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Midas User`s Manual - Center for Structural Biology

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1. H L L fl L L S S I S S where the hue is interpolated in a counterclockwise direction when the interpolation factor f is positive and clockwise when it is negative APPENDIX 1 88 UCSF MidasPlus points are used for a molecular surface LINES Every two vertices describe a line sINE STRIP Each vertex is connected to the previous vertex in a line INE LOOP A LINE LOOP is like a LINE STRIP but the last vertex is connected to the first TRIANGLES Every three vertices describe a triangle TRIANGLE STRIP The first three vertices are a triangle and each subsequent vertex forms a connected triangle with the previous two TRIANGLE FAN The first vertex is the center of a fan and the subsequent vertices form triangles around the center QUADS Every four vertices describe a quadrilateral QUAD STRIP The first four vertices are a quadrilateral and each subsequent pair of vertices forms a quadrilateral with the previous two POLYGON The vertices form a polygon It should be noted that since MIDAS cannot display solid surfaces it will never use some of the above types e g TRIANGLE STRIP However ribbonjr can in fact accept all the above types Thus if one developed a pro gram that employed one of the non MIDAS types or wrote a filter that added such types to a MIDAS generated PDBRUN file ribbonjr could be used to display the result
2. See also conic ksdssp 2 4 66 Rlabel Usage rlabel atom_specification Usage rlabel atom_specification Rlabel enables residue labeling of the first displayed atom of each residue in atom_specification Such labeling is enabled by default in MIDAS rlabel may be used to turn off display of residue labels See also label 2 4 67 Rock Usage rock axis angle frames wait_frames Usage rock axis Rock will rotate the selected structures back and forth about the x y or z axis The angle indicates the number of degrees the structure rotates at the fastest point in the sinusoidal period an angle value of 9 corresponds approximately to a 90 degree arc The cycle time for rock is approximately 2 4 seconds This corresponds to 18 frames forward and 18 frames back 15 frames per second If arguments are omitted defaults will be used These defaults are 0 wait_frames infinite frames angle of 3 and y axis MIDAS continues to process commands while the requested motion is in progress To have command processing pause until the motion is finished use the wait command If rock does not work it is likely you have failed to select the target models See also freeze select wait UCSF MidasPlus 46 UCSF MidasPlus 2 4 68 Roll Usage roll axis angle frames wait_frames Usage roll axis Roll will rotate the selected structures about the x y or z axis continuously If axis is an integ
3. If no atom_specification is given all open models are colored Examples color green 2 HIS color all histidine residues in model 2 green color 20 s 3 color model 3 s surface color 20 midway between blue and magenta color red b 0 4 color all bonds in the fourth residue of model 0 red color blue s 1 e lt 5 color all atom surfaces on model 1 with electrostat ic potential less than 5 kcal mole per elementary charge the color blue color red color blue color red every atom that is blue Ranges of colors may be mapped onto models based on either surface electrostatic potential or atom temperature factor A range of color is specified by either keywords or numbers such as blue red or 16 32 By default color hues are interpolated counterclockwise on a standard color wheel the e designation changes the interpolation to be in the clockwise direction For example blue to red interpolated counterclockwise goes through magenta whereas clockwise interpolation goes through green To color models by electrostatic potential use the surface designation s with the color range The ends of the color range are mapped to the lowest and highest potential values of all open models The color of a surface point is the color in the color range that corresponds to its electrostatic potential in the potential range If boundary conditions are given i e e gt e lt the colors are mapped within the boundaries Similarly for temperature factors
4. bond_length r bond_ratio DESCRIPTION Longbond examines each bond MIDAS lists in CONECT records and if the bond length exceeds the user specified threshold issues a MIDAS bond command to remove the bond This command is useful for cleaning up structures for which MIDAS generates unreasonable bonds By default Jongbond remove each bond whose length exceeds 1 5 times its typical length derived from the types of the bonded atoms The ratio of 1 5 may be overridden using the r flag If the l flag is given then the bond length is compared against the absolute distance bond_length rather than the type dependent length BUGS Some bond removal commands issued by longbond may be ignored by MIDAS because a residue would then be broken into two disconnected pieces In such cases the user needs to create the proper connecting bonds and then reinvoke longbond AUTHOR Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 139 UCSF MidasPlus MAKEMS 1 MAKEMS 1 NAME makems MidasPlus delegate for convenient generation of molecular surfaces MIDAS COMMAND SYNTAX Command delegate start ms makems DESCRIPTION Makems is a MidasPlus delegate that takes an atom specification and then generates and displays the corresponding solvent accessible molecular surface Makems only works correctly when surfacing a single model it cannot correctly surface multiple models If multiple models are present when makems i
5. Further 3D graphics annotations are USER GFX COLOR red green blue color specification User defined graphics object color same format as the USER COLOR record above Color records may appear outside or within graphics primitives and apply to the following primitive or vertex USER GFX NORMAL n n n A normal vector for the next vertex USER GFX VERTEX xyz A vertex with given coordinates USER GFX FONT font size font name This annotation switches subsequent label text to the given font name and font size USER GFX TEXTPOS xyz This annotation sets the position of the next label see below USER GFX LABEL text This annotation places a label starting at the current text position The label text must be between double quotes The quoted text follows the ANSI C language rules for string constants that is a backslash character starts an escape sequence a backslash double quote character sequence indicates a double quote and so on APPENDIX 1 89 UCSF MidasPlus Annotation Record Formats For the C format specification the leading Us The Fortran formats include reading the word Us ER is left out and the format given below starts in column 7 ER Annotations marked with a dagger are required Annotation C format Fortran format Annotation Headers PDBRUNt PDBRUN 2d 6A1 6A1 X 12 EYEPOS EYEPOS 9 3f 9 3
6. See also clip 2 4 35 Ksdssp Usage ksdssp options The ksdssp Kabsch and Sander define secondary structure of proteins command computes the regions of secondary structure in the displayed models Many PDB files have their secondary structure information supplied in HELIX and SHEET records but some do not and ksdssp is useful in these cases The MIDAS rib bonjr command requires secondary structure information in order to make an accurate rendering of displayed models To do the secondary structure calculation the ksdssp command invokes a separate program also called ksdssp which is described in Appendix 6 of this manual Options given to the ksdssp command are passed on to the ksdssp program so consult Appendix 6 for a description of the options Typically running ksdssp without any options does a reasonable job of computing secondary structure nonetheless in some cases UCSF MidasPlus 34 UCSF MidasPlus options are necessary Note that the PDB file and output file arguments mentioned in the ksdssp manual page should never be supplied to the ksdssp command within MIDAS they should only be given when the ksdssp program is run outside of MIDAS See also ribbonjr 2 4 36 Label Usage label atom_specification Usage label atom_specification Atoms and residues are labeled appropriately Atom_specification may include any atoms residues or models The residue sequence number and type ap
7. The makemark command reserves name for use in future mark commands The makemark com mand with no argument returns a list of currently reserved mark names A reserved mark name can be freed for reuse with makemark See also mark 2 4 42 Makems Usage delegate start ms makems The makems delegate computes and displays the solvent accessible molecular surface of a MIDAS model Details of this delegate s usage can be found in Appendix 6 of this document See also open surface vdw 2 4 43 Mark Usage mark name atom_specification The mark command associates the given name with the set of atoms specified The mark can be used in later atom specifications with the syntax mark name which will intersect the set of marked atoms with any other parts of the atom specification This is explained in detail in Referencing Models Residues and Atoms in Part II of this manual The mark name can also be used in a pdbrun command to limit the atoms involved to those in the mark UCSF MidasPlus 36 UCSF MidasPlus Note that the makemark command must be used to reserve the mark name before the mark command can be used Using mark will remove the specified atoms from the named mark Also note that the mark com mand marks additional atoms with the given name Atoms marked with that name from previous mark com mands are still so marked To mark just the atoms given in the mark command it would be necessary to first cl
8. As a consequence on SGI systems the midas executable is a front end program that first queries the system to determine the type of graphics hardware present and then executes either midas irisgl or midas opengl depending on which should provide better performance The heuristics used by the midas front end program were determined empirically from the various graphics hardware types available to us at UCSF and may not cover every system type correctly particularly more esoteric hardware options Nonetheless we believe them to be correct for 95 of SGI workstations If you believe you have a system where the incorrect back end program is selected you can test this out by executing the alternate back end directly as described below To have midas choose a different back end for your workstation permanently lIt also makes no performance difference for these color schemes since MIDAS optimizes half bonds of the same color into a single draw UCSF MidasPlus 85 UCSF MidasPlus edit the file usr local midas resource glgraphics as per the comments contained in that file To determine which back end program midas is selecting execute midas noexec which will print out the name of the back end program with noexec appended which should be ignored In the simple case where you want to run the back end with no arguments or with just a session file argument you can do so with no problem If you want to use command line opt
9. See also copy 2 4 10 Cd Usage cd path_name Cd changes the current working directory to path_name If you are not familiar with the concept of directories and path names see UNIX for Beginners Kernighan and the description of the cd com mand in section 1 of the UNIX User s Manual Note that all subsequent commands that have filename argu ments are executed in the new working directory for example pdbrun record save source write etc Example ed crodna 2 4 11 Center Usage center atom_specification Center places the center of the atoms in the atom_specification at the center of the screen See also window UCSF MidasPlus 24 UCSF MidasPlus 2 4 12 Chain Usage chain atom_specification Usage chain atom_specification The chain command draws pseudobonds between the specified atoms undisplaying all others This is particularly useful for displaying the backbone atoms of a protein chain is similar to display except that only bonds chains are undisplayed labels etc remain Example chain ca chain all alpha carbons See also display show 2 4 13 Clip Usage clip plane units frames wait_frames Usage clip plane The clipping planes may be moved relative to their current position by a specified number of units Units is a positive or negative distance in angstroms A positive number moves the plane towards the user A negative number moves it away from the u
10. The format of a group file is most easily understood by providing an example This is the contents of the group file for S pheny file name S Ph UCSF MidasPlus 83 UCSF MidasPlus 1 S phenyl 2 new S 0 000 0 000 0 000 3 new C 0 000 0 000 0 000 4 new C 0 000 0 000 0 000 5 new C 0 000 0 000 0 000 6 new C 0 000 0 000 0 000 7 new C 0 000 0 000 0 000 8 new C 0 000 0 000 0 000 9 read internal coordinates for new group 10 10n3 n2 1 75 105 0 60 0 11 2 1 O nd 1 4 120 0 60 0 12 A B20 A 120 0 180 0 13 FAR 2 eh Le 120 0 0 0 14 pE SA Bo 2 sg 20 0 0 0 15 65 4 3 1 4 120 0 0 0 16 220 139 14 120 0 0 0 Line 1 is the descriptive name of the chemical group Lines 2 through 8 identify the atoms that com pose the group There is one line per atom in the group The only significant field on these lines is the second field which is the name of an atom in the group Note that to ensure uniqueness addgrp will append a number to the atom name so in MIDAS the final names of atoms in this group would be S1 C2 C3 etc The other fields must be present but are otherwise ignored Line 9 marks the end of the lines describing group atoms It should be present verbatim The lines that follow give information as to how each atom is positioned relative to other atoms in the group and possibly also with respect to atoms mentioned on the addgrp command line that invoked this group file The atoms in the gro
11. x exponent Control the exponent used in exponential averaging of distances involving pseudo atoms Unless given the c flag noeshow does exponentially weighted averaging of distances involving pseudo atoms If a constraint involves n atoms on one end and m atoms on its other end then the weighted average distance is gt C C nm nem exponent 1 exponent where c is the coordinate position of the ith atom The default exponent is 6 Use of the D flag prevents the division by n m Errors Noeshow displays error messages in the MIDAS reply area Errors typically occur when there are problems matching atom names in the constraint file with those in the PDB file Frequently in such cases many error messages are generated In the Iris GL version of MIDAS only the last few of these can be seen in the reply area If it is necessary to see all the error messages at once this can be done by running noeshow outside of MIDAS The first step is to get a PDB file from MIDAS to use as input to noeshow In MIDAS issue the command pdbrun cat gt inputfile This will save an annotated PDB file describing the current MIDAS display into a file called inputfile Next from a shell window run usr local midas lib midas noeshow options_used_in_Midas lt inputfile The output from the above command will be a series of MIDAS commands The output commands that start with echo are the ones that would display messages in the
12. CA CD CB er OD Isoleucine CG2 ee CB cG1 cD1 APPENDIX 2 92 Leucine CD2 Za CB CG X cpb1 Lysine CB CG CD CE NZ Methionine CB CG SD CE Proline N CA CD CB Wa Serine CB OG Threonine OGI CB XcG2 Valine G1 CB cG2 Tyrosine CD1 CE1 e SS CB CG CZ OH cD2_CE2 Phenylalanine CD1 CE1 yn N CB CG CZ cD2 _CE2 Tryptophan CE3 CB CG CD2 CZ3 CD1 CE2 CH2 Ne cz UCSF MidasPlus Appendix 3 Special Characters and Symbols Used in MIDAS The following table describes symbols which have special meaning to MIDAS In addition to these symbols several special characters are available for use in command line editing users of the EMACS text editor will readily recognize most of these special editing characters Symbol Function Usage z gt b gt APPENDIX 3 model number residue atom name range name separator whole wildcard match partial wildcard match single character wildcard every nth residue or atom zone specifier temperature factor model_number where model_number is an integer residue where residue is a residue name residue sequence number or range of residues atom_name where atom_name is an atom name or range of atoms specifies a range of atoms such as CB beta carbon to the last atom in residue branch a range of residues such as 35 66
13. Import PDB for opening PDB files and Save As for saving sessions Each one will bring up a panel to navigate the file system and UCSF MidasPlus 7 UCSF MidasPlus select the file or session name of interest If you already know the precise location of the PDB file or session it is probably faster to use the open load or save commands respectively From this point on there are many MIDAS commands available for manipulating the model These are described in detail in Part II Command Reference Guide of this document The following categories of commands are provided to help you get started For information on The pertinent commands are Adding groups or new residues addgrp addaa delete swapaa swapna Coloring models color intensity set Displaying molecular surfaces surface vdw vdwopt Interactive manipulation of models assign select Labeling model components label rlabel Making videos rock roll set sleep source wait Recovering coordinates fix getcrd save write Rotating bonds rotat brotat reverse assign angle Selective display of model components chain display show Viewing in stereo stereo 1 3 On Line Help MIDAS features an on line help system All commands documented in Part II of this manual are also available on line The command help command will produce a short synopsis of the specific command in question The command help without any arguments produces a list of all available MID
14. The commands available in MIDAS are summarized in the following tables and described individually in detail on subsequent pages 40n the NeXT machine note that if MIDAS is started by opening a file with a pdb extension or by double clicking on the MidasPlus appli cation icon then MIDAS will be running in the user s home directory UCSF MidasPlus 15 UCSF MidasPlus Input Output bs copy load open pdbopen save write Model Movement align assign cofr freeze move rock roll select setcom speed turn Structure Information angle discern distance getcrd label ribbonjr rlabel Display Control center chain clip color display intensity label3d objdisplay push pop rainbow reset ribbonjr savepos scale section set unset show stereo thickness UCSF MidasPlus MidasPlus Commands and Utilities Grouped by Function Commands marked with an asterisk are not used directly at the MIDAS command prompt but are instead used either at the UNIX com mand line or via the MIDAS delegate facility Their use and features are documented in Appendix 6 of this manual convert pdbrun style file to ball and stick printable PostScript send display image to a printer or file load a saved session into MIDAS open a PDB file solvent accessible surface or object file for display PDB file browser save a MIDAS session output a model into a file align two atoms along the z axis assign function
15. This file neon dat is read from the current working directory of midas The example below lists the default control parameters used when the neon dat file is missing Input is free format one control parame ter per line 0 Tubetype O all atoms 1l smooth 2 bent 3 straight 3 Sphere density 1 rough 5 high resolution 1 Dash flag O no dashes 1 draw dashes 1 Object flag O no objects l draw objects 0 CPK flag O normal Render output 1 CPK output 0425 Stick thickness Angstroms 0 50 Tube thickness Angstroms 0 10 Dash thickness Angstroms 0 10 Object thickness Angstroms 0 04 Density thickness Angstroms 0 Atom rendering O stick l ball amp stick 0 25 Atom size Fraction of vdw radius ball amp stick mode 0 0 50 Depthcue Percent O n 1 y fraction aft intensity 0 0 0 0 0 B factor Range O n 1 shade to color 2 rainbow min max 1 0 1 0 1 0 Befactor color RGB red green blue 5 Number of dashes Number drawn between each pair of atoms 1 0 1 0 0 0 Dash color RGB red green blue 0 30 Dash offset Dist from atom to first dash Angstroms 0 40 Dash space ratio 0 0 dots 0 4 dashes 1 0 solid line 4 00 CA conect distance Angstroms CONTROL CARDS Tubetype Backbone atom representation all atoms smooth tube bent tube or straight tube The color of the tube representation corresponds to the color of the a carbon Sphere density APPENDIX 6 149 UCSF MidasPlus NEON 1 NEON 1 Dens
16. Use the dms program to generate the surface An example command for creating a surface is dms dfr a d 0 5 g logfile i site o dfr dms where UCSF MidasPlus 65 UCSF MidasPlus dfr is the name of the PDB file a indicates that all atoms are to be included in the calculation If this flag is missing only amino acids are included in the calculation d 0 5 indicates the density of points on the surface g logfile directs informative messages from the program to the file logfile i site directs dms to calculate the surface for the entire molecule but report the surface for only those atoms and residues selected in the file site odfr dms directs the output from the program i e the surface to the file dfr dms At UCSF the dms program should always be run in the background using the submit command This prevents long running jobs from adversely affecting interactive users Thus the command line for the above example becomes submit dms dfr a d 0 5 g logfile i site o dfr dms 4 The progress of the dms program may be monitored in two ways 4a Use the ps command to see if the program is running 4b Read the logfile i e the file name given with the g flag and the submit out file created by submit If the program is left to run overnight it is a good idea to check these two files before leaving the laboratory to make sure the program didn t run into immediate difficulty and stop The c
17. com pound name sequence At most one compound may be selected using either the mouse or up and down arrow keys The MIDAS residue sequence number and the optional information of the selected com pound is displayed below the browser in the sequence field and information window respectively Viewdock operates in one of three modes examine prune and identify In examine mode when the user selects an entry in the browser the compound is automatically displayed in MIDAS and any previously displayed compounds are undisplayed picking in MIDAS has no effect In prune mode when the user picks a compound in MIDAS the compound is discarded selecting an entry in the browser does not affect what is displayed in MIDAS In identify mode when the user picks a compound in MIDAS the compound is selected in the browser selecting an entry in the browser does not affect what is displayed in MIDAS When the selected entry in the browser is undeleted the button below the information window is labeled as Discard clicking on the button will make the selected entry marked When the selected entry is marked or deleted the button is labeled as Restore clicking on the button will make the selected entry The name of a compound its MIDAS residue number and its discard state are shown in the compound undeleted APPENDIX 6 186 UCSF MidasPlus VIEWDOCK 1 VIEWDOCK 1 The menu bar items include Exit Terminate viewdock Viewdock can save c
18. ATO 1 N VAL 0 5330 155770 154090 3330 146 ATO 2 CA VAL 1 650 16 390 15 360 0 96 1 50 ATO 3 gt IE VAL 2 670 15 670 16 230 3 18 1 43 ATOM 4 O VAL S10 216 250 172200 O0872 1248 ATO 5 CB VAL 1 760 17 680 16 180 1 77 1 47 ATO 6 CG1 VAL 3 120 185 390 152900 4 37 1 50 ATO 7 CG2 VAL 0 630 18 680 15 930 2 42 1 51 ATO 8 D VAL 0 250 15 310 14 410 4 96 1 46 ATO 9 HA VAL 2 200 16 520 14 420 2 30 1 50 ATO 10 HB VAL 1 750 17 420 17 260 2 08 1 62 ATO 11 1HG1 VAL 3 210 18 510 14 820 0 21 1 60 ATO 12 2HG1 VAL 3 230 19 250 16 460 0 92 1 57 ATO 13 3HG1 VAL 3 910 17 600 16 200 1 79 1 56 ATO 14 1HG2 VAL 0 270 18 120 15 640 3 19 1 55 ATO 15 2HG2 VAL 0 440 19 240 16 860 0 54 1 56 ATO 16 3HG2 VAL 0 940 19 370 15 130 2 66 1 57 Note in this example that All hydrogens appear after the other atoms of the residue e Atom 9 HA is attached to atom 2 CA The remoteness indicator A is the same for these atoms There are three hydrogen atoms connected to CG1 These three all have the same remoteness indi cator but contain a distinguishing digit in column 13 Thus each has a unique name It is not necessary to use a digit as a prefix to the atom name when only one hydrogen is attached to a given atom 3 5 More on Connectivity and Templates MIDAS has an algorithm for constructing atom connectivity based on interatomic distances With reason able coordinate data this algorithm generally prod
19. Object thickness Radius in angstroms of lines and dots in graphics objects Density thickness Radius in angstroms of electron density lines the density itself is not changed of course Atom rendering Controls whether atoms are represented as sticks or balls and sticks Atom size Radius of balls in ball and stick mode as a fraction of the van der Waals radius specified by midas Depthcue fraction The first value turns depthcuing on or off The second value is the fractional intensity of atoms at the back of the image B factor range Control of coloring by temperature factor The first value controls the coloring type Type 0 turns the option off so the model will be colored as displayed Type 1 creates a gradient of color start ing with the B factor color specified below for atoms with lowest temperature factor to the displayed color for atoms with highest temperature factor Type 2 creates a gradient of color blue magenta red orange yellow from lowest to highest temperature factor value The second and third values specify the minimum and maximum temperature factors over which the gradient of color is calculated Atoms with temperature factors above and below the values are colored yellow and blue respectively If both values are 0 0 the minimum and maximum values are deter mined from the displayed atoms B factor color The RGB red green blue color of atoms with lowest temperature factor Used with B factor APPENDI
20. The color coded results are displayed on the highest numbered open model The same flags used to control pseudo atom averaging D and x also control the ensemble averaging see Options section The c flag however is ignored for ensemble averaging If you want simple numerical averaging for the constraints use x 1 instead of c Normally noeshow will give equal weight to each member of an ensemble It is possible however to give the members unequal weightings This could be useful for example if the ensemble had been generated by a program such as PARSE 1 which assigns a probability to each member of the ensemble To indicate the weights to noeshow there must be a line in each PDB file as follows USER STRUCTURE WEIGHT weight where weight is any non negative number Note that there are two spaces after the USER Structures lack ing a line such as the above will be given a weight of 1 0 and therefore if no structures have the above line all will have equal weight Showing possible H H interactions Noeshow has one capability that is designed to be used primarily without a set of distance constraints it can show all hydrogens within a given cutoff distance of one or more designated hydrogens The general procedure to do this is to use the marking mechanisms discussed in the Restricting display section to designate both the hydrogens of interest marked with noemark1 as well a
21. i dms_file 0 esp_file q charge_file a pdb_file r n c cutoff e epsilon p len W V SEE ALSO specifies a dms surface input file The electrostatic potential is calculated for all points of this surface Use the dms 1 program with the n flag to calculate normals to gen erate dms_file If the p flag see below is given a value of 0 the normals need not be calculated by dms 1 indicates the annotated dms surface file to which the calculated electrostatic surface is output The option q charge_file supplies an alternate charge file for residue types The default file used is usr local midas resource charges esp Instructions for constructing alternate charge values are contained in the default file The q flag must precede the name of the Protein Data Bank format file a flag to which the alternate charge file is applied Thus a series of command line parameters q file a db1 q file2 a db2 may be used to associate alternate charge files with specific models is the name of the Protein Data Bank format file containing the coordinates for the associated dms surface file and any other atoms which should be included in the elec trostatic calculation The potential is calculated only for those surface points in dms_file but all atoms in pdb_file are used in the calculation indicates that the dielectric constant is dependent on the distance from the atom or charge
22. 34 37 Residue sequence number right integer 38 Code for insertions of residues character 39 40 Type of helix right integer 41 70 Comment left character SHEET 1 5 SHEET character 8 10 Strand number in current sheet right integer 12 14 Sheet identifier right character 15 16 Number of strands in current sheet right integer 18 20 Initial residue name right character 22 Chain identifier character 23 26 Residue sequence number right integer 27 Code for insertions of residues character 29 31 Terminal residue name right character 33 Chain identifier character 34 37 Residue sequence number right integer 38 Code for insertions of residues character 39 40 Strand sense with respect to previous right integer The following fields identify two atoms the first in the current strand and the second in the previous strand which are hydrogen bonded to each other These fields should be blank for strand 1 42 45 Atom name as per ATOM record left character 46 48 Residue name right character 50 Chain identifier character 51 54 Residue sequence number right integer 55 Code for insertions of residues character 57 60 Atom name as per ATOM record left character 61 63 Residue name right character 65 Chain identifier character 66 69 Residue sequence number right integer 70 Code for insertions of residues character tHelix types are Right handed alpha default Right handed omega Left handed omega 1 Left handed alpha 2 3 Right
23. H If the output format is ps causes binary data to be hex encoded Though raw binary format is more space efficient many printers cannot print binary data unless it is hex encoded Note that future versions of conic may make hex encoding the default and the H flag would turn it off S scale_factor Zoom in on the center of the image by the specified factor The size of the window remains unchanged W Force MIDAS to wait until conic has exited before continuing NeXT DIFFERENCES The s option is not supported Only the TIFF and Encapsulated PostScript file formats are supported You should place the output in a file whose name ends with tiff or eps so the Workspace may open it correctly MIDAS simulates the effects of the s option CONFIGURATION FILE The scene computed by conic is described by a list of options in a configuration file If the configuration file is absent or the option is omitted then a default value will be used Lines beginning with are com ments and are ignored All other lines are options which begin with a keyword and are followed by space separated values The available options are listed below ambient r g b Set the ambient light to the given RGB value which is three floating point intensities ranging from Oto 1 The default ambient lighting is 0 2 0 2 0 2 antialias mode Set the antialiasing algorithm Mode may be none for no antialiasing 3 2 for mapping 3x3 cal culation pixels onto
24. MIDAS COMMAND SYNTAX Command pdbopen directory dir index file DESCRIPTION Pdbopen is a MidasPlus delegate that presents an X Motif user interface that allows users to browse through an index of the Protein Data Bank PDB coordinate entries examine information associated with each entry and open entries in MIDAS Pdbopen may be invoked with the following flags directory Set the directory to use as the PDB repository The default directory is mol pdb index Set the file to use as the PDB entry index The default index file is found in index entries idx in the PDB repository directory Pdbopen reads the PDB index file and then displays two windows an index browser and an entry inspector Each PDB entry consists of several fields including its PDB ID code compound information and ascession sic date The browser lists short forms of PDB entries of interest while the inspector displays all the fields of a selected PDB entry The index browser consists of a text list a menu bar and two buttons The text list consists of PDB entries one per line displayed in a scrollable region At most one entry in the text list may be selected using the mouse and additional information about that entry is displayed in the entry inspector The menu bar has three entries Sort Show and Hide The Sort menu will sort the entries displayed in the text list according to the chosen field the Show and Hide menus will show and hide the chosen fi
25. This com mand assumes that model n is already in orientation from If models other than n are selected APPENDIX 6 144 UCSF MidasPlus MROTATE 1 MROTATE 1 they will also be affected by the rotations and translations that mrotate generates snapshot name Take a snapshot of the current orientation and associate name with it The standard MIDAS com mand savepos name is also executed automatically so the orientation may be recovered later in MIDAS using the com mand reset name Note that only the orientation i e the atomic positions are saved other attributes such as colors and whether atoms are displayed are ignored Name may be used in later interp and store com mands as either the from or to orientation stop Terminate the delegate store filename from ton This command does exactly the same thing as interp except the MIDAS commands are appended to file filename instead of being sent to MIDAS BUGS Makes too many assumptions about where models are in MIDAS SEE ALSO MidasPlus User s Manual APPENDIX 6 145 UCSF MidasPlus MS 1 MS 1 NAME ms calculate a solvent accessible molecular surface SYNOPSIS ms file a d density e file g file i file s file n r b e w radius o file NOTE The ms command has been obsoleted by the dms command It is recommended that dms 1L be used instead of ms Dms alleviates many of the shortcomings of ms such as handling of chai
26. addgrp add a new group to a residue bond make a bond between two atoms delete delete a group from a residue gennuc generate DNA RNA structure from sequence data longbond break excessively long bonds pdb2group create addgrp style group description from PDB file swapaa exchange one amino acid for another swapna exchange one nucleotide for another Multi Model Positioning match superimpose two models matrixcopy copy transformation matrix from one model to another matrixget output a transformation matrix to a file matrixset set a transformation matrix from a file set set options especially independent and refmodel watch graphically monitor interatomic distances watchopt specify parameters used by watch command Command documented in Appendix 6 UCSF MidasPlus 17 UCSF MidasPlus density gd midasmovie noeshow viewdock System Access cd midaspop midaspush stop system dnacheck fixatname ksdssp uncryst unmtrix Script Support mrotate read record sleep source update wait Auxiliary Program Support delegate echo help makemark mark matrixcopy matrixget matrixset pdbrun pickabort pickatom run update Video Support expr smpte fade videodisk UCSF MidasPlus Cooperation with Non MidasPlus Packages display X PLOR electron density maps display energy contours generated by Peter Goodford s GRID program show molecular dynamics trajectories display NMR constraints on a
27. and it adds an alpha channel to the file so that the resulting image can be composited onto other backgrounds vV Print progress messages A Ignore USER COLOR USER RADIUS and USER MATPROP records present in the input file Since the MIDAS pdbrun command provides USER COLOR and USER RADIUS records for each atom this flag must be used if atomic information is coming from MIDAS but a color scheme specified in an atom information file is desired see the COLORING THE MOLECULE section of this manual page C Force conic to display full spheres at the near clipping plane This option affects those spheres whose centers lie across the near clipping plane from the viewer but whose nearest extent crosses the clipping plane conic always discards spheres whose centers are closer than the clipping plane By default conic shows the sphere with a portion cut away With this option the entire sphere is shown It should be noted that the cut away depiction is inaccurate in two regards the partially cut spheres still cast full shadows and no part of a sphere is shown if its APPENDIX 6 105 UCSF MidasPlus CONIC 1 CONIC 1 center is in front of the clipping plane even though it may extend through the plane Typically these inaccuracies are not noticeable but in some situations such as using point light sources they may produce odd looking results F Set the image size to be the full screen
28. changed and the rotation again along the bond from the fixed to the rotating section is counter clockwise In assigning multiple bond rotations to a model two rotations cannot affect a common set of atoms unless one affected set is a complete subset of the other That is rotations must be properly nested Examples UCSF MidasPlus 47 UCSF MidasPlus rotation 1 1 1 c8 c9 assign rotation to the bond between c8 and c9 in the first residue of model 1 rotation 3 1 2 C 3 N assign rotation 3 to the bond between atom C in residue 2 and atom N in residue 3 See also brotation reverse assign fix fixreverse roll turn 2 4 70 Run Usage run cmd cmd_args Run passes its arguments cmd and cmd_args to the shell for execution and takes the output from these as a series of MIDAS commands The user may interrupt the execution of the MIDAS commands by pressing the ESC key Execution of the current command is completed before processing the interrupt Note that MIDAS first searches the directory usr local midas ib midas for cmd before examining the rest of the user s execution path This is useful to avoid name conflicts between MIDAS commands using the run pdbrun delegate mechanism and UNIX commands of the same name See also pdbrun system 2 4 71 Save Usage save session_name Save stores the model orientations bond rotations distance calculations slider assignments and user options for the current session in a MI
29. filename Read executes the contents of the named file s as a list of commands Read differs from source in that source updates the display after each command while read only updates the display after all commands are done See also record source run pdbrun 2 4 61 Record Usage record filename Record saves all the commands remembered by the set record command in the file filename Saved commands can later be re executed with a read or source command although the command file should first be edited since the record command itself will be in the file Record is very useful for creating demonstra tion scripts for later playback Note that there is normally a set record in the system startup file distributed with MIDAS so that by default all typed user input is remembered Thus all commands used since MIDAS startup can be saved easily with record This is useful for reproducing results or applying commands used on one set of models to a different set of models See also read set source 2 4 62 Redraw Usage Redraw atom_specification This command no longer does anything It is provided for backwards compatibility with old MIDAS command scripts 2 4 63 Reset Usage reset list view_name Reset returns models back to saved orientations In each MIDAS session the original orientation of the first model s opened is saved as view_name default This orientation may be retrieved by the command reset or the
30. or O2 Thus a residue contains a fixed number of atoms with specific names The pattern of bonding between the atoms is termed connectivity The connectivity within a residue must form a connected graph of uniquely named atoms Since the atoms are uniquely named the bonding can be defined in an unambiguous manner The definition of a MIDAS residue includes both connectivity and atom naming information If you use a PDB file with non unique atom names in some residues MIDAS will still display it however you will not be able to address atoms uniquely When residues are used to build models the connectivity of atoms is the same for each occurrence of any given residue in the model For example if we build a residue named gly then each time a gly residue appears in the model protein it will have the same basic pattern of connectivity of atoms and the same atom names MIDAS uses files called templates to name each residue s atoms and the connectivity of those atoms Each template consists of a map which describes how the atoms are connected and which atoms link the residue to other residues If a template doesn t exist for a particular residue then MIDAS will use atomic radii and dis tances to connect atoms within the residue In most cases you can safely forget about the existence of template files partially because MidasPlus usually gets the connectivity right and because you can fix the connectivity with Mi
31. tripled lines cs Complex small as Complex but smaller than normal size Not all font faces are available in all the types The cross table of availability is p s d c t cs roman e e greek italic e e script cyril all gothic The name used to open the font with the label3d open command is made by composing the font face name with the type name separated by a hyphen So the roman font face in the complex type would be referred to as roman c Typically one would use the the most detailed type available for the font face unless a very large number of labels are going to be used when perhaps a simpler type might be employed BUGS Good vector fonts are hard to come by FILES usr local midas resource label3d fonts system font directory SEE ALSO MidasPlus User s Manual AUTHOR Conrad Huang Computer Graphics Laboratory UCSF Eric Pettersen Computer Graphics Laboratory UCSF Hershey font conversion ACKNOWLEDGEMENTS The Hershey Fonts were originally created by Dr A V Hershey while working at the U S National Bureau of Standards The format of the Font data distribution not the format used by label3d was origi nally created by James Hurt Cognition Inc 900 Technology Park Drive Billerica MA 01821 APPENDIX 6 138 UCSF MidasPlus LONGBOND 1 LONGBOND 1 NAME longbond remove long bonds from structure MIDAS COMMAND SYNTAX Command pdbrun conect longbond
32. 0 000 0 000 0 000 new C 0 000 0 000 0 000 new C 0 000 0 000 0 000 read internal coordinates for new group 1 0 n3 n2 1 4 120 0 60 0 21 0 n3 4 120 0 180 0 32 1 0 4 120 0 0 0 43 2 1 sak 1205 0 18070 Po Be go 2 AL 4 120 0 0 0 bo J3 2 4 120 0 0 0 60 Lp 2 4 120 0 0 0 Group file format is also described in detail in Chemical Group Description Files in part 3 of the MidasPlus manual COMMAND ARGUMENTS The required command line arguments to pdb2group are the names of anchor_atom n3_atom and n2_atom The anchor_atom is the first atom to be listed in the computed group file N3_atom and APPENDIX 6 162 UCSF MidasPlus PDB2GROUP 1 PDB2GROUP 1 n2_atom refer to atoms in PDB_file and are used to compute bond and dihedral angles between the group and the rest of the molecule they do not appear in the group file Atoms in the PDB file which are con nected to anchor_atom only through n3_atom will not appear in the group file The PDB file must contain only one residue The title of the group file is the group_description if given or the PDB file name otherwise If the PDB file is read from standard input the title is EXAMPLE Although lysine is provided as a standard group for purposes of illustration the derivation of a group file describing a lysine side chain is shown here Creating the PDB input file Creating the PDB input file by hand is a tedious procedure but may be necessary if you have no
33. 1 00 0 00 ATO 4 0 VAL A 8 813 17 657 5 941 1 00 0 00 ATO 5 CA VAL A 6 317 19 598 5 527 1 00 0 00 ATO 6 CG1 VAL A 6 959 20 999 5 376 1 00 0 00 ATO 7 CG2 VAL A 1 4 819 19 636 5 383 1 00 0 00 ATO 8 N EU A 2 9 259 18 958 4 152 1 00 0 00 ATO 9 CA EU A 2 10 715 18 872 4 330 1 00 0 00 ATO 10 C EU A 2 11 156 20 058 5 187 1 00 0 00 This error often does not become apparent until the residue is labeled and the resulting model is found to be missing a CB atom If the MidasPlus program is used to implicitly construct the model then it will draw a bond to the closest atom and silently ignore the other set of coordinates This is one of the reasons it is sometimes advisable to construct a template using gentpl since this program is more rigorous in checking for input errors see section 3 6 for more details Residues Out of Sequence In the following example notice that the second residue SER appearing in the file is erroneously num bered residue 5 MIDAS will accept this input without complaint The resulting model will have residue 5 connected to residue and residue 3 This is all well and good but only if it is what was originally intended If however residue number 5 was to appear between residue 4 and residue 6 then it should have appeared in that order in the PDB file Thus if one finds that residues are connected in an incorrect order the ordering UCSF MidasPlus 75 UCSF MidasPlus and not the numbering in the da
34. 15 Color Usage color color_name color_name s U Lb Lv Lc atom_specification The color command allows the user to selectively color bonds labels and surfaces by model residue and atom Other graphics objects see Non Molecular Graphics Objects in Part IID have colors embedded in their definitions and are unaffected by the color command Color_name is a name that has been previ ously defined by the colordef command A special color_name is byatom which is a simple attempt at determining color from atom name Atom name prefixes and their corresponding colors are as follows CL BR magenta FE gray C gray O red N light blue H D digit white S yellow I F magenta B gray others blue These colors are coded into MIDAS and cannot be easily changed Other built in color_names are described in the colordef command Optionally the user may specify one of the designations s l b or v to color surfaces labels bonds and van der Waals surfaces respectively In the absence of these specifiers MIDAS colors everything i e bonds surfaces labels and van der Waals surfaces of all specified atoms Note that the solvent accessible surface and the van der Waals surface may be displayed simultane ously and thus colored separately See the surface and vdw commands in this document The atom_specification uses the standard MIDAS syntax Note that the color command will not work i e models may not be uncolored
35. APPENDIX 6 112 UCSF MidasPlus DISCERN 1 APPENDIX 6 DISCERN 1 operators include and which correspond to addition subtrac tion division multiplication and exponentiation respectively The precedence of the operators is the normal arithmetic one and parentheses may be used to override The list of supported functions is sqrt square root sin sine cos cosine acos arccosine exp exponential log natural logarithm and abs absolute value An example of a property command is property diffsq 4 5 2 Properties with numeric names are predefined to correspond to data columns e g 1 corresponds to data column 1 size keyword value pair major keyword value pair minor keyword value pair color keyword value pair These commands redraw the selected model using different display parameters based on the keyword value pair arguments Major and minor are the axes lengths of the ellip soid size is a scale factor applied to both axes color is the color of the ellipsoid The supported keywords are listed below property name Specifies that the display parameter will be interpolated using values computed with property name In the special case where name is none the default display parameter will be used bmin value Specifies the lower bound for the data values If this keyword is not used the minimum value for the specifi
36. Command documented in Appendix 6 16 UCSF MidasPlus window display the entire molecule on the screen Molecular Surfaces dms calculate a solvent accessible molecular surface esp calculate electrostatic potential makems compute and display solvent accessible surface of an atom specification pdb2site convert PDB file to dms site file surface display a model s solvent accessible surface vdw display van der Waals surface vdwopt set van der Waals surface options Presentation Graphics conic display shadowed space filling image ilabel label an SGI image with arbitrary text itops convert an SGI image or TIFF file to Color PostScript label3d create labels that neon ribbonjr can render neon generate a molecular model with solid stick bonds and shadows ps2illustrator convert copy output to Adobe Illustrator format ribbonjr display secondary structure ribbon image stereoimg show rendered stereo pair stereops2illustrator convert stereo copy output to Adobe Illustrator format Bond Rotation angle monitor bond or dihedral angle assign assign functions to sliders brotation initiate a backwards bond rotation fix make bond rotations permanent fixreverse fix and reverse bond rotation reverse reverse the direction of a bond rotation rotation initiate a bond rotation speed set the control speed of sliders and spaceball Structure Creation Modification addaa add an amino acid to the end of a molecule
37. MIDAS object format is described in detail under Non Molecule Graphics Objects in Part III of the MidasPlus manual Inventor format is the standard Silicon Graphics format inventor output may be viewed using ivview 1 SceneViewer 1 or showcase 1 Rayshade and pov output are for use with raytracers of the same name The format description may be found with in the raytracer docu mentation Screen is not actually a file format instead the ribbon representation is displayed directly on screen using the OpenGL or Silicon Graphics GL library there is no output file Tiff output requires that an output file be specified though it needs to use the screen to calculate the image The default output format is screen even if an output file is specified except on NEXTSTEP systems where neither screen nor tiff formats are supported To use other formats use the f command line flag see below Capturing Screen Images in Part III of the MidasPlus manual discusses saving converting and printing ribbonjr images COMMAND LINE FLAGS The command line flags interpreted by ribbonjr are a Do not display any atoms using balls and sticks By default all non mainchain atoms and bonds are displayed b r g b r g b r g b Set the background color in RGB format each component ranges between 0 and 1 If one set of RGB values is given then the entire background is set to that color If two sets are given the backgroun
38. MIDAS reply area Note that one of the out put commands starts with rm This is to get MIDAS to remove a temporary file that noeshow produces APPENDIX 6 158 UCSF MidasPlus NOESHOW 1 NOESHOW 1 You may wish to remove this temporary file yourself by typing in the output rm command to the shell window less the leading Mardishow Mardishow is used to display constraints that are in MARDIGRAS input format and can be used to display constraints in MARDIGRAS output format though noeshow can be used to display MARDIGRAS output also as outlined in the Distance constraint preparation section above This section will outline the salient differences between using noeshow and mardishow Mardishow displays constraints in the two MARDIGRAS formats directly i e the constraints do not need to be converted to an intermediate format unlike the procedure for noeshow Since neither MARDIGRAS input nor MARDIGRAS output format constraints have an energy well asso ciated with them displayed constraint violations are color coded differently than in noeshow When show ing MARDIGRAS output format constraints mardishow constructs a fake energy well by using the given upper and lower bounds to define the floor of the energy well The edges of the well are placed 0 5 angstroms beyond the given bounds this margin can be changed with the d option Coloring is then as in n
39. NAME GENTPL 1 gentpl generate a MIDAS template from a Protein Data Bank coordinate file SYNOPSIS gentpl r residue i infile c radiifile DESCRIPTION Gentpl is a utility program for generating a MIDAS template from a Protein Data Bank coordinate file Standard input is assumed unless otherwise specified One file is produced the ASCII instruction file residue ins where residue is the residue name specified on the command line These files are placed in the directory defined by the MODELS variable in the user s program environment see Building and Modifying MIDAS Templates in Part III of the MidasPlus User s Manual specifies the residue name This name must correspond to the residue name as it appears in the Protein Data Bank input file specifies an input file The input must be in standard Brookhaven Protein Data Bank for mat The file may contain data other than the coordinate data for the specified residue but these extraneous records are ignored specifies a file containing the radii of the atoms used to calculate the connectivity If no file specified the program uses as default usr local midas resource connect tpl The format of the radii file is a series of records containing the atom name followed by the atom radius in angstroms At least one space must appear between the atom name and the radius indicates verbose mode and is useful for tracking down errors The radii fi
40. OO PIXE VEILS E AEE EAE EEE wees ede ocd ees note PYG VA A AE EE cic ce tacos beh Seber be sark age ba dae eRe E eee KSOSS Dinie fe shs cana eessndesnves bene tes cte a A taduad a E EE a feds TO DOM EEPE AREA A Labeucebs Mest undone ne fviaeens de fcapaecesde celeb vee oteaaate eset Seo ede Makemark i n cactevin ne cae casa snes ee sug etsy va ates AENT Matrixcopy Matrixget Matrixset 0 eee eeeeeeseessecseesseceecesecnecsseeeeeesees Midasmoviesie s3 0 a a dd ee a eee aes Midaspush Midaspop eseecesceesceeceseeeeeeeeecseeseecaeesaecsecaecseceseeeeensees A CON e EE nose Bust acai ses nite Mani Mise nee tsa rethiaes Pdbr n ss se echoed oie Ridin eae eE E A eda ea a iin Pickatom Pickabort corrr errie i a i eenia TAR TA m0 o E E E EEA EN ESET leeti ala0 ANO E doves scent fonts Mech E EEES E E EE EEEE Reveleson r E E E S E e r E E T EN E RiDDON IR ennnen e N a A E AE EE Rl bel nemetan cee r E hoa sca Fahad E Bo cas EA ESEESE teh ii Selesi see deeseaseetssh eevee ded Re Set Unset otc eh SOCOM eae eree E EEES EEE ioa Speedracer SUELO ieda Stereoimg eeeseeeseeseseeereerorsrerererserees SLOP T Watch Watchopt eee WiNdOW sisirin araras Part III Advanced Concepts o e Connectivity and Templates o oo Molecular Surfaces cecceeseeseeeeeeeeeeees VDW Surfaces ceeeeeeeeesseceeeees Solvent Accessible Surfaces Running Dms Directly Electrostatic Potential Molecular Surf
41. PDB file cone x y zr g b dx dy dz angle Define a cone light The absolute Cartesian coordinates of the light source are x y z The color of the light is given by r g b The Cartesian direction of the cone light is given by dx dy dz and the half angle of the cone is angle degrees eyergb APPENDIX 6 106 UCSF MidasPlus CONIC 1 CONIC 1 Conic places an additional point light source which coincides with the eye position The purpose of this light source is to weakly illuminate shadowed areas so that they have discernible features rather than a uniform color The eye option sets the color of the point light source The default value is 0 3 0 3 0 3 format image format Use the given image format if possible see the f option above fov angle Sets the field of view half angle in degrees The default value is 15 degrees input file Use file as the Protein Data Bank file lightx yzrgb Add an infinite light source to the scene being computed The direction of the light source is specified by x y z The color of the light source is specified by r g b By default conic defines a light source with direction 1 1 1 and color 1 1 1 The default light source is removed if other sources are specified via the light option location x y Sets the image location on the screen This parameter is only meaningful if the output is to the screen i e for output format screen Is_flags flags Change the default flags of subse
42. PDB file containing the desired group and no model building tools are available If so refer to Protein Data Bank Format in part 3 of the MidasPlus User s Manual for the exact format description You would need to create a file containing a single residue containing the group of interest with explicit CONECT records for all atoms in the file A much more pleasant alternative if you have a PDB file on hand with the group in it or can make a basic PDB file containing the group that MIDAS can display is to use MIDAS to generate the final PDB input file The procedure would be to open the starting PDB file in MIDAS limit the display to the residue of interest and then run the command pdbrun conect nouser cat gt final_PDB_input_file To continue the example of generating a lysine side chain group description file if the standard PDB entry lgcn were open in MIDAS as model 0 then the following commands would be used show 0 12 display only lysine residue pdbrun conect nouser cat gt lysgroup in save PDB file with CONECT records into lysgroup in Running pdb2group Referring to the SYNOPSIS section above the anchor_atom specified on the command line should be the first added atom of the new group when the group is added to an existing structure N3_atom and n2_atom are atoms that are not in the new group but that the new group connects to N3_atom connects directly to the anchor_atom and n2_atom connects to n3_atom
43. So in the lysine group example the appropriate pdb2group command would be pdb2group a CB 3 CA 2 C d Lysine lysgroup in gt lysgroup out SEE ALSO MidasPlus User s Manual AUTHORS Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 163 UCSF MidasPlus PDB2SITE 1 PDB2SITE 1 NAME pdb2site convert a PDB file into a DMS site file SYNOPSIS pdb2site i PDB_file o site_file DESCRIPTION Pdb2site reads a Protein Data Bank file and converts it into a site file suitable for use with the i flag of dms 1 The i argument specifies the input PDB file If no input file is given pdb2site will read from stan dard input The o argument specifies the output site file If no output file is given pdb2site will write to standard output Pdb2site is frequently used in conjunction with MIDAS to generate a site file for use with dms 1 The pro cedure would be to display the atoms of interest in MIDAS and then type the command pdbrun pdb2site o site_file This would generate a file called site_file which is in the format appropriate for a dms site file SEE ALSO dms 1 MidasPlus User s Manual Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description AUTHOR Conrad Huang Computer Graphics Laboratory University of California San Francisco APPENDIX 6 164 UCSF MidasPlus PDBOPEN 1 PDBOPEN 1 NAME pdbopen Midas delegate for browsing and opening PDB entries
44. The following property descriptions are mandatory field number Each data point has number values associated with it This includes the three Cartesian coordinates so the minimum value for number is 3 data This must be the last property description Subsequent lines in the file are treated as data points The following property descriptions are optional count number There are approximately number data points This value is only advisory and discern will only use it to guide memory allocation strategy nside number Ellipsoids will be drawn with number longitudinal lines The default value of this pro perty description is 5 It must be at least 3 nlayer number Ellipsoids will be drawn with number latitudinal lines The default value of this property description is 1 It must be at least 1 and odd size number If the user does not issue a size command ellipsoid axes lengths will be scaled by a fac tor of number The default value of this property description is 1 directional Normally ellipsoids are drawn with the major axis parallel to the z axis This property description specifies that for each data point the three columns following the initial Cartesian coordinates form a direction vector for the major axis of the ellipsoid Each line following the property descriptions is treated as a single data point Each data point is represented as a list of floating point numbers The first three items in the list form the initial C
45. Way House Elms Parade Oxford OX2 9LL England or by contacting Peter Goodford himself at peter biop ox ac uk APPENDIX 6 128 UCSF MidasPlus GENNUC 1 GENNUC 1 NAME gennuc Generate double helical DNA or RNA structures SYNOPSIS gennuc t structure type sequence file DESCRIPTION Gennuc generates a Protein Data Bank PDB formatted file of coordinates on standard output representing double helical DNA or RNA structures built from standard base pair coordinates Valid structure type code s are brl right handed B DNA in Langridge configuration bra right handed B DNA in Arnott configuration bls left handed B DNA in Sasisekharan configuration ara right handed A DNA in Arnott configuration arn right handed A RNA in Arnott configuration apr right handed A RNA in Arnott configuration The base pair input sequence is read from the named file or standard input if no sequence file is given Valid codes for DNA are A T C and G for adenine thymine cytosine and guanine Valid codes for RNA are A U uracil C and G Either uppercase or lowercase characters may be used Invalid codes are noted but otherwise ignored SEE ALSO Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description BUGS Doesn t know about Z DNA AUTHORS T E Ferrin and N Pattabiraman Computer Graphics Laboratory University of California San Francisco APPENDIX 6 129 UCSF MidasPlus GENTPL 1
46. a bond from CA to C draw a bond from C to O lift up the pencil and move it back to C draw a bond to OXT you will find a pattern of connectivity for glycine such as can be found in any standard biochemistry text 3 Templates specify connectivity only and do not give any information about bond angle or bond length In MIDAS connectivity is determined by the MOVE and DRAW instructions in the template files not by the distance between atoms unless no template exists If the user provides coordinates for glycine in which the distance from the C to the O is 10 angstroms MIDAS is constrained to draw the long bond because of the connectivity specification in the glycine template It is the user who defines the tem plates and ultimately controls which atoms are connected 4 The observant reader may have noticed that the carboxyl acid group contains two oxygen atoms OXT and O If this GLY residue is the terminal amino acid in a peptide chain then both oxygen atoms are appropriate to the model If however the residue appears within a sequence of amino acids then only one oxygen is appropriate and the bond to the atom named OXT is not drawn but instead a bond is drawn between the END atom in this example a carbon and the START atom of the next residue typically a nitrogen in the case of amino acids MIDAS decides which bonds not to draw in this case by ignoring atoms which appear in the template but for which the user p
47. a keyword and some values The pdbrun command of MIDAS generates output of this format The keywords that conic uses are COLOR RADIUS and MATPROP COLOR is followed by three floating point RGB intensities and a color specification RADIUS is followed by a floating point number representing the atom radius in angstroms MATPROP is followed by the three parameters to the matprop option in the configuration file Once a COLOR RADIUS or MATPROP is given it applies to all of the succeeding atoms in the file An example of the extended format follows USER COLOR 0 000 1 000 0 000 green USER RADIUS 1 800 USER MATPROP 0 500 0 250 16 000 ATOM 1I HIS 1 49 168 26 701 10 916 1 00 16 00 If the input fails to specify the color radius or material properties of an atom conic uses an atom informa tion file to supply missing values The file contains comment lines which begin with and information lines which have either five or eight fields atom type radius an RGB triple and optionally three material property values see the matprop keyword in the CONFIGURATION FILE section for the meaning of material property fields and their default values The atom type is either one or two characters and is used APPENDIX 6 108 UCSF MidasPlus CONIC 1 CONIC 1 to match the atom type in the PDB input The atom type is a special case and matches any atom which does not match any other information lines Using an atom informat
48. a multi font label To make the label B sheet start with the command ll label 0 43 N b Note that there is a trailing space at the end of the above command so that the text that will be appended later sheet will have a space separating it from B The attributes of the new label could now be set with justify right bottom use g colordef dgreen 0 0 0 6 0 0 color dgreen The remainder of the label would be appended with append sheet The appended part of the label would be set to roman font and the entire label given additional space from the structure with the commands Making a title use r offset 2 0 Since titles are not associated with any particular atom one creates a title at the origin with a command such as label Structure and use scale and position to size and position it scale 2 position 14 6 35 The above position command places the title in the lower right area of the screen and due to the positive z in front of the molecule This z positioning is useful in stereo views Finishing labeling It is rarely desirable to stop the label3d delegate since the label positions then can no longer be updated to compensate for model rotations However occasionally the user may wish to remove all current labels and start over In this case do not use the MIDAS delegate stop command Instead use the label3d command stop Thi
49. aliasing as per the above 3 12 1 1 Competing with Background Jobs If your MIDAS workstation is also used for long running background computation jobs you may experience degraded performance due to the fact that memory areas containing MIDAS code and data may be swapped out to disk in favor of background jobs when the MIDAS user is not actively manipulating the model or typing commands If it is desirable to have MIDAS wire down its memory areas and prevent them from being swapped out you can do so with the devopt memlock on command If you get an error message when executing this command then your system administrator did not enable this option when installing MIDAS The MidasPlus Installation Guide describes how your system administrator can enable the option if it is desired to do so 3 12 2 SGI Specific Performance Issues In the MidasPlus 2 0 release the MIDAS binary provided for SGI systems was written using the Iris GL graphics library Since that time SGI has transitioned to the OpenGL graphics library and new SGI systems support OpenGL natively i e their graphics hardware is designed for OpenGL and support for Iris GL pro grams is provided through compatibility libraries Conversely older systems with native Iris GL hardware support OpenGL through compatibility libraries This raises a performance issue in that some graphics boards exhibit markedly degraded performance when used with the non native type of library
50. all known page types The p option sets the page type the default is Letter The r option rotates the image so it is in landscape mode instead of portrait mode The g option gamma corrects the image data by the given amount Depending on the printer this value should range from from 0 9 to 2 2 the default is the same value as is used for the screen The s option scales the image by the given amount The a option overrides the s option and automatically scales the image to fit the page type If the r option is given as well then the image is optionally rotated for the best fit The i option makes one pixel match one square PostScript unit Otherwise a pixel is normally shrunk to give the PostScript image the same size as the screen image The b option sets the number of bits per color to download 8 is equivalent to 24 bit RGB other possible values are 1 2 or 4 For printers with small color gamuts you can speed up printing by using a value smaller than the default of 8 The q option suppresses all informational and error messages quiet The z option will remove zap image file after conversion The 8 option tells itops to generate binary 8 bit PostScript The resulting output cannot be sent to most PostScript printers but is approximately half the size The E option changes the output to be an Encapsulated PostScript file that is meant to be included in other documents It wil
51. atom name is C then the atom is carbon and so forth for N nitrogen O oxygen etc MIDAS creates a surface around each atom clipping off areas of overlap to create a Corey Pauling Koltun CPK type model The radii and density of dots used can be changed with the vdwopt command in MIDAS 2 A solvent accessible surface may be calculated for any molecule This surface is defined by rolling a theoretical water probe around the van der Waals surface of the molecule and using the contact and reentrant points to determine the surface This type of surface is smooth free of seams between atoms since the surface is determined by a probe water molecule These two types of molecular surface representation differ significantly in their speed of generation and utility Vdw surfaces are generated quickly and do not break or tear with bond rotations Solvent accessible surfaces take approximately 100 times longer to compute and the surface tears with bond rotations 3 2 1 VDW Surfaces The vdw command in MIDAS will display the van der Waals surface for all atoms of a MIDAS model or a subset of atoms as described in the Command Reference Guide section of this document The user selects those atoms residues and models for which the surface is displayed Often the user does not want the surfaces of all atoms both interior and exterior displayed but rather only the surfaces of those atoms which comprise
52. command reset default Other orientations may be saved using the savepos command Savepos view_name UCSF MidasPlus 44 UCSF MidasPlus and retrieved using the reset command reset view_name For a list of existing view_names give the command reset list See also align push pop savepos window 2 4 64 Reverse Usage reverse rotation_number Reverse reverses the direction of a bond rotation If the direction is reversed then the portion of the molecule which rotated previously as delineated in the rotation command description remains fixed and vice versa in subsequent rotations Also the rotation angle is reset to zero degrees Warning In assigning multiple bond rotations to a model two rotations cannot affect a common set of atoms unless one affected set is a complete subset of the other That is rotations must be properly nested In executing reverse reversing the bond rotation may cause such a conflict and be disallowed Reversing bond rotations must be done in an appropriate order such that all intermediate combinations are legal see rota tion See also brotation rotation fixreverse 2 4 65 Ribbonjr Usage ribbonjr options The ribbonjr command produces an aesthetic representation of the secondary structure of the displayed molecule s in a manner reminiscent of a Jane Richardson drawing The current model orienta tion and coloring is retained There are many options which are detailed fully i
53. field contains the residue sequence number Notice that as the residue changes from his tidine to serine the residue number changes from 1 to 2 Two like residues may be adjacent to one another so the residue number is very important for distinguishing between them The next three data fields contain the X Y and Z coordinate values respectively The next data field is the occupancy and is not used by MIDAS The final data item is an optional atom temperature factor The glucagon data file continues in this manner until the final residue is reached ATO 239 N THR 29 3 391 19 940 12 762 1 00 21 00 ATOM 240 CA THR 29 2 014 19 761 13 283 1 00 21 00 ATO 241 C THR 29 826 19 943 12 332 1 00 23 00 ATO 242 O THR 29 932 19 600 11 133 1 00 30 00 ATO 243 CB THR 29 1 845 20 667 14 505 1 00 21 00 ATO 244 OG1 THR 29 1 214 21 893 14 153 1 00 21 00 ATO 245 CG2 THR 29 3 180 20 968 15 185 1 00 21 00 ATO 246 OXT THR 29 317 20 109 12 824 1 00 25 00 TER 247 THR 29 Note that this residue includes the extra oxygen atom OXT on the terminal carboxyl The TER record ter minates the amino acid chain A more complicated protein fetal hemoglobin consists of two amino acid chains alpha and gamma and two heme groups The first ten lines of the PDB file for this molecule appear as ATO 1 N VAL A 6 280 17 225 4 929 1 00 0 00 ATO 2 CA VAL A 6 948 18 508 4 671 1
54. handed pi Left handed gamma 4 5 Oaornan Right handed gamma 2 7 ribbon helix Right handed 3 10 10 Polyproline Parallel is indicated with 1 anti parallel with 1 Strand 1 has sense indicator 0 UCSF MidasPlus 70 UCSF MidasPlus For those who are familiar with the FORTRAN programming language the following format descrip tions will be meaningful For those users unfamiliar with FORTRAN ignore this gibberish ATOM HETATM Format A6 I5 1X A4 A1 A3 1X A1 14 A1 3X 3F8 3 2F6 2 SSBOND Format A6 1X I3 1X A3 1X A1 1X 14 4X A3 1X A1 1X 14 CONECT Format A6 11I5 HELIX Format A6 1X 13 1X A3 2 1X A3 1X A1 1X 14 A1 12 A30 SHEET Format A6 1X 13 1X A3 12 2 1X A3 1X A1 14 A1 12 2 1X A4 A3 1X A1 14 A1 3 3 2 Examples of PDB Format Glucagon is a small protein of 29 amino acids in a single chain The first residue is the amino terminal amino acid histidine which is followed by a serine residue and then a glutamine The beginning portion of the PDB file appears thus ATO 1 N HIS 49 668 24 248 10 436 1 00 25 00 ATOM 2 CA HIS 50 197 25 578 10 784 1 00 16 00 ATO 3 HIS 49 169 26 701 10 917 1 00 16 00 ATO 4 O HIS 48 241 26 524 11 749 1 00 16 00 ATO 5 CB HIS 51 312 26 048 9 843 1 00 16 00 ATOM 6 CG HIS 50 958 26 068 8 340 1 00 16 00 ATO 7 ND1 HIS 49 636 26 144 7 860 1 00 16 00 ATO 8 CD2 HIS 51 797 26 043 7 286 1 00 16 00 ATO 9 CEL HIS 49 691 26 152 6 454 1 00 17 00 A
55. i flag Residue sequence numbers involving letters may cause problems W Change the water probe radius from the default radius of 1 4 angstroms This parameter must be between 1 0 and 2 0 The output consists of a series of atom and surface point records with the same format for the first six fields Each atom is followed by the surface points if any which belong to it These first six fields are in the following format residue name sequence number atom name x coordinate y coordinate z coordi nate For an atom record the seventh field is A For a surface point record the seventh field begins with an S followed by a C or R according to whether the point is part of contact or reentrant sur face This is followed a digit used for depicting different density levels The eighth field is the molecular surface area associated with the point in square angstroms If the n flag is specified the next three fields are the unit normal vector pointing outward from the surface Informative messages and errors are written to the standard error output unless a g file is specified The calculation takes about 5 seconds per atom for molecules of fewer than 1000 atoms and 7 seconds per atom for larger molecules timings are for a VAX780 The chemical elements that the program can currently handle are those which the author has found to occur in molecules of interest and whose van der Waals radii could
56. image format as described in the preceding two sections Such files can then be converted to printable PostScript files with the itops 1 utility described in Appendix 6 Itops produces PostScript on standard output which can be redirected to a file or piped directly to a print spooler either lpr or lp depending on your system s setup A typical command issued from the UNIX command line to pro duce a printout from an image file would be itops a r saved_image lpr Pprintername The a flag allows auto scaling to best fit the image on the printed page and the r flag allows the image to be optionally rotated 90 degrees for best fit Consult the itops manual page for other options 23 Note that despite the fact that conic can produce PostScript with the f ps flag the product is Encapsulated PostScript that while suitable for inclusion in other documents cannot be printed directly To produce directly printable conic PostScript the procedure above of producing a TIFF or SGI image file and converting it must be followed 3 6 4 Inclusion of Images in Documents The preparation involved in including an image in a document largely depends on the type of document itself which can be anything from a web page to a journal publication Most popular web browsers can directly image TIFF files and all graphical browsers can image GIF files so images saved in those formats are typically used in w
57. in the MIDAS command window The list of commands is given below Other than open and use all dis cern commands are applied to a single selected model there can only be one selected model at any given time open model_number datafile_name Open the file datafile_name and display it in MIDAS as model model_number If model_number is absent use the lowest available model number This command also makes the newly opened model the selected model use model_number Make model model_number the selected model symbol nside ns nlayer n aspect na Redisplay the selected model using ellipsoids with ns longitudinal lines nl latitudinal lines with the ellipsoid compressed length to width by a factor of na Any of the three specifications may be omitted in which case the value will remain unchanged For a newly opened object the default values for ns nl and na are 6 1 and 1 0 respectively property name formula Define or list a property for use with the size major minor and color commands If for mula is omitted the formula for computing property name is listed otherwise the for mula will be used for computing property name any previously defined formula is dis carded The formula consists of data columns the usual arithmetic operators and sim ple function calls Data columns are introduced by the character followed by the column number columns are numbered starting from one not zero Arithmetic
58. input to widely available raytracers see also x option Unfortunately due to the large triangles used to render the bicubic patches shadows generated by these raytracers look wrong in certain places Due to this limita tion the pov output actually turns off shadow computation g Display guide atoms at their true Cartesian coordinates Normally when atoms are displayed guide atoms are displayed at interpolated locations on the ribbon rather than at their Cartesian coordinates which may not be on the ribbon since the ribbon is not guaranteed to pass through the guide atom Displaying guide atoms on the ribbon typically makes the image look better because side chains are attached to the ribbon itself rather than hanging in space h Turn off half bond mode Normally bonds are drawn as two cylinders each with the color of the closer atom Turning off half bond mode makes ribbonjr use half as many cylinders making interactive performance considerably better l ambient diffuse specular shininess Set the lighting parameters of ribbons balls and sticks The values are the ambient diffuse and specular reflectance and shininess of the material All values should be between O and 1 The default values are 0 5 0 5 0 5 and 0 5 respectively m draw mode Select the ribbon representation The supported modes are 3D and flat The 3D mode produces Jane Richardson type ribbon representation of the molecule The flat mode produces two cur
59. labels to be any point size The default font size is 12 The default font on the SGI is raster which is not scaleable so setting a font size for it has no effect linewidth Controls the thickness with which bonds are drawn The default is 1 and larger values produce thicker lines and slower interaction On some systems if anti aliasing is turned on lines cannot be wider than 1 devopt smooth off will turn off anti aliasing molpath A colon separated list of directories that will be searched for PDB files by the open com mand Tildes can be used to refer to user s home directories la csh 1 If the PDB file is not found in any of the molpath directories or the current directory then MIDAS will attempt to be smart and treat the molpath directories as PDB distribution style directories and look for the file again This only occurs if the given file name is 4 charac ters long i e it seems to be a standard 4 character PDB identification code If so then the molpath directories will be searched for a subdirectory with a 2 character name the same as the middle 2 characters of the PDB ID code If such a subdirectory exists then it will be searched for a file by the name of pdbidcode ent For example if attempting to open 1gcn the molpath directories will be searched for gc pdb1 gcn ent nameplate Controls the placement of the MidasPlus logo on the bottom of the screen A value of 0
60. mark command documentation for further details For maximum efficiency a delegate should prevent MIDAS from transmitting pdbrun information that is not of interest The pdbrun keywords nouser do not include USER records and noobj do not include non molecular graphics object descriptions are used for this purpose It is also possible to write delegates that start MIDAS instead of the other way around If midas is started with the d delegate_name option then midas will treat its standard input and output as a delegate of the given name which make it possible for midas to be started as a subprocess from a delegate program Other Resources and Information As a delegate implementor you may be able to reduce your work considerably by being aware of the follow ing e MIDAS can display non molecular graphics objects composed of lines dots and or text This maybe of use if your delegate needs to graphically annotate the displayed molecules See section 3 10 Non Molecular Graph ics Objects for more details e The MidasPlus distribution provides C and C libraries to simplify PDB format input and output There are man pages for pdb and pdb that describe the routines provided and how to access them e Source code for some MidasPlus delegates is provided in the directory usr local midas resource examples delegates Examining the source code may help clarify some aspects of delegate design and
61. ms or dms utility used to gen erate solvent accessible surfaces and that the surface should be associated with the indicated model_number model_number cannot be omitted in this case Optionally a surface file surface_filename may be specified as a fourth argument in which case the ms or surface keyword would be omitted The opened surface is associated with the open model An opened surface file is not initially displayed since it may be quite large See the surface command for displaying all or part of an open surface MIDAS can read ms and PDB files that have been compressed using the UNIX compress command Compressed ms and PDB files use substantially less disk space than regular files There is no need to first uncompress the files or to specify any special keyword on the open command line If open is used with the object keyword the file is assumed to specify a non molecule graphic object and can be opened as a new model or associated with an existing model Each line in the object file is a command or text If it is text then it is displayed in the current color and font at the current position All of the commands start with a period and are as follows UCSF MidasPlus 40 UCSF MidasPlus comment text comments C text comments font name size set font and size color color_designation set color see below cmov x y z set character position dot xy z show dot at position marker x y z show marker at position
62. mxy z move to location move xy z move to location dxy z draw line from last location draw xy z draw line from last location The color_designation parameter to the color directive can be simply a single MIDAS color including user defined colors see colordef or two colors and a mixture fraction separated by commas The mixture fraction is a number between zero and one that indicates the relative amounts of the two colors to use to get the actual color Zero indicates use exclusively the first color while one indicates use only the second color If the autocolor option has been set using the command set autocolor then each newly opened model without color definitions will be given a unique color so that different models can be easily dis tinguished To close a model use open followed by the model number If a model is closed and another model opened with the same model number then none of the transfor mations applied to the previous model are applied to the newly opened model Note that this is in direct con trast to some previous versions of MIDAS where all the transformations were applied in order to facilitate docking If docking is necessary one model s transformation matrix can be applied to another model with the matrixget matrixset commands Filename may be a pathname to a file or the name of a file in the current working directory To change directories use the cd command See also cd makems match write
63. on the fieldmerge manual page APPENDIX 6 184 UCSF MidasPlus VIDEODISK 1 VIDEODISK 1 AUTHOR Greg Couch APPENDIX 6 185 UCSF MidasPlus VIEWDOCK 1 VIEWDOCK 1 NAME viewdock Midas delegate for browsing DOCK output USAGE viewdock m PDB_file DESCRIPTION One of the problems of dealing with DOCK output is that there is a large number of compounds to examine and MidasPlus does not offer a simple interface for browsing through these compounds Some compounds may be discarded immediately upon visual examination since they obviously do not fit well others may need to be examined further depending on their scores format described below file named on the command line starts MIDAS to display the compounds and presents a panel for examining manipulating and annotating compound information If a file named PDB_file info is present viewdock assumes that it is from a previous session and will use the additional compound information from that file If viewdock is invoked with the m flag MIDAS will not be invoked this option may be used to scan through the PDB file without having to look at all the atomic coordinates Viewdock is a MidasPlus delegate that reads a list of compounds from a Protein Data Bank PDB format The PDB file that viewdock reads should be an edited version of the extended PDB file produced by DOCK The file contains a list of compounds each of which consists of a set of REMARK recor
64. open command is used to open prepared MIDAS solvent accessible surface files followed by the surface command to display the surface Alternatively the vdw command may be used to display the model s van der Waals surface Display of this surface requires no advance calculation and is more convenient unless the solvent accessible surface is specifically desired Examples surface 0 display the surface for model 0 surface 1 5 display the surface for model 1 residue 5 surface 1 5 32 64 undisplay surface for model 1 residues 5 32 and 64 See also makems vdw 2 4 86 Swapaa Usage swapaa new_residue_type preserve residue Swapaa replaces residue with a new_residue_type residue Both the old and new residue must be stan dard amino acids New_residue_type is a three letter residue name residue is a single residue specified by number e g 21 or unique residue name e g LYS The side chain of the new residue will be in stan dard conformation unless the preserve keyword is given in which case as much of the existing conformation as possible is saved Preserving conformation can cause rings to become nonplanar e g swapping in a PHE for a LYS while preserving conformation The temperature factor for the new residue is set to the highest currently found in the model UCSF MidasPlus 56 UCSF MidasPlus 2 4 87 Swapna Usage swapna new_residue_type preserve residue Swapna replaces residue with a new_resid
65. options you may want to change at times 3 12 1 Issues Common to All Platforms There are two aesthetic options normally enabled in MIDAS that you may want to disable for increased performance anti aliasing smoothing of line segments and half bond coloring Disabling anti aliasing will result in lines with considerably more noticeable stair stepping artifacts but can significantly increase performance on some platforms particularly those with no hardware anti aliasing support Anti aliasing is turned off with the command devopt smooth off Disabling half bond coloring means that bonds drawn between atoms of different colors will not be half one color and half the other Instead the entire bond will be the color of one of the two endpoint atoms This makes little visual difference for uniformly colored models or models colored on a per residue basis but may be unsatisfactory for models colored on a per atom basis But since MIDAS only has to draw one line for each bond instead of two disabling half bond mode can result in a two fold speedup on some plat forms Half bond mode is disabled with the command set halfbond It should be noted that if you use thicker lines than the default via the set linewidth command this has much the same impact on performance as anti aliasing and in fact combines with anti aliasing If you wish to use increased line widths but experience sluggish performance you should investigate disabling anti
66. penalty would APPENDIX 6 153 UCSF MidasPlus NOESHOW 1 NOESHOW 1 begin to be applied The distances where the energy penalty reaches a maximum is taken to be 0 5 angstroms beyond the given bounds on either side The default value of 0 5 can be changed by giving the v option flag to xplor2amber followed by the desired distance As described later the bounds of the energy well determine whether the constraint will be shown as satisfied or violated see the Basic usage section Xplor2amber will normally interpret segids in the X PLOR constraint file as chain IDs in the con verted file The e chain_ID option to xplor2amber will cause it to give all atoms the specified chain ID Note that specifying chain_ID as a quoted space will give the atoms no chain ID even if segids are present in the X PLOR constraint file DIANA DIANA format constraints are handled in almost the same manner as the just described X PLOR format constraints The only differences are that the conversion script is diana2amber instead of xplor2amber and that instead of specifying a single bounds file on the command line separate lower and upper bounds files in that order are specified Also there is no c option for diana2amber AMBER SANDER namelist Running the sander2amber conversion script as shown in the SHELL COMMAND SYNTAX sec tion above will produce a file of equivalent constraints in AMBER INTERFACE format Since AM
67. residue type The VDW ra dii data files that MIDAS uses for models with and without explicit hydro gens are respectively usr local midas resource midas vdw hydrogen and usr local midas resource midas vdw default Use the default or hydrogen options below to return to default values hydrogen Indicates that hydrogen atoms are included in the model and van der Waals radii should not compensate for missing hydrogens The result is smaller atom radii and distinct hydrogen atoms default Indicates that van der Waals radii should compensate for missing hydrogen atoms Vdwopt default undoes the effect of vdwopt hydrogen extend len Increases all van der Waals radii by the constant len angstroms Multiple extends are not additive instead the last extend has precedence define atom_type radius Indicates that all atoms with an atomic symbol of atom_type should be as signed a van der Waals radius of radius angstroms See also vdw 2 4 94 Version Usage version Version reports information about which version of MIDAS is currently being executed and is displayed in the reply area of the MIDAS window It is useful to supply this information when reporting MIDAS bugs so that it is possible to determine if the problem has already been solved in a more recent ver sion of the program UCSF MidasPlus 59 UCSF MidasPlus 2 4 95 Wait Usage wait wait_frames Wait suspends command processing for the given number of wait_frames or
68. residues 35 through 66 or a range of colors such as red blue shades of red magenta and blue separates names or ranges in an atom specifier but does not indicate a specific order e g 1 CA CB CG or 21 30 45 matches whole atom or residue names For example 0 CA selects the alpha carbon atoms of all residues matches partial atom or residue names e g 0 C matches all atoms whose names begin with C used for atom and residue names only For example G selects all three letter residue names beginning with G For example 5 selects every fifth residue in the se quence z lt zone and zr lt zone select all residues within zone angstroms of the indicated atoms za lt zone selects all atoms not residues within zone angstroms Using gt in stead of lt results in the complementary set of atoms b gt temp_factor selects all atoms with temperature factors greater than temp_factor b lt temp_factor selects all atoms with temperature factors less than temp_factor For example b gt 20 b lt 25 selects all atoms with tempera ture factors greater than 20 and less than 25 93 UCSF MidasPlus Symbol Function Usage e gt electrostatic potential e gt potential selects all atoms with electrostatic potentials greater than potential e lt potential selects all atoms with electrostatic potentials less than potential For example e gt 10 e lt 20 selects all atoms with electrostat ic potentials between 10 a
69. start atom FE1 is correct but the connection to the following residue should be made via FE2 instead of INC The file can be edited to read RESIDUE FEA START FE1 DRAW O DRAW FE2 DRAW NA DRAW NB DRAW NC END FE2 Sometimes gentpl is unable to generate a template from the PDB file because the atoms in the file are too far apart to determine the correct connectivity An error message appears indicating unreachable atoms gentpl uses a standard list of atomic radii for determining connectivity This list is located in usr local midas resource connect tpl Atoms falling within the standard distances in the list are joined Any atoms which are not joined to the main body of the residue are reported as unreachable atoms One approach to solving the unreachable atoms problem is changing the standard radii to larger values so that atoms which failed to bond before can be appropriately connected To do this one can 1 Make a copy of the atomic radii file in your own private directory using the command cp usr local midas resource connect tp connect 2 Edit connect to increase the atom radii so that the appropriate connections can be made 3 Use the gentpl program to create the new template For example if the residue for which we want to build a template is VLX and this residue occurs in the PDB file glx pdb the command used is gentpl r VLX i glx pdb c connect where connect is the name of
70. surface usr local midas bin neon alias quit stop alias rainbow pdbrun all nouser rainbow alias ribbonjr pdbrun surface ribbonjr alias stereoimg run stereoimg devopt move_windows on set record set text set labels set control 95 assign useful functions to the first few sliders pre assign some bond rotations define standard color names a few useful aliases aliases that start with only expand at beginning of commands several commands are actually pdbrun aliases preneon is useful if several neon outputs must be combined before conic processing help those new users by default keep the three MIDAS windows in same relative positions start remembering commands for later recording show command line and reply area show distance angle and rotation monitors show control panel UCSF MidasPlus set verbose autocolor halfbond set refmodel 1 newly opened models oriented same as lowest open model set reassign new slider assignments override old set molpath pdb mol pdb usr local midas resource pdb directories searched to locate PDB files APPENDIX 4 96 UCSF MidasPlus Appendix 5 The MidasPlus Delegate Mechanism What are delegates MIDAS has a rich command language and users can specify nearly all operations by typing them in on the keyboard Occasionally however it is useful to have other computer programs compose the commands This func tionality is partially provided by the
71. that is supposedly in PDB format you should consult the Protein Data Bank Format section in Part III of this manual which discusses the details of PDB file format as well as solutions to common problems found in non conformant PDB files If you already have a PDB format file that is known to be correct or you want to try out MidasPlus with one of the test files included with the software distribution the following section shows you how to quickly display a model and then manipulate it If MIDAS responds sluggishly on your system consult the Perfor mance Issues with Midas section in Part II of this manual for possible remedies 1 1 Displaying the Model The MidasPlus display program is used to display the PDB file To invoke the MidasPlus display pro gram give the command midas on SGI or Digital DEC Alpha workstations or open usr local midas bin Midas app on NeXT workstations This will bring up three windows a main modeling window a command and reply area below the main win dow and a sideview and controls area to the right of the main window Depending on your system the main window may be automatically sized and placed or you may be presented with a rubberband box for sizing and placing the main window In either case the secondary windows will place themselves in the correct rela tionship to the main window If you move the main window the others will follow and retain their same re
72. the MidasPlus package 2Based on Python http www python org UCSF MidasPlus 2 UCSF MidasPlus Acknowledgements The original version of MIDAS was written by Prof Thomas Ferrin and Dr Conrad Huang Dr Huang is also the principal author of MidasPlus the MidasPlus delegate facility and many of the current MidasPlus delegates Eric Pettersen and Greg Couch have also contributed significantly to the large effort required in programming test ing and documenting the many features the MidasPlus system offers All of these individuals are still affiliated with our laboratory The Laboratory Director is Prof Thomas Ferrin Thanks are due to many of our existing MidasPlus users for countless suggestions over the years that led to improvements in the system The development of Midas Plus is supported by the National Institutes of Health National Center for Research Resources NCRR P41 RR 01081 T Ferrin Principal Investigator Because a substantial portion of the funding for our laboratory comes from a NCRR grant P41 RR 01081 from the National Institutes of Health it is critically important that publications resulting from work using the MidasPlus system or incorporating graphical images produced with MidasPlus acknowledge our laboratory We ask that a statement similar to the following be used Molecular graphics images were produced using the MidasPlus package from the Comput er Graphics Laboratory University of California San Franc
73. the atomic radii file just edited Gentpl searches through the PDB file for the specified residue and uses the atomic radii in the connect file to generate the connectivity of atoms and the corresponding MIDAS template If this method fails to produce an accurate template the user must resort to creating the template instruction file with a text editor Refer to the previous section for a description and example of the connectivity instruc tion file Look at some of the ins files in the template library usr local midas resource midas models to use as examples Do not worry about the order in which the DRAW and MOVE commands appear in your instruc tion file as long as they correctly specify the connectivity and there is a path from the START atom to all other atoms in the residue 3 6 Capturing Screen Images It is frequently desirable to use MidasPlus images in contexts other than an interactive modeling session such as in publications web pages or presentations This section discusses saving screen images to disk in various formats some format conversions for saved files and how to print saved files as well as some tips for screen photography 3 6 1 Saving Screen Images to Disk The ability to save screen images to disk is important for several reasons e It is the first step in printing images e Saved images can be incorporated easily into web pages or otherwise electronically disseminated e Saved images can be annotated or othe
74. the molecular surface of a molecule The molecular surface resembles the van der Waals surface of a molecule except that crevices between atoms are smoothed over and interstices too small to accommodate the probe are eliminated The surface includes cavities in the interior of the molecule even if they are not accessible to a solvent molecule coming from the outside The molecular surface calculated is that defined by F M Richards 1977 Ann Rev Biophys Bioeng In particular the calculated molecular surface is that traced out by the surface of the probe sphere rather that the probe sphere s center According to Richards definition the molecular surface consists of two parts contact surface and reentrant surface The contact surface is made up of those parts of the molecular van der Waals surface that can actually be in contact with the surface of the probe The reentrant surface is defined by the interior facing part of the probe when it is simultaneously in contact with more than one atom Dms reports the amounts of contact and reentrant surface area and the combined total surface area on the standard error output see the g flag below File is an input file of coordinates The input file must be in the Protein Data Bank format The first letter or first two letters of the atom name is used to determine the element type By default implicit hydrogens are included for carbon nitrogen and oxygen atoms thus aro
75. the surface of the molecule or the surface of an active site It can be a tedious process in MIDAS to select each of these surface atoms individually or even residue by residue The zone specifiers in atom specifications section 2 1 4 provide a convenient way to select specific sites of interest Example of Site Selection Suppose the user wants to display the surfaces of only those atoms within a certain distance of a particular set of atoms or coordinate positions as in determining an active site of a molecule If the receptor s PDB file were opened as model zero and the ligand s PDB file were opened as model one the following command vdw 1 za lt 8 will show the vdw surface of only those atoms within 8 angstroms of any ligand atom coordinate value If the user wishes to change the test radius from 8 angstroms to 12 angstroms for example the command line is vdw 1 za lt 12 See section 2 1 of this document for additional details on how to specify atoms and zones around atoms 3 2 2 Solvent Accessible Surfaces There are two approaches to creating solvent accessible surfaces for use with MIDAS The first easier approach is to use the makems delegate while in MIDAS itself to interactively specify what atoms or models to surface Makems will then invoke the dms program appropriately to compute the solvent accessible surface and display the resultant surface in MIDAS While simple this approach has some limitations that may make i
76. the time the map file is created It is generally a few percent of the unit cell size center atom Defines the center of the contoured region The easiest way to specify the central atom is by using the MIDAS pick mechanism described under Atom Picking in Part II of the MidasPlus manual display mapfile_prefix model_number contour_level contour_color contour_level contour_color The display command generates the electron density contours at the specified contour levels in the specified colors and opens them as model model_number Up to four con tour level color pairs can be specified Mapfile_prefix is one of the X PLOR map file names specified on the delegate start command line with the map extension removed Contour maps can be closed using the open model_number command and can be turned off and on with the objdisplay model_number command Note that density only examines the first character of any command keyword so for instance the command display could be shortened to disp or just d if desired EXAMPLES The following commands would be used to open contour maps at levels 2 0 colored blue and red around the iron atom in residue HEM from the X PLOR file dens map as model in MIDAS delegate start dens density dens map Read the data from the X PLOR map file dens map dens center 0 HEM FE Center the contours about the iron atom in the HEM residue dens display dens 2 0 blue 2 0 red Display contours
77. to each surface point specifies neutral spheres Charges are summed within the cutoff radius defining the sphere and an equal and opposite charge is spread uniformly across the sphere surface indicates the cutoff radius in angstroms The default value is 10 0 Epsilon is the dielectric constant or if the r flag is specified epsilon is the factor that is multiplied by the distance in angstroms to give the effective dielectric The default value is 1 0 calculates the potential at a distance len angstroms from the surface Positive values of len lie outside of the surface while negative values lie within the surface The default value of len is 1 4 angstroms indicates that the electrostatic potential of each point should be appended to the corresponding line in the input dms_file indicates verbose mode Auxiliary information e g the number of points found for each atom is reported dms 1 midas 1 MidasPlus User s Manual AUTHOR Conrad Huang UCSF Computer Graphics Laboratory The idea of neutral spheres came from Paul Weiner while he was a graduate student in the Department of Pharmaceutical Chemistry UCSF APPENDIX 6 121 UCSF MidasPlus EXPR SMPTE 1 EXPR SMPTE 1 NAME expr smpte evaluate SMPTE expressions SYNOPSIS expr smpte d time codel operation time code2 DESCRIPTION Expr smpte computes the result of the given SMPTE time code binary expression SMPTE time codes are given in a HH MM SS
78. use the I b or v UCSF MidasPlus 26 UCSF MidasPlus designation and specify boundary conditions using b lt and b gt The default designation maps bond color by temperature factor and surface color by electrostatic potential For finer distribution of potentials and temperature factors broader color ranges should be used For example blue red maps only 120 degrees of the color wheel whereas cyan yellow maps 240 degrees Alter natively the interpolation direction may be changed by specifying the c designator Examples color blue red s 0 color lowest potential surface blue and highest red Intermediate potentials are mapped to shades of magenta color red blue b 0 color the bonds of the lowest temperature fac tor atoms red and highest blue color 8 32 s 0 e gt 20 e lt 20 color ms surfaces with potential 20 kcal mole per elementary charge cyan color 8 and with potential 20 kcal mole per ele mentary charge orange color 32 Intermedi ate potentials are mapped to shades of blue magenta and red Note that displaying many colors especially color ranges has the potential of slowing down interactive response time significantly See also colordef colorrename 2 4 16 Colordef Usage colordef color_name red green blue Usage colordef color_name existing_color_name colordef adds the given color_name to the list of color names that MIDAS recognizes A color name is an arbitrary sequence of letters digits an
79. user can supply commands by typing g gd_command parameters at the MIDAS command prompt Many commands need additional parameters and all parameter values remain set until the user wishes to change them by supplying other values COMMANDS Basically the commands of gd can be classified into two categories commands used in conjunction with the contouring and display of three dimensional energy maps output by GRID and commands used to gen erate GRID input files after the user has defined which atoms need to be included in the GRID box The list of commands is given below GRID CONTOURING COMMANDS These commands all have to do with the contouring and visualization of three dimensional energy maps output by GRID color color_spec Color_spec can be simply a single MIDAS color including user defined colors see the colordef command in the MidasPlus manual or two colors and a mixture fraction separated by commas with no blanks The mixture fraction is a number between 0 and 1 and indicates the relative amounts of the two colors to use Zero indicates use exclusively the first color while 1 indi cates use only the second color The default value for color_spec is gray The color com mand can be used for coloring the GRID box boundaries see the show_box command min and max labels and energy contours see the contour command 66 cz level contour_level Contour_level is the le
80. vertical bar in the right margin area of the manual such as shown with this paragraph Changes additions and bug fixes are also detailed in the Release Notes document Thus users already familiar with MidasPlus can quickly determine what has changed UCSF MidasPlus 3 UCSF MidasPlus in the current release E mail Communications about Midas The UCSF Computer Graphics lab maintains several e mail addresses related to MidasPlus e midas inquiry cgl ucsf edu Inquiries about your current license obtaining new licenses or getting new MidasPlus releases e midas bugs cgl ucsf edu Bug reports for MidasPlus programs e midas ideas cgl ucsf edu Requests for enhancements or other suggestions Also check MidasPlus Web Resources in Part I of this manual for information about MidasPlus related web pages UCSF MidasPlus 4 UCSF MidasPlus Part I Getting Started MidasPlus is capable of displaying 1 Molecular structures from information contained in Protein Data Bank PDB format files 2 Van der Waals surfaces associated with molecular structures 4 3 Molecular surfaces computed by the DMS program or 4 Graphics objects consisting of text lines and or points MidasPlus expects input PDB files to adhere fairly well to the PDB standard However some software packages generate PDB files with poor conformance to the PDB standard If you have trouble displaying a file
81. via the control panel See Manipulating the Model in Part I of this manual for further details Examples select 1 selects model 1 select 1 5 8 selects models 1 and 5 through 8 See also assign 2 4 76 Set Unset Usage set keyword value Usage unset keyword There are two types of display options in MIDAS those that act as off on toggles and those that vary over a range of values For the toggle type of option set with the appropriate keyword enables the option and set keyword or unset keyword disables the option For value type options set keyword value sets the value while set keyword displays the current value Although initially all toggle options are disabled MIDAS sets certain options on at the beginning of each session by reading the initialization file usr local midas resource midas midas rc See Appendix 4 of this document for a list of the display options enabled during initialization See also devopt The available MIDAS display options are see next page UCSF MidasPlus 50 UCSF MidasPlus Set Unset Toggle Options Keyword Function autocolor cofg control filenames fullscreen halfbond independent labels ortho reassign record showsphere text verbose Gives each newly opened model a different color Puts a at the center of rotation for the selected models The default center of rotation is at the center of mass of the selecte
82. will try to switch the video to a stereo format when going into stereo and back when leaving stereo If your monitor has to be switched by hand to show stereo then you may want to turn this option off On SGI s if the default visual is a stereo visual then you will want to turn this off stereo_monitor format SGI only Choose the setmon 1 format e g 1280x1025 _96s for stereo Low end systems interlaced stereo can only pick str_rect or str_bot High end systems may have multi ple choices normal_monitor format SGI only Choose the setmon 1 format e g 72 to return to after leaving stereo This is initial ized from the value of sbin nvram monitor The default is 60 which matches SGI s default stereo_pointer_adjust on off DEC only On older DEC systems e g ZLX series when the monitor goes into interlaced stereo the mouse does not Turn on to compensate OpenGL related These options trade off visual aesthetics for speed when they are turned off the graphics is faster They are all on by default smooth on off Turns antialiasing of lines and points on and off Turning this option off can speed up line draw ing by a factor of 3 DEC Alphas with the old PXG graphics are unusable unless smooth is off and not much better anyway antialias_points on off Controls whether points are antialiased must be set before smooth is turned on dither on off On systems with a low number of graphics b
83. 0 puts it to the extreme left 1 0 puts it to the right UCSF MidasPlus 52 UCSF MidasPlus Set Unset Value Options continued Keyword Function refmodel Specify the model number to use as a reference coordinate system for newly opened models For example if refmodel is set to 0 then the coordinates of a newly opened model will be subjected to the same scaling rotation and translation that model 0 is currently undergoing The models can be individually manipulated thereafter If refmo del is unset then newly opened models will not be subjected to any transformations If refmodel is set to 1 then the lowest model number in use will be used as the basis for transforming newly opened models viewdist The distance from the viewer to the screen in inches This information is needed to correctly compute stereo projections Its default setting is appropriate for most modeling work but the value may have to be increased if a demonstration is being given where many people are further from the screen than normal vpsep Amount of vertical separation between left and right eye images in stereo mode in scan lines This option should only have to be set once for each machine with stereo It con trols the vertical convergence of the left and right images when the stereo system is turned on Once the correct value is determined empirically it should be put in usr local midas resource midas midas rc The easiest
84. 00 0 00 ATO So Je VAL A 8 436 18 338 4 977 1 00 0 00 ATOM 4 0 VAL A 8 813 17 657 5 941 1 00 0 00 ATO 5 CB VAL A 6 317 19 598 Se OAT 00r 0 00 ATOM 6 CG1 VAL A 6 959 20 999 5 376 1 00 0 00 ATO 7 CG2 VAL A 1 4 819 19 636 5 383 1 00 0 00 ATO 8 N EU A 2 9 259 18 958 4 152 1 00 0 00 ATO 9 CA EU A 2 10 715 18 872 4 330 1 00 0 00 ATO 10 C EU A 2 11 156 20 058 5 187 1 00 0 00 This data file appears initially much the same as the file for glucagon with the exception that the fifth data field now contains the single character chain indicator In this case the chain indicator is A indicat ing the alpha chain of the hemoglobin molecule This field was simply blank in the glucagon example At the end of chain A the heme group records appear UCSF MidasPlus 72 UCSF MidasPlus ATOM 1058 N ARG A 141 6 576 12 834 10 275 1 00 0 00 ATOM 1059 CA ARG A 141 8 044 12 831 10 214 1 00 0 00 ATOM 1060 C ARG A 141 8 186 14 096 9 365 1 00 0 00 ATOM 1061 O ARG A 141 T091 25 139 9 6712 2 00 0 00 ATO 1062 CB ARG A 141 8 579 11 531 9 580 1 00 0 00 ATOM 1063 CG ARG A 141 8 386 11 441 8 054 1 00 0 00 ATOM 1064 CD ARG A 141 8 727 10 045 7 568 1 00 0 00 ATOM 1065 NE ARG A 141 9 095 10 056 6 143 1 00 0 00 ATOM 1066 CZ ARG A 141 9 268 8 931 5 414 1 00 0 00 ATO 1067 NH1 ARG A 141 8 602 8 795 4 282 1 00 0 00 ATOM 1068 NH2 ARG A 141 10 097 7 962 5 830 1 00 0 00 ATO 1069 OXT A
85. 1 20 480 1 00 0 00 HETATM 1110 CBD HEM A 1 8 992 6 848 20 968 1 00 0 00 HETATM 1111 CGD HEM A 1 8 998 6 529 22 465 1 00 0 00 HETATM 1112 O1D HEM A 1 9 693 5 683 22 895 1 00 0 00 HETATM 1113 02D HEM A 1 8 276 7 153 23 229 1 00 0 00 ATOM 114 C ACE G 0 7 896 18 462 1 908 1 00 0 00 ATOM 115 O ACE G 0 7 246 18 839 922 1 00 0 00 ATO L16 CH3 ACE G 0 9 415 18 301 1 832 1 00 0 00 ATOM 117 N GLY G 1 7 354 18 174 3 077 1 00 0 00 ATOM 118 CA GLY G 1 5 904 18 282 3 283 1 00 0 00 ATO 1119 C GLY G L PELSD 1912 12930 1 400 000 ATOM 1120 Oo GLY G 1 7 026 20 248 2 448 1 00 0 00 ATO 1121 N HIS G 2 8 300 18 533 3 176 1 00 0 00 ATOM 1122 CA HIS G 2 9 565 19 224 2 889 1 00 0 00 UCSF MidasPlus Here the TER card is implicit in the start of a new chain The new chain identifier is G The file continues in the same pattern as before until the entire gamma chain and its associated heme group have been specified Remember that the spacing of the data fields is crucial Refer to the table given previously to deter mine the precise columns in which data must appear If a data field does not apply it should be left blank For example a protein which consists of a single amino acid chain has no chain identifier and thus column 22 is blank 73 UCSF MidasPlus From this example it is apparent that Protein Data Bank format relies on the concept of residues much in the same way as MIDAS uses templates The same rules apply f
86. 2 k2 1 000 k3 1 000 and or restraint at1 1 H23 at2 1 H25 r1 0 0 r2 1 8000 r3 2 5980 r4 4 5980 k2 10 0 k3 10 0 grpatl 1 H23 1 H24 and or restraint at1l 275 at2 290 r1 0 0 r2 1 8000 r3 2 5980 r4 4 5980 k2 10 0 k3 10 0 grpatl 275 276 AMBER SANDER namelist format amp rst iat 37 35 iresid 1 atnam 1 H8 atnam 2 H2 2 rl 0 000 r2 2 895 r3 2 945 r4 4 945 rk2 10 000 rk3 10 000 amp end and or rst iat 108 1 igr2 143 144 145 0 rl 0 000 r2 3 315 r3 3 395 r4 55895 APPENDIX 6 159 UCSF MidasPlus NOESHOW 1 NOESHOW 1 rk2 10 000 rk3 10 000 amp end X PLOR distance constraint format assign resid 6 and name HB resid 7 and name HN J 4 60 252 1 0 assign resid 34 and name HB resid 39 and name HN 4 0 3 7 2 5 assign resid 37 and name HB1 resid 39 and name HN 4 0 2 2 1 0 assign resid 23 and name HB resid 26 and name HB 4 0 5 2 4 0 assign resid 22 and name HB2 resid 24 and name HN y 4 0 2 2 1 0 assign resid 20 and name HB resid 22 and name HN J S20 27 2e0 d DIANA low and high bound constraint format 14 TYR HN 10 VAL O 2 00 1 00E 00 H Bond 13 ARG HN 14 TYR HN 2 90 1 00E 00 N i N it1 11 VAL HA 14 TYR HN 5 00 1 00E 00 ha i hn i 3 14 TYR HA 17 ALA QB 3 80 1 00E 00 ha i hb i 3 14 TYR HA 29 LEU QD1 3 80 1 00E 00 helixl helix2 14 TYR OR 15 VAL QG2 7 80 1 00E 00 sequential 18 LEU QD1 1
87. 2x2 image pixels or 2x2 for mapping 2x2 calculation pixels onto single image pixels Antialiasing improves the picture quality at the expense of computation time The time increase is proportional to the number of pixels computed modulo the startup time Thus for small molecules which have low startup times going from mode none to 2x2 will increase the computation time four fold The relative increase is less for large molecules since the startup time for large molecules is a significant fraction of total computation time The default antialias mode is none atinfo file Use the given file as the atom information file which contains default information on how each type of atom should be colored Coloring the molecule is described in greater detail below This option has no effect if conic is invoked from within MIDAS as MIDAS fully specifies atom colors and radii backgroundrgb rgb rgb Set the background color for the image If only one RGB value is given then the entire back ground is set in that color If two RGB values are given then the background is interpolated between the two colors from bottom to top If three RGB values are specified then the background is smoothly interpolated from the first color at the bottom of the image to the second color in the middle to the third color at the top The default background color is 0 0 0 NOTE if this option is given in the configuration file it will override any color specified in the input
88. 4 TYR OR 7 80 1 00E 00 24 ASP O 28 ALA HN 1 80 1 00E 00 hbond 25 GLY HA1 28 ALA HN 5 00 1 00E 00 aH i HN i 3 AMBER torsion information format Final Restraint Analysis for coords min8 rst Restraints deviations and energy contributions pencut 00 First atom Last atom curr value target deviation penalty CA CYX 16 lt CB CYX 16 212 978 210 000 2 978 863 CA SER 17 CB SER LAS 29 656 30 000 344 SOLT N SER 19 CA SER T9 158 920 60 000 000 000 CA SER 19 B SER 19 41 668 90 000 000 000 CA CYX 202 CB CYX 20 188 804 210 000 000 000 N ARG 23 CA ARG 23 59 704 60 000 7296 009 X PLOR torsion information format Number of dihedral angle constraints 130 overall scale 200 0000 3 GIN C 4 LYS N 4 LYS CA 4 LYS C Dihedral 126 639 Energy 0 000 C 1 000 Equil 157 500 Delta 0 86 1 Range 30 000 Exponent 2 4 LYS C 5 THR N 5 THR CA 5 THR C Dihedral 111 196 Energy 0 000 C 1 000 Equil 120 000 Delta 0 00 0 Range 30 000 Exponent 2 APPENDIX 6 160 UCSF MidasPlus NOESHOW 1 NOESHOW 1 FEEDBACK Feel free to mail suggestions or questions to pett cgl ucsf edu NOTE Noeshow and mardishow are perl scripts and as such require a perl command interpreter in order to work Most systems already have a perl interpreter installed If yours does not one is provided in the MidasPlus distribution Consult the MidasPlus Installation Guide for further details REFERENCES 1 Ulyanov NB Schmitz U Kumar A J
89. AS and some ancillary programs which may be used in conjunction with MIDAS for specific modeling problems Beginning users may wish to skip this section on first reading Included are descriptions of e Connectivity and templates e Calculation and display of a molecular surface e Calculation of electrostatic potential for a surface e Details of Protein Data Bank format e Saving printing screen images e Photographing screen images e Displaying non molecular objects e Using Midas in conjunction with a web browser e Performance issues with Midas Note The descriptions include sample command lines In these examples the model name used is dfr an acronym for dihydrofolate reductase a system which has been extensively modeled The user s own file names should be substituted for dfr when running commands 3 1 Connectivity and Templates Many macromolecules in nature such as proteins and DNA are long chains of component molecules amino acids and nucleic acids MIDAS uses the same approach in building molecular models Small com ponent molecules are chained together to build complex models In MIDAS these building blocks are called residues Each residue is made up of atoms which are connected in a specific pattern Each atom in the residue has a unique name usually combining a key letter such as C for carbon N for nitrogen etc and additional letters to uniquely identify it For example atoms may be named CA C1 C2 N1
90. AS commands The help facility is very useful for both the novice and experienced MIDAS user and obviates constantly referring to the User s Manual for every command 1 4 Tutorials There are three tutorials available for MidasPlus One of these is available from the World Wide Web one from the MidasPlus distribution CD ROM and one is available from both To determine if the CD ROM tutorials have been installed on your system check whether the main tutorials directory usr local midas tutorials exists If it does the tutorials have been installed If not you may want to have your administrator install them Also if you mount the distribution CD ROM on your system you can access the tutorials in the Midas 2 1 tutorials directory on the CD ROM The main tutorials directory has two subdirectories cgl and glasfeld The cgl subdirectory contains exercises developed for a MidasPlus class taught at UCSF It is an introduction to most of the features of MidasPlus as well as some basic UNIX commands The README file in the cgl subdirectory has instructions on that tutorial s usage The glasfeld subdirectory contains a hypertext tutorial developed for use in a course taught by Arthur Glasfeld at Reed College It not only teaches many commands in MidasPlus but also many aspects of structural biochemistry You can use this tutorial by pointing your favorite web browser at file usr local midas tutorials glasfeld intro html This tutorial is al
91. AS to revert to the default center of mass that it normally computes See also cofr 2 4 78 Show Usage show atom_specification Usage show atom_specification Show displays the specified atoms and removes all others in those models from the display Models not involved in atom_specification will be unaffected Note that this differs from the display command in that the show command displays only those atoms specified and will undisplay all others Show removes the specified atoms completely from the display See also chain display 2 4 79 Sleep Usage sleep number_of_seconds Sleep causes MIDAS to pause for number_of_seconds seconds and then resume operation This com mand is useful in command scripts where a break in the action is required See also wait 2 4 80 Source Usage source filename filename Source reads one or more command files of MIDAS commands Source differs from read in that source will display the results of each command as it is executed while read only updates the display after all commands have completed The user may interrupt the execution of the source file by pressing the ESC key MIDAS completes exe cution of the current command before processing the interrupt UCSF MidasPlus 54 UCSF MidasPlus See also read run pdbrun 2 4 81 Speed Usage speed value Speed changes the speed of functions activated by the sliders or spaceball Thus the sensitivity of the d
92. Additional copies of this manual are available for 10 each including postage by writing to MIDAS Software Distribution Computer Graphics Laboratory School of Pharmacy University of California San Francisco CA 94143 0446 Please include a check or money order payable to The Regents of the Univer sity of California with your request Sorry but purchase orders cannot be accepted Orders received without payment enclosed will be returned unprocessed Copyright 1983 1985 1989 1991 1994 1997 by The Regents of the University of California All rights reserved Introduction Background The MidasPlus molecular visualization system is a collection of programs developed by the Computer Graphics Laboratory at the University of California San Francisco UCSF The major component of the MidasPlus system is an interactive graphics display program MIDAS Molecular Interactive Display and Simulation designed for the display and manipulation of macromolecules such as proteins and nucleic acids Many ancillary programs are also part of the system and allow for such features as computing the solvent accessible surface of a molecule calculating electrostatic potentials and so on MidasPlus is the most recent in a series of interactive molecular graphics systems whose direct lineage extends back to the first developments in molecular graphics at Project MAC Massachusetts Institute of Technology in 1964 2 National Institutes of Health NIH
93. BER s older force field Weiner et al models nucleotides as separate phos phate and sugar base residues Dnacheck recombines the sugar base residues with the phosphate residues to form complete PDB nucleotide residues 3 Reversed direction PDB format requires that DNA strands be specified starting from the 5 end Some files have strands that start from the 3 end Dnacheck reverses the order of the residues in these strands Dnacheck does not unfortunately correct RNA file deficiencies CONFIGURATION FILES AND BLUEPRINTS Dnacheck works in four steps A reads a configuration file describing a list of blueprint files and some naming conventions associ ated with the blueprints and then reads the blueprints B applies the blueprints to the input file to take care of type 1 problems as described in the DESCRIPTION section above C applies simple heuristics to take care of type 2 problems D takes care of type 3 problems by applying simple heuristics to the first two residues of a chain to determine whether strand reversal is necessary Blueprints are simply PDB format files each containing the ATOM or HETATM records of a single residue followed by CONECT records The CONECT records must be present and may be generated using the pdbrun command in MIDAS The format of the configuration file is most easily explained by example The following is part of the default configuration file blueprint T synonym THY
94. BER SANDER constraints already describe an energy well the mapping to an AMBER INTER FACE energy well description is straightforward MARDIGRAS output Although mardishow is capable of displaying MARDIGRAS output format constraints without conversion it may nonetheless be desirable in certain circumstances to convert the constraints for use with noeshow in order to make use of features only present in the latter program Such a conversion is a two step process First the constraints are run through the mardi2amber program to convert them to AMBER SANDER namelist format The mardi2sander program is provided with the MARDIGRAS package and is documented there The second step is to convert the AMBER SANDER format constraints to AMBER INTERFACE format as detailed in the paragraph above Torsion angle constraint preparation You need not have torsion angle constraint information in order to use noeshow or mardishow such infor mation is optional In fact mardishow cannot display torsion angle constraint information only noeshow can Noeshow uses the output torsion angle restraint information from the SANDER AMBER module rather than the input torsion angle info This is because it uses the energy penalty information provided by AMBER to color the torsion constraints A sample of the kind of information it expects can be found in the Con straint formats section of this document Torsion angle information from X PLOR can be conve
95. CHA HEM 1 16 124 33 461 10 405 1 00 0 00 HETATM 978 CHB HEM 1 11 350 32 580 12 046 1 00 0 00 HETATM 979 CHC HEM 1 9 326 34 709 7 887 1 00 0 00 HETATM 980 CHD HEM 1 1 42 138 353 379 6 119 1 00 0 00 incorrect HETATM 976 FE HEM 1 12 763 34 157 9 102 1 00 0 00 HETATM 977 CHA HEM T 16 124 33 461 10 405 1 00 0 00 HETATM 978 CHB HEM 1 11 350 32 580 12 046 1 00 0 00 HETATM 979 CHC HEM 1 9 326 34 709 7 887 1 00 0 00 HETATM 980 CHD HEM t 14 138 35 379 6 119 1 00 0 00 A MidasPlus utility fixatname easily corrects the above misalignment It is fully documented in Appendix 6 of this manual Incorrect Secondary Structure Display Nucleotides There are several possible causes of problems when attempting to show nucleotide structures with rib bonjr including variant atom name nomenclature reversed order of residues standard is 5 to 3 and separate sugar and phosphate residues they should be combined A MidasPlus utility dnacheck corrects all of these faults as well as a few other minor problems Dnacheck is fully described in Appendix 6 of this document 3 3 5 Hand Edited PDB Files Duplicate Atom Names One possible editing mistake is the failure to uniquely name all atoms within a given residue Notice in the following example that two atoms in residue VAL are named CA ATO 1 N VAL A 6 280 17 225 4 929 1 00 0 00 ATO 2 CA VAL A 6 948 18 508 4 671 1 00 0 00 ATO 3 C VAL A 8 436 18 338 4 977
96. DAS pdbrun command executes a program and provides a PDBRUN format file see Appendix 1 as standard input to that program Any standard output of the program is interpreted as MIDAS commands and executed Such a program that used PDBRUN version 5 can be made to work with MidasPlus 2 1 by changing its invocation alias from alias old program pdbrun old program to alias old program pdbrun pdbrun6to5 old program A few pdbrun programs produce modified PDBRUN files as their output Their output is then piped to another program as input An example of such a program is neon which pipes its output to conic for rendering Such programs using PDBRUN version 5 must employ pdbrun5to6 in their updated aliases to work with MidasPlus 2 1 Consult the pdbrun5to6 manual page for details SEE ALSO pdbrun5to6 1 midas 1 MidasPlus User s Guide AUTHOR Greg Couch UCSF Computer Graphics Laboratory APPENDIX 6 168 UCSF MidasPlus PS2ILLUSTRATOR 1 PS2ILLUSTRATOR 1 NAME ps2illustrator convert Midas copy file PostScript to Adobe Illustrator format SYNOPSIS ps2illustrator lt copy file gt Illustrator file DESCRIPTION Ps2illustrator reads in a PostScript file generated by the MIDAS copy command and converts it to an Adobe Illustrator format file for inclusion in desktop publishing documents SEE ALSO stereops2illustrator 1 midas 1 BUGS Depends on the csplit and nawk programs that might not be available on all platforms A
97. DAS session file The model coordinates are saved in PDB format Since the model orientations are stored in the session file and not the data files PDB files produced with save do not have their coordinates transformed To get transformed coordinates use the write or pdbrun com mand To restart a saved session from the UNIX command line use the command midas session_name Also the load command can be used to restore a saved session into MIDAS replacing the ongoing modeling session Note that if bond rotations have been made and the user wishes to have the saved PDB files reflect the new conformation the fix command must be invoked before the session is saved It should also be noted that save only saves the state of MIDAS itself and not the state of associated MIDAS delegates Delegates active when the session is saved will not be active when the session is restored See also fix load pdbrun stop write UCSF MidasPlus 48 UCSF MidasPlus 2 4 72 Savepos Usage savepos view_name Usage savepos view_name Savepos saves the current model orientations and associates view_name with it If view_name is miss ing the name default is used The view may be retrieved using the reset command A view may be forgotten using the command savepos view_name This saves space in session files For a list of all existing view_names give the command savepos list See also align reset push pop wind
98. DAS will send the command pickabort to the requesting delegate The commands and replies described above are primarily for use by delegate application programmers The only important point that a user needs to remember is that typing pickabort will terminate a delegate picking request without actually selecting an atom The pickatom command is only valid when sent by a delegate and has no effect when typed at the keyboard See also delegate picking 2 4 58 Push Pop Usage push Usage pop Push saves the current orientation of all open models on an image stack Pop retrieves the last pushed orientation Any number of model orientations may be saved on the stack memory allowing and retrieved on a last in first out basis See also align reset savepos window For those unfamiliar with the concept of a stack think of a pile of pictures which is created by pushing pictures one at a time onto the top of the pile and in which pictures are retrieved one at a time by taking the top picture off the pile UCSF MidasPlus 43 UCSF MidasPlus 2 4 59 Rainbow Usage rainbow model_number The rainbow command colors model chains from end to end continuously from red to blue This can sometimes be of assistance in visually following chain connectivity in a complicated structure Full details of the use of this command can be found in Appendix 6 of this document 2 4 60 Read Usage read filename
99. DB file generate times codes for use with videodisk utility Fade from one Iris image to another control V LAN videodisk Command documented in Appendix 6 18 UCSF MidasPlus Miscellaneous alias cd colordef colorrename devopt gentpl help midas tty run2ses set unset stop version UCSF MidasPlus define or display command aliases change current working directory define color name rename color name set device specific option generate a MIDAS template from a PDB coordinate file show information about MidasPlus commands terminal based version of MIDAS display program convert pdbrun style file to MIDAS session file set options terminate the current MIDAS session report MIDAS version number Command documented in Appendix 6 19 UCSF MidasPlus The actions of many MIDAS commands may be reversed by preceding them with the tilde character This is essentially an undo for the following commands UCSF MidasPlus Reverse Command Functions Command Function alias delete an alias angle remove an angle monitor assign deactivate sliders bond remove a bond between two atoms brotation remove a backwards rotation chain break chaining for all atoms listed clip halt an ongoing clipping operation cofr use default center of rotation display remove atoms from the display distance remove a distance calculation label remove a
100. ECT 7 11 Atom serial number right integer 12 16 Atom serial number covalent bond right integer 17 21 Atom serial number covalent bond right integer 22 26 Atom serial number covalent bond right integer 27 31 Atom serial number covalent bond right integer 32 36 Atom serial number hydrogen bond right integer 37 41 Atom serial number hydrogen bond right integer 42 46 Atom serial number salt bridge right integer 47 51 Atom serial number hydrogen bond right integer 52 56 Atom serial number hydrogen bond right integer 57 61 Atom serial number salt bridge right integer Atoms whose chemical symbols as distinct from remoteness indicator are one letter long are left justified in columns 14 16 Those which are two characters long e g zinc symbol ZN are left justified starting in column 13 Refer to the Brookhaven document Protein Data Bank File Record Formats for details UCSF MidasPlus 69 UCSF MidasPlus Protein Data Bank Format continued Record Columns Data Justifi Data Type cation Type HELIX 1 5 HELIX left character 8 10 Helix serial number right integer 12 14 Helix identifier right character 16 18 Initial residue name right character 20 Chain identifier character 22 25 Residue sequence number right integer 26 Code for insertions of residues character 28 30 Terminal residue name right character 32 Chain identifier character
101. FF format where HH is the number of hours MM is the number of minutes 00 59 SS is the number of seconds 00 59 and FF is the frame number 00 29 Leading zeros after a colon are required The time codes may be abbreviated by omitting earlier parts i e 12 would be frame 12 and 2 05 would be frame 5 in the third second Relative time codes may have a negative sign prefix The d option turns on support for the Drop Frame Time Code The SMPTE standard time code drops frames numbered 00 and 01 each minute except for every 10th minute to compensate for NTSC variance from real clock time This option is not implemented yet SEE ALSO videodisk 1 AUTHOR Greg Couch APPENDIX 6 122 UCSF MidasPlus FADE 1 FADE 1 NAME fade fade from one SGI image to another SYNOPSIS fade 1 loop s steps p pause e shell_command from_image to_image DESCRIPTION Fade reads two image files displays the first image and fades to the second image Both image files must be in SGI Image Library RGB format and must be identical in size If the l argument is given fade will alternately fade from one image to the other for Joop times The default value of loop is one The s argu ment specified the total number of frames displayed during the fade including the starting and ending frames As steps increases the fade becomes smoother but takes longer The default value of steps is 40 The p flag specifies the number of cloc
102. IDAS first searches the directory usr local midas ib midas for command before examining the rest of the user s execution path This is useful to avoid name conflicts between MIDAS commands using the run pdbrun delegate mechanism and UNIX commands of the same name The all option specifies that all atoms not just those that are displayed should be sent to the given command The conect sic option specifies that PDB standard CONECT records should be generated for all resi dues even if they have standard connectivity MIDAS places USER records in the PDBRUN file to indicate display information such as atom colors view direction clipping planes etc The nouser option specifies that no USER records should appear in the file The noobj keyword causes just GFX type USER records to be omitted from the file The surface key word causes USER GFX VERTEX records to be placed in the file for displayed VDW or solvent accessible surfaces The mark name option specifies that only those atoms referenced by the named mark should be sent to command Note that unless the all option is given as well only those marked atoms that are also displayed labeled vdw ed or surfaced will be sent Specifying more than one mark name option results in the union of the given marks being sent Any output from command is interpreted as MIDAS commands and executed Control returns to MIDAS when the pdbrun command terminates The pdbrun comman
103. OESHOW 1 There is a somewhat more complicated method for restricting constraint display that offers finer grain con trol than the above method It involves using the relatively new mark and makemark commands of MIDAS You may want to read the documentation for the above two commands in the MidasPlus manual if you are unfamiliar with them These commands allow you to mark a set of atoms with a name If you mark a set of atoms with the name noemark1 then noeshow will only show constraints where at least one end involves an atom in the marked set If you also mark some atoms with the name noemark2 then noeshow will only show constraints where one end is in the first set and the other end is in the second set For example makemark noemark1 would create the mark name noemark1 for use and mark noemark1 12 14 would mark all atoms in residues 12 through 14 with the name noemark1 Running noeshow at this point would show only those constraints that had at least one end in residues 12 to 14 Note that running the mark command with the same name a second time will add to the set of marked atoms not replace the set with a new set To replace you would have to clear the mark with mark name and then mark with the new set Structure Ensembles To determine constraint satisfaction across an ensemble of structures displayed in MIDAS noeshow uses exponential averaging R to the minus sixth
104. RG A 141 8 973 13 984 8 310 1 00 0 00 TER 1070 ARG A 141 HETATM 1071 FE HEM A 8 133 8 321 15 014 1 00 0 00 HETATM 1072 CHA HEM A 8 863 8 752 18 417 1 00 0 00 HETATM 1073 CHB HEM A 10 362 10 946 14 389 1 00 0 00 HETATM 1074 CHC HEM A 8 482 7 374 11 743 1 00 0 00 HETATM 1075 CHD HEM A 6 982 5 180 15 773 1 00 0 00 HETATM 1076 N A HEM A 9 452 9 545 16 178 1 00 0 00 The last residue in the alpha chain is an ARG arginine Again the extra oxygen atom OXT appears in the terminal carboxyl The TER record indicates the end of the peptide chain It is important to have TER records at the end of peptide chains so that MIDAS does not attempt to connect the end of one chain to the start of another The atom number residue type chain indicator and residue number in the TER record are optional In the example above the TER record is correct and should be present but MIDAS would have bro ken the molecule chain at that point even without a TER record because HETATM residues are not con nected to other residues or to each other The heme group is a single residue made up of HETATM records Note that the residue numbering begins again with 1 as the new chain begins At the end of the heme group associated with the alpha chain the gamma chain begins HETATM 1109 CAD HEM A 1 7 582 6 73
105. S In addition we began to distribute copies of this system including documented source code which has pro ven to be an excellent training tool as well as a starting point for other molecular modeling packages The system has continued to evolve often in response to new ideas received directly from MIDAS users There are now more than 500 sites running MidasPlus in 38 states and 30 countries Nearly 1 400 publications have resulted from work done at the UCSF Computer Graphics Laboratory using MIDAS and MidasPlus MidasPlus In order to take advantage of the substantial advances in graphics display technology and workstation func tionality and performance in the mid 1980 s we decided in 1989 to rewrite the MIDAS system This work was done during the winter of 1989 and the resulting system was named MidasPlus MidasPlus has significantly increased functionality and performance compared to its predecessor This was accomplished while maintaining compatibility with the original MIDAS command language More recently we have focused our efforts towards providing a software development framework for others to build on We view the extensibility of MidasPlus as critical to its success and have concentrated on providing an open architecture and developer friendly environment This allows programmers to add new commands and MidasPlus is a trademark of the UCSF Computer Graphics Laboratory IR Langridge and A W MacEwan in P
106. S window until it is the correct aspect ratio If the t option is given the MIDAS window will be brought into the correct aspect ratio by trimming one dimension This may result in part of the image being clipped but will also result in less blank screen area For optimal screen filling reshape the MIDAS window to about the same aspect ratio as half the screen and get the image you want before running stereoimg s Show the image immediately with imgview 1 Without this flag the image is deposited in the output file and not displayed 0 Deposit the image into the named output file instead of the default stereoimg tiff p Use the named rendering program to generate the pair image Legal values for the renderer flag are conic ribbonjr and neon This flag is mandatory vV Make the pair in a fashion appropriate for use with a mechanical stereo viewer typically used with journal publications Each eye image will have a square aspect ratio If you convert the image to PostScript with the itops 1 program giving a scale factor with the s option to itops of 0 375 will produce a final image where each eye image is 2 5 inches square a typical size used in journals Other scale factors can be used for larger or smaller images C This flag indicates the end of arguments for stereoimg Any arguments which follow the C flag will be passed on to the rendering program NeXT DIFFERENCES On NEXTSTEP ribbonjr does not work as a renderin
107. SCRIPTION Density is a MidasPlus delegate for displaying electron density contour maps generated from X PLOR map files The map files must be of the formatted type When requested density will create a MIDAS object representing the electron density at one or more contour levels and open it for display as a user specified model number Density assumes that the structure associated with the electron density is open as model 0 and therefore rotates and translates the density object it creates to align it with model 0 The user can specify the size of the grid to be created and where it is centered Density is a program designed to run in conjunction with MIDAS using the MidasPlus delegate mechanism The standard way that density is invoked is for the user to start a MIDAS session and issue the MIDAS com mand delegate start dens density mapfile mapfile2 which runs density with the specified formatted X PLOR map files and tells MIDAS to pass commands beginning with dens through to density for further processing The commands that density can handle are described below COMMANDS When density is acting as a delegate for MIDAS as in the example above the user can give it commands by typing dens density_command in the MIDAS command window The list of commands is given below size grid_units Specifies the size of the grid that is to be contoured The default size is 20 units The size of an individual grid unit is determined by X PLOR at
108. THE alias C5M C7 CSA alias O4 O1 alias O1P OA alias O2P OB The first line states that there is a blueprint that should be applied to residues named T By convention the file name of the blueprint is the same as the name of the residue to which it applies The second line states that this blueprint should also be applied to residues named THY or THE The third line states that atoms named C7 or C5A should be renamed C5M The fourth through sixth lines add simi lar name translations The configuration file consists of a series of these blueprint descriptions Residues in the input file match ing a blueprint are altered to have the same residue type as the blueprint name atoms in the residues are translated if they match one of the aliases and atom record types ATOM vs HETATM are modified to match those in the blueprint If there are residues in the input file that do not match any blueprints they are left unmodified APPENDIX 6 119 UCSF MidasPlus DNACHECK 1 DNACHECK 1 COMMAND OPTIONS c file F A Specify the name of the configuration file The default configuration file that dnacheck uses is config The configuration file must be in either the current directory or the default directory see C below Convert any residue which is not connected to other residues to be a hetero residue i e the PDB records for the atoms of the re
109. TO 10 NE2 HIS 1 51 046 26 090 6 098 1 00 17 00 ATO TLN SER 2 49 788 27 850 10 784 1 00 16 00 ATOM 12 CA SER 2 49 138 29 147 10 620 1 00 15 00 ATOM 13 eE SER 2 47 713 29 006 10 110 1 00 15 00 ATO 14 0 SER 2 46 740 29 251 10 864 1 00 15 00 ATO 15 CB SER 2 49 875 29 930 9 569 1 00 16 00 ATO 16 OG SER 2 49 145 31 057 9 176 1 00 19 00 ATO 17 N GLN 3 47 620 28 367 8 973 1 00 15 00 ATO 18 CA GIN 3 46 287 28 193 8 308 1 00 14 00 ATO 19 C GLN 3 45 406 27 172 8 963 1 00 14 00 Notice that each line or record begins with the record type ATOM The atom serial number is the next item in each record Although each atom in the file is given a unique serial number this information is not required by MIDAS The atom name is the third item in the record Notice that the first one or two characters of the atom name consists of the chemical symbol for the atom type All the atom names beginning with C are carbon atoms N indicates a nitrogen and O indicates oxygen The next character is the remoteness indicator code which is transliterated according to 3BuxrM NR DR OINMUQAWS UCSF MidasPlus 71 UCSF MidasPlus The last character of the atom name is a branch indicator if required The next data field is the residue type Notice that each record contains the residue type In this exam ple the first residue in the chain is HIS histidine and the second residue is a SER serine The next data
110. UTHOR Scott Dixon SmithKline Beecham Pharmaceuticals APPENDIX 6 169 UCSF MidasPlus RAINBOW 1 RAINBOW 1 NAME rainbow rainbow color molecule chains MIDAS COMMAND SYNTAX Command rainbow modelnumber DESCRIPTION Rainbow colors each chain in the specified model s all models if none specified from red to blue transit ing through yellow green and cyan in the process This may be of some assistance in tracing tangled molecule chains Since standard PDB files are ordered from N to C terminus this means that rainbow colors the N terminus red and the C terminus blue By default rainbow projects its color scheme across the entire model s requested even if parts of those models are not displayed This is because the rainbow command in MIDAS is an alias that expands to pdbrun all nouser rainbow which causes all model information to be sent to rainbow To restrict the coloring to just the displayed regions you would have to type pdbrun nouser rainbow at the MIDAS command prompt LIMITATIONS NOTE BUGS Rainbow will frequently not work correctly if the device option colormap is on from the MIDAS com mand devopt colormap on In colormap mode there is only a fixed number of colors available frequently less than rainbow needs to make a spectrum Rainbow is a perl script and as such needs a copy of the perl interpreter in the directory usr local bin Perl is supp
111. X 6 150 UCSF MidasPlus NEON 1 NEON 1 coloring type 1 Number of dashes Controls the number of dashes drawn between pairs of atoms Dash color The RGB red green blue color of dashed lines Dash offset Controls the distance in angstroms between the center of atoms and the ends of the dashed lines so that dashes do not bump into the model Dash space ratio Controls the relative proportions of dash and intervening space A value of 0 0 gives dots 0 4 is good for dashed lines and 1 0 gives a solid line CA connect distance Cutoff distance in angstroms for determining if the backbone tube will be drawn between subse quent a carbons of each model For example if residues 1 10 and 30 40 of a model were displayed the cutoff would be used to find the break between residues 10 and 30 If unwanted breaks occur this value should be increased Note that if tubetype is 0 this parameter is ignored and CONECT records are used to establish connectivity RUNNING NEON A copy of the file usr local midas resource neon dat should be present in your current working directory Default values will be used if the file is not found To create an image set the desired parameters in neon dat In the interactive window of midas display orient and color the model or models of interest Enter the command neon p to preview the image After a short pause a small conic window will open displaying the image Option flags following the neon com m
112. _frames if specified indicates the number of frames to wait before beginning the clip section will halt an ongoing section Frames and wait_frames default to and 0 respectively These parameters are useful for controlling the rate of clipping and are helpful when constructing MIDAS command scripts and making videos MIDAS continues to process commands while the requested motion is in progress To have command processing pause until the motion is finished use the wait command See also thickness clip wait UCSF MidasPlus 49 UCSF MidasPlus 2 4 75 Select Usage select atom_specification Usage select model_number model_range Usage select all For each Usage above Usage select Select selects a model or models for subsequent move rock roll and turn commands as well as interactive mouse manipulations If the argument to select is an atom specification then the model s containing those atoms will be selected If select is used with the keyword all then all models will be selected select all will then revert to the previous selection state This feature is convenient for switching back and forth between moving models relative to one another and global motion of all models Otherwise the argument s to select should be one or more model numbers or ranges of the form separated by spaces Note that model_number cannot include a symbol The selection status of models can also be controlled
113. a list of space group definitions Each space group definition con sists of a set of symmetry operators divided into levels Each symmetry operator describes how to transform atomic coordinates in fractional crystallographic coordinates A symmetry operator is only applied if its level is less than or equal to the output level The following is a single space group definition 1 spacegroup R 3 2 level 0 3 x Yr 4 y x y 5 y x X 6 level 1 7 x 1 3 VUE 2 35 BAP IZ 3 8 y 1 3 x y 2 3 z 2 3 9 y x 1 3 x 2 3 z 2 3 10 x 2 3 y 1 3 z 17 3 11 y 2 357 x S yo Ft 273 wer 1 3 12 y x 2 3 Sst 13x ca 143 Line 1 indicates that this is the definition for the space group named R 3 The name is used to compare against the space group symbol found in columns 56 through 66 of a PDB CRYST record Line 2 specifies that the subsequent symmetry operators are assigned a level of zero Lines 3 4 and 5 are symmetry opera tors Line 3 defines a symmetry operator that regenerates the input atomic coordinates this operator is typ ically present Lines 4 and 5 define two symmetry operators that generate new subunits Line 6 specifies that subsequent symmetry operators are assigned a level of one Lines 7 through 12 define six symmetry operators that generate new subunits Each symmetry operator is defined by three formulae which transform the x y and z coordinates respec tiv
114. a newly opened object the display parameters are for size major and minor and white for color unless overridden in the data file axes x xname y yname z zname Define the property values to use for Cartesian coordinates Any of the axis 113 UCSF MidasPlus DISCERN 1 DISCERN 1 specifications may be omitted in which case the previously defined property will be used For a newly opened object the xname yname and zname properties are 1 2 and 3 respectively i e the first three columns are the Cartesian coordinates direction x xname y yname z zname Define the property values to use for the direction of ellipsoid major axes For a newly opened object if the data file contains the directional property see below the xname yname and zname properties are 4 5 and 6 respectively i e the three columns after the Cartesian coordinates are the direction vector If the data file does not contain the directional property then all ellipsoids will be oriented with their major axes parallel to the z axis Any of the axis specifications may be omitted in which case the previously defined property is used If no property has been defined for any of the three axes the ellipsoids will remain parallel to the z axis FILE FORMAT The format of the data file that discern will read consists of a series of property descriptions followed by the data values
115. aces ccccccccccesesesesesessseeeees Protein Data Bank Format ccceeeeeee Examples of PDB Format Common Errors in PDB Format Files 00 0 0 cccccccccccccececesesesesesessseeseees Program Generated PDB Files e eee ceesecseceeeneeeseeseeesees Hand Edited PDB Files Modeling Hydrogen Atoms eee Hydrogens in Protein Data Bank Files 00 ee eeeeeseceeeeceeeeeneeceneeeneeeeeeees More on Connectivity and Templates Building and Modifying MIDAS Templates 20 0 0 eeeeeeeeeeeeeeee Capturing Screen Images 0 0 0 eee eee Saving Screen Images to Disk Converting Image Files to Other Formats 0 0 eee eee cee ceeceseeeeeeees Printing Screen Images Inclusion of Images in Documents iii 49 49 50 50 54 54 54 54 55 55 55 56 56 56 57 57 57 58 58 58 59 59 60 60 60 6l 63 63 63 64 65 66 67 71 74 74 75 76 76 77 78 79 79 80 81 81 Making Videos iisscniinen Giant pianists Be Maes ea iota 82 Screen Photography cssssscssssscisctesas ssstses sesssaedschsshepsatsescsssdohstachs sbanstvesaastevtscksteonconsed 82 Non Molecular Graphics Objects 0 0 0 eee eee eeceseeeeeceeeeecaeeseecaeesaeceeceaeceseeeeeensees 83 Chemical Group Description Files oc ee eeeeeeeseeeeeceesseceesaececeaecneeeeeseeesees 83 Web Browsing PDB Files with Midas 00 eee ce ceececeeeeeeceeeeeeeeseeeneesaecaecnaeeaes 84 Performance Iss
116. ames TL Probability assessment of conformational ensembles sugar repuckering in a DNA duplex in solution Biophysical Journal 1995 Jan 68 1 13 24 AUTHOR Eric Pettersen UCSF Computer Graphics Laboratory ACKNOWLEDGEMENTS Noeshow and mardishow could not have been written without the assistance and encouragement of Dr Shauna Farr Jones Xplor2amber was written with the assistance of Dr Bryan Finn and Dr David Schweisguth and xplor2tors with the assistance of Dr Brian Jones Diana2amber was written with the assistance of Dr Michael Zawrotny APPENDIX 6 161 UCSF MidasPlus PDB2GROUP 1 PDB2GROUP 1 NAME pdb2group generate Midas group file from Protein Data Bank PDB file SYNOPSIS pdb2group a anchor_atom 3 n3_atom 2 n2_atom d group_description PDB_file DESCRIPTION Pdb2group takes a PDB file with explicit CONECT records even for standard residues such as amino acids and generates a group file suitable for use with midas 1 The group file is used by MIDAS commands such as swapaa swapna and addgrp and defines the connectivity and relative position of a group of atoms The generated group file is written to standard output FILE FORMAT A group file consists of a series of text lines and can be divided into four parts The first part is the title and is a single line description of the group e g 4 OH phenyl The second part is the list of atoms in the group and is a series
117. ameter for which the user substitutes the appropriate name digit etc User Contributed Software Programs marked with asterisks in the preceding table are user contributed software which has been incor porated into the MidasPlus distribution Such programs are unsupported in the sense that bug reports and sug gested enhancements for these programs will not receive the same priority as for core parts of the MidasPlus distri bution This is not to say that bug reports or enhancement requests for user contributed software will be ignored just that since the source code may not have been written at UCSF the time required to determine how to change the code may make such a change impractical Nonetheless user contributed software has extended MidasPlus functionality in many significant ways and we encourage you to contribute any software developed at your site Contributions for MidasPlus distribution must include e All source code necessary to compile your program along with instructions as to how to perform the compilation for example a README and Makefile e Full documentation of the use of the program preferably in Unix manual page format the source for the discern manual page is in usr local midas src contrib discern discern 1 as an example e A demo that can be run to verify that the software is working correctly when we receive it To notify us of your desire to contribute software either send
118. and correspond to options of conic which control the appearance of the image and whether the image is saved in a file for later use PRENEON To create a complex image multiple outputs of neon can be saved combined and then sent to conic to draw the final image The Midas command preneon runs only neon and the output must be directed to a file If the output of preneon is not directed to a file it is returned by default to midas which will have to work its way through many lines of invalid commands The preneon command does not accept any com mand line flags EXAMPLES 1 To have a quick look at an image Command neon p 2 To save a full screen image in the file figure i Command neon F o figure i 3 To create a complex image with a ligand shown as sticks and the binding site shown as space filling atoms set neon dat for sticks display just the ligand and save the output of neon in the file site Command preneon gt site Turn on the CPK flag in neon dat and display just the binding site atoms Append the output of neon to the file site Command preneon gt gt site Send the combined information in the file site to conic using Conic parameters from the file param and save the full screen image in the file figure i Command conic c param F o figure i site APPENDIX 6 151 UCSF MidasPlus NEON 1 NEON 1 FURTHER EXAMPLES The demonstration images included on the MidasPlus distribution CD show how to achiev
119. and generate and display a graphics object depicting the distance constraints and torsion angle constraints if any For the curious graphics objects are discussed in the Non Molecular Graphics Objects section of the MidasPlus manual though it is not necessary to read that section to use noeshow effectively The graphics object will be opened in the lowest unused model number Distance constraints will be depicted as lines connecting the atoms involved in the constraint If one of the atoms is actually a pseudo atom composed of several atoms then the constraint will be drawn to the nearest of the atoms The distance constraints will be colored according to how well they are satisfied Color Meaning red distance exceeds both upper bounds yellow distance between the upper bounds green distance satisfies constraint cyan distance between lower bounds blue distance less than both lower bounds Note that by default noeshow does not display the satisfied constraints the a flag causes them to be displayed Torsion angle constraints if any will be displayed as cages surrounding the central bond of the dihedral The coloring of the cage is as follows Color Meaning AMBER Meaning X PLOR red energy penalty gt 4 0 violation gt 10 degrees orange energy penalty gt 1 0 violation lt 10 degrees yellow energy penalty gt 0 0 satisfied but within 5 degrees of violated green energy penalty 0 0 sati
120. aracter as a delimiter For example label 1 color 32 s 1 color green b 1 If a large system is being displayed it might be advantageous to use such a compound command since the graphics image is drawn only after the entire command has been executed Each description of the MIDAS commands in this document contains a line indicating the correct usage of the command The usage includes the command name appearing in boldface print followed by command line parameters in italic or roman print Parameters appearing in italics require substitution of the appropriate name digit etc by the user Parameters appearing in roman print are literals and should be typed in as they appear in the usage line Parameters which appear inside square brackets are optional All parameters not appearing inside square brackets are required for the command to execute Keyword parameters are sometimes separated by vertical bars which indicate that the keywords are mutually exclusive Parameters named atom_specification always refer to a selection of atoms residues and or models as described in section 2 1 Note that omitting atom_specification is the same as specifying all atoms in all models MIDAS accepts abbreviated forms for all commands Abbreviations are disambiguated by ranking com mands by frequency of use For example rec may be substituted for record Typing re happens to mean reset instead of read
121. are below with a standard HELIX record present as a reference record HELIX 1 A PHE 6 EU 26 1 USER FLIP PHE 6 USER XSECTION PHE 6 LEU 26 xsection type USER NORIBBON PHE 6 LEU 26 EXAMPLES The demonstration images included on the MidasPlus distribution CD show how to achieve a variety of striking effects and give detailed instructions on how each image was made If these demonstration images have been installed on your system they will be found in usr local midas demos images The README index file there has further information If the demonstration images have not been installed on your system you need to mount the distribution CD ROM and you will find the images in the CD ROM directory Midas 2 1 demos images SEE ALSO Carson M and Bugg C E Algorithm for ribbon models of proteins Journal of Molecular Graphics Vol 4 1986 pp 121 122 conic 1 dnacheck 1 ksdssp 1 midas 1 showcase 1 BUGS Residues with ring structures on the mainchain may not be depicted correctly FILES usr local midas resource ribbonjr xs default default cross section file usr local midas resource midas models ins default residue drawing templates AUTHORS Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 176 UCSF MidasPlus RUN2SES 1 RUN2SES 1 NAME run2ses convert a PDBRUN file into a Midas session SYNOPSIS run2ses i PDBRUN_file o session DESCRIPTION R
122. are numbered If the letter T appears in place of a 1 in the coordinate values MIDAS accepts the input and sets those coordinate values equal to 0 000 Thus if the user finds some atoms grossly misplaced in the MIDAS model the corresponding error in the PDB file may be the use of l instead of 1 Such errors may be readily located if the text of the data file appears in uppercase since a text editor may be invoked to search for all occurrences of the lowercase letter l 3 4 Modeling Hydrogen Atoms 3 4 1 Hydrogens in Protein Data Bank Files Users who have coordinate values for hydrogen atoms may include those values in the PDB data file using the Brookhaven Protein Data Bank convention for hydrogen atoms The conventions for hydrogen atoms in PDB files are as follows 1 Hydrogen atoms appear as ATOM records following the ATOM records of all other atoms of a particu lar residue 2 The name of each hydrogen atom is determined by the name of the atom to which it is connected The first space of the name column 13 is an optional digit to be used if two or more hydrogens are attached to the same atom The second column 14 is used for the chemical symbol H The next two columns contain the remoteness indicator one or two characters of the atom to which the hydrogen is attached For example UCSF MidasPlus 76 UCSF MidasPlus
123. artesian coordinates for the data point this may be changed using the axes command see above There must be the same number of elements in the list as the number specified by the field property description EXAMPLES The following is a sample data file field 7 size 0 2 nlayer 3 directional data APPENDIX 6 114 UCSF MidasPlus DISCERN 1 DISCERN 1 0001 02 01 0 2 0 100 5 0 4 01 0 0 8 010 2 5 3 0 0 25 1 2 The following are MIDAS commands that may be used to display the data file as described in the DESCRIP TION section above disc open discern data Open the data file and display it disc color property 4 min blue max red Color the data points based on column 4 and make the minimum value correspond to blue and maximum to red Intermediate values will map to colors ranging from blue to cyan through magenta to red disc size property 5 min 0 1 max 0 5 Make the ellipsoid size correspond to column 5 and map the minimum value to 0 1 angstrom and maximum to 0 5 angstrom BUGS There is no way to change the direction vector from columns 4 5 and 6 SEE ALSO MidasPlus User s Manual AUTHOR Conrad Huang Computer Graphics Laboratory UCSF Chris Bayly UCSF APPENDIX 6 115 UCSF MidasPlus DMS 1 DMS 1 NAME dms calculate a solvent accessible molecular surface SYNOPSIS dms file a d density g file i file n w radius v o file DESCRIPTION Dms calculates
124. assigned a rotation_number between 0 and 15 inclusive either by the user or automatically by MIDAS Once a bond rotation is activated the rotation may be manipulated and controlled by assigning the rotation to a slider via the assign command The MIDAS sys tem startup command file pre assigns bond rotations 0 through 4 to sliders they can be de assigned if neces sary Alternatively the turn command can be used to set the angle of the bond rotation to an exact value The rotation number and current bond angle are reported on the top of the display screen If only atom and atom2 are specified the angle reported is relative to the beginning position i e the position when the assignment was made If four atoms are specified then the torsional angle is reported The rotation command removes the rotation and returns the bond to its original conformation use the fix command to preserve the new conformation When a bond is rotated part of the model remains fixed and the remainder rotates For a rotation in a side chain the backbone side will remain fixed and the side chain will rotate For a rotation in the back bone the beginning residues of the structure will remain fixed and the terminal residues will rotate The rota tion looking along the bond from the fixed to the rotating section is clockwise If the brotation command which see is used instead of rotation then the rotating and fixed portions as described above are inter
125. at levels 2 0 colored blue and red in model 1 Since the grid size was APPENDIX 6 110 UCSF MidasPlus DENSITY 1 DENSITY 1 not explicitly specified it defaults to 20 units CAVEATS The contour maps should always be rotated and translated in synchrony with model O the structure Should they ever be mistakenly manipulated out of alignment they can be realigned by using the MIDAS matrixcopy command Different areas of the protein can be contoured at the same time by specifying a new center and opening additional contour maps into other model numbers SEE ALSO MidasPlus User s Manual AUTHOR Christian Schafmeister UCSF APPENDIX 6 111 UCSF MidasPlus DISCERN 1 DISCERN 1 NAME discern MidasPlus delegate for visualizing multidimensional data MIDAS COMMAND SYNTAX Command delegate start disc discern DESCRIPTION Discern is a MidasPlus delegate for qualitatively visualizing three dimensional points with additional asso ciated values Discern generates MIDAS object files that represent data points as ellipsoids The center of the ellipsoid represents the Cartesian coordinates of a data point The color size and lengths of the major and minor axes of the ellipsoids represent the additional values The ellipsoids are displayed using longitu dinal and latitudinal lines By varying the number of these lines one can get different representations For example using 3 longitudinal and 1 latitudinal lines yields
126. ates the location sense anti parallel etc and registration with respect to the previous strand in the sheet if any of each strand in the model One record per strand The following table describes the format for each record type The record type appears in columns to 6 of each line of a PDB file This record type determines the kind and format of information on the remainder of that line Note that the data appears in specific columns This refers to the spaces on the line in which the data appears For example in an ATOM record the first four places contain the record type ATOM The next two places are blank The 7th through 11th places contain the atom serial number The serial number is right justified so if the serial number is 1 for example the digit 1 will appear in the 11th place and the other places will be blank For the atom with serial number 100 the number will appear in places 9 through 11 leaving places 7 and 8 blank It is necessary to reproduce this format exactly in order for MIDAS to interpret the data properly Any deviation is likely to cause errors preventing the successful construction of a model Note that HELIX and SHEET records are only required if you intend to use the midas ribbonjr com mand to render a Jane Richardson type ribbon depiction of the model The ribbonjr command uses infor mation contained in these records to determine what parts of t
127. be located in the literature The atoms currently recognized are Element Radius H 1 20 C 1 90 N 1 50 O 1 40 F 1 35 P 1 90 S 1 85 Cl 1 8 Fe 0 64 Cu 1 28 Zn 1 38 Br 1 95 I 2 15 BUGS Atoms must be consecutively numbered in the PDB file for correct results AUTHOR Michael Connolly University of California San Francisco APPENDIX 6 147 UCSF MidasPlus MS 1 MS 1 LIMITATIONS 6000 atoms Also there cannot be more than 8000 waters involved in overlapping reentrant surface remo val This is generally not a problem unless you have a large protein with many internal cavities and you have not used the d flag to reduce the density FILES r intermediate file of reentrant surface points binary a intermediate file of reentrant surface points ASCII s intermediate file of reentrant surface points sorted 22222 intermediate file of contact surface points ASCII 072277 intermediate file of all surface points k intermediate file from getcoord e intermediate file of atoms inside ellipsoid b binary file of coordinates for buffering DIAGNOSTICS Many and varied Be sure to examine the g file and submit out before you leave a background job running overnight APPENDIX 6 148 UCSF MidasPlus NEON 1 NEON 1 NAME neon generate a molecular model with solid stick bonds and shadows MIDAS COMMAND SYNTAX Command neon conic options Command p
128. cd GRID variables to user defined values and are used by makegrid to generate the GRID input file npla number_of_planes_per_Angstrom Sets the GRID variable NPLA Defaults to 1 probe probe_type Sets the type of the probe Defaults to the water probe oh2 See the GRID manual for other possibilities KNOWN BUGS The color of an object i e energy contour min max label and GRID box boundaries has to be defined before the actual object is drawn Once displayed there is no way to change its color except by deleting the object open model_number redefining its color with color color_spec and regenerating the object using the appropriate command Dashed lines cannot be produced If gd is used to show energy contours it must be running on a machine with the same integer and floating point binary format as the machine that produced the GRID energy contour data file Naturally if the GRID computation was performed on the same machine that gd is running on contouring will work AUTHOR Hans De Winter Laboratory of Medicinal Chemistry REGA Institute of Medical Research Minderbroedersstraat 10 B 3000 Leuven Belgium APPENDIX 6 127 UCSF MidasPlus GD 1 GD 1 REFERENCE 1 Goodford P J A computational procedure for determining energetically favorable binding sites on biologically important molecules 1985 J Med Chem 28 849 857 The GRID program can be obtained from Molecular Discovery Ltd West
129. ce constraints are in AMBER INTERFACE format they need no further preparation to be used by noeshow If you have constraints in MARDIGRAS input format they are ready for use in mardishow see the Mardishow section below Constraints in other formats will need to be converted If you are not certain what format your constraints are in examples of each are provided in the Constraint formats section below Constraints in AMBER INTERFACE format have an energy well for each constraint There are two upper bound values and two lower bound values The lower of the two upper bound values is where if the distance exceeds the bound an energy penalty begins to be applied in the AMBER simulation and the higher upper bound value is where the penalty reaches a maximum The lower bounds are similar but apply to short distances Some constraint formats e g X PLOR describe only one upper and one lower bound How this is mapped to the AMBER INTERFACE type constraint style depends on the conversion procedure The conversion procedure for the various formats are X PLOR Running the xplor2amber conversion script as shown in the SHELL COMMAND SYNTAX section above will produce a file of equivalent constraints in AMBER INTERFACE format The bounds given in the X PLOR constraint file are taken as describing the floor of the energy well required for the AMBER INTERFACE format description i e the distances where an energy
130. cent addition of the MIDAS commands run pdbrun and delegate have made it relatively easy to extend MIDAS functionality with auxiliary programs Several such programs have been contributed to the MidasPlus distribution and are described in this section These support programs are typically invoked from within MIDAS The manual pages for MIDAS and all associated utility and support programs are included here and the table below summarizes the function of each program MidasPlus Program Suite Program Name Function bs create printable PostScript ball and stick representation of molecule conic generate CPK style molecular models with shadows discern visualize multidimensional data density display X PLOR electron density maps dnacheck correct nonstandard PDB files of nucleotide structures dms calculate a solvent accessible molecular surface esp calculate electrostatic potential fixatname correct AMBER pseudo PDB files so they are in standard PDB format gd display GRID generated energy contours gennuc generate ideal DNA RNA structures from sequence data gentpl generate a MIDAS template from a Protein Data Bank coordinate file ilabel label an SGI image with arbitrary text itops convert SGI image or TIFF to color PostScript ksdssp generate HELIX and SHEET records for PDB files lacking them label3d create labels with correct depth for stereo or neon longbond break excessively long bonds midas MidasPlus molecular interactiv
131. construct his or her own set of MIDAS templates and use these alone or in combination with the existing MIDAS library of tem plates A program exists to automatically construct new template files when needed see gentpl in Appendix 6 for details 3 5 1 Building and Modifying MIDAS Templates Occasionally it is necessary to modify existing templates For example gentpl sometimes generates templates with incorrect START and END atoms This results in the use of the wrong atoms to connect the current residue to the previous and next residues in the chain To correct this problem the user may edit the template directly To do so invoke the standard system text editor on the appropriate ins file which should be found in the user s private models directory The default private models directory is HOME models This can be overridden by setting the MODELS environment variable If that directory doesn t exist nor does the default models directory then the template will be found in the current directory Since ins suffix files contain only simple character text they can be edited directly The name of the START atom and the END atom can be changed as needed see previous section for additional information on the format of template files For example suppose gentpl generated the following template RESIDUE FEA START FE1 DRAW O DRAW FE2 DRAW NA DRAW NB DRAW NC UCSF MidasPlus 78 UCSF MidasPlus END NC The
132. d color is interpolated from the first to the second color starting at the top going down wards If three sets are specified the background color interpolates from the first color at the top of the image to the second color in the middle to the third color at the bottom This option is only meaningful when the output format is screen The default background color is black 0 0 0 APPENDIX 6 171 UCSF MidasPlus RIBBONJR 1 RIBBONJR 1 c color scheme Select the color scheme to use for the ribbon The supported color schemes are residue struc ture and xsection In the residue scheme the ribbon corresponding to a residue will have the same color as the residue s guide atom In the structure scheme the color is determined by the secondary structure type helix strand or turn the actual colors are specified using the H S and T flags see below In the xsection scheme the color is determined by the residue cross section type see x flag below The default color scheme is residue e shell command Execute the shell command when the image has finished drawing Ribbonjr will not exit after executing the shell command see the p flag below f output format Select the output format The supported formats are midas inventor rayshade pov screen and tiff The default output format is screen or midas if drawing to the screen is not supported on the system e g NEXTSTEP systems The rayshade and pov formats are
133. d cross section that instead of being smooth is composed of a series of short flat segments The ribbon appears similar to the default ribbon but with ribs running down the ribbon s length A scale factor Specify the scale factor between the radius of an atom and the radius of the sphere that represents the atom in ball and stick mode The default scale factor is 0 2 For some images you may also want to use the r option to increase the sphere subdivision and thereby get better looking balls B scale factor Specify the scale factor between the radius of a bond s atoms and the radius of the cylinder that represents the bond in ball and stick mode The default scale factor is 0 2 For some images you may also want to use the r option to increase the sphere subdivision and thereby get better looking balls D width height Specify the window dimensions when output format is screen or tiff The default dimensions are obtained from USER records in the PDB input file If no dimensions are specified in the PDB file they are set to 645x484 E helix extension When ribbonjr constructs the ribbon representation it uses the guide atom coordinates as the basis of its control points When using B splines the ribbon corresponding to a helix tends to be very slender because the spline does not interpolate through the control points To produce helices of a reasonable radius the coordinates of helical g
134. d facilitates extensions to the normal MIDAS command set In particular both the conic and the ribbonjr commands are implemented using pdbrun As mentioned above a PDBRUN file is passed as input to command This PDBRUN file describes not only current model coordinates but also other aspects of the modeling environment such as clipping plane positioning etc Modeling environment annotations are supplied in various types of USER records described in detail in Appendix 1 The PDBRUN file has three principal sections The first section Annotation Headers has global modeling information The second section Per Molecule Annotations has molecular data for each model Each model s data starts with a USER FILE record and is terminated with an END record The serial numbers in ATOM HETATM and TER records incre ment continuously from one model to the next Due to field widths this imposes a limit of 99999 atoms in a scene Any PDB records present in the model s original source file and not normally interpreted by MIDAS e g REMARKS are preserved and placed just after the USER FILE record The data for non molecular graphics objects are also in this section bounded by USER OBJECT and USER ENDOBJ records The third section Annotation Trailers contains records specifying the angles and distances being explicitly monitored in the current view Throughout fields in PDB records that are not wide enough to hold their associated values are fille
135. d in other documents whereas standard PostScript can be printed directly In fact such itops output can be printed by piping directly to pr 1 or p 1 obviating an intermediate disk file UCSF MidasPlus 80 UCSF MidasPlus On SGI systems the imgcopy program can convert SGI image files to a variety of formats Consult the imgcopy manual page for details of usage A listing of the formats that imgcopy can convert to can be obtained by running the imgformats program On NeXT systems the free Omnilmage app program can convert between a wide variety of image file formats If you don t already have it point your favorite web browser at http omnigroup com Software Omnilmage If you re an adventurous sort with a C compiler the freely available netpbm suite of image tools can perform a wide variety of image format conversions Netpbm is available for anonymous FTP from the sites listed in the table below Site Directory Geographic Locale wuarchive wustl edu graphics graphics packages NetPBM USA ikaros fysik4 kth se pub netpbm Sweden ftp informatik uni oldenburg de pub netpbm Germany peipa essex ac uk ipa src manip England ftp rahul net pub davidsen source USA 3 6 3 Printing Screen Images The MIDAS display program s copy command will print the current MIDAS modeling session view To print images from ancillary rendering programs such as ribbonjr conic and neon one must first capture image files in TIFF or SGI
136. d input if no file names are specified Fixatname prints the corrected PDB file on standard output BUGS Atoms with two character atomic symbols are misaligned as mentioned above SEE ALSO MidasPlus User s Guide AUTHOR Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 124 UCSF MidasPlus FIXSES 1 FIXSES 1 NAME fixses update pre MidasPlus 2 0 session files SYNOPSIS fixses sessionname ses DESCRIPTION Sessions saved with version of MidasPlus prior to release 2 0 require minor modifications to work correctly with versions 2 0 and later Fixses performs these modifications AUTHOR Greg Couch UCSF Computer Graphics Laboratory APPENDIX 6 125 UCSF MidasPlus GD 1 GD 1 NAME gd a MidasPlus delegate which serves as an interface between MIDAS and Peter Goodford s GRID pro gram 1 MIDAS COMMAND SYNTAX Command delegate start g gd r file_name If the r flag is used then all communication between gd and MIDAS is recorded in file file_name DESCRIPTION Gd is a MidasPlus delegate to allow the visualization of three dimensional energy maps output by Peter Goodford s GRID program 1 Gd contours these maps at user defined energy levels which are then displayed by MIDAS along with the molecules under study Gd can also produce GRID input files with correct BOT XYZ TOP XYZ coordinates for the molecules or parts of molecules of interest When gd is acting as a delegate for MIDAS the
137. d models The center of rotation can be changed with the cofr command and the center of mass of a model can be set with the setcom command If the independent toggle option is on a will be displayed at the center of rotation of each individual model Displays the control panel Makes MIDAS display the filenames of the open models in the top left corner of the win dow above any bond rotation monitors Makes MIDAS resize itself to use the full screen Useful if MIDAS is started without a desired f option If then unset MIDAS will revert to its original size Atoms are colored by halfbond connections to other atoms instead of each atom having one whole bond associated with it Note that using halfbond mode may degrade response time If set models rotate about their own centers of mass otherwise models rotate about the combined center of mass Turns on distance rotation and angle monitoring labels Uses orthographic instead of perspective projection If set multiple assignments to a single slider see assign will cause reassignment i e only the last assignment will apply If unset then multiple assignments will accumulate i e all will apply Initiates remembering of subsequent typed user commands Note that commands that implicitly generate additional commands e g read source run pdbrun are remem bered but not expanded Issuing a new set record when record mode is already set resets remembering from scratch
138. d underscores A color name may be redefined at will The red green and blue arguments must be floating point numbers between zero and one inclusive By convention red green blue cyan yellow magenta white gray grey and black are predefined In OpenGL versions of MIDAS all X window system color names are also predefined They can be listed by running the program usr bin X11 showrgb Also for backwards compatibility the integers from 0 to 65 are in fact color names that are predefined and may not be redefined UCSF MidasPlus 27 UCSF MidasPlus Numerical Color Mapping colordef value Equivalent color Color name red green blue number green 1 0 0 1 0 0 0 cyan 8 0 0 1 0 1 0 blue 16 0 0 0 0 1 0 magenta 24 1 0 0 0 1 0 red 32 1 0 0 0 0 0 yellow 48 1 0 1 0 0 0 white 0 1 0 1 0 1 0 black 64 0 0 0 0 0 0 gray grey 65 0 5 0 5 0 5 Examples colordef activesite red create a special color for the active site On the NeXT there is a color called colorpanel that is constantly redefined to be the same as the current color in the color panel when the Color Panel is active The colorpanel color can be used in com mands just like any normal color name See also color colorrename 2 4 17 Colorrename Usage colorrename color_name new_color_name colorrename replaces the given color_name with the new_color_name The new color name is an arbitrary sequence of letters digits and u
139. d with asterisks instead Details of the meaning and format of the USER records employed by pdbrun can be found in Appen dix 1 A discussion of the motivation for and design criteria of the PDBRUN format can be found in G S Couch E F Pettersen C C Huang and T E Ferrin Annotating PDB files with scene information J Mol Graphics 13 153 158 1995 UCSF MidasPlus 42 UCSF MidasPlus See also delegate run save system write vdwopt 2 4 57 Pickatom Pickabort Usage pickatom Usage pickabort These commands are used in conjunction with the MIDAS delegate facility see Appendix 5 A delegate program can request that the user select a particular atom on the display by first sending a pickatom command to MIDAS verifying that the command has been accepted by MIDAS then waiting for the user to select an atom and for MIDAS to send the indication of the selected atom back to the delegate program When MIDAS accepts a pickatom command from a delegate it will reply with Waiting for pick If another delegate program is already waiting for an atom to be selected MIDAS will reply with Already picking for delegate XXX After MIDAS accepts a pickatom command and the user selects an atom the command that MIDAS sends to the delegate is of the form pickatom model_number residue_sequence atom_name If instead of selecting an atom the user types pickabort MI
140. dasPlus commands once the model is displayed see the bond command Templates are discussed in more detail in More on Connec tivity and Templates section 3 5 3 2 Molecular Surfaces MIDAS represents molecules by drawing three dimensional wire frame stick figures on the screen Users often want to characterize the surfaces of these molecules as well This can be accomplished in several ways within MIDAS the two basic types are space filling solid models and surfaces represented by a densely spaced dot surface Surfaces represented by dots offer greater interactivity since they can be manipulated in real time in the same way as wire frame models Space filling models on the other hand offer shading and UCSF MidasPlus 63 UCSF MidasPlus shadows and produce photographic quality images these models are generated using the conic command see Appendix 6 for full details Note that although MIDAS renders dots surfaces that are manipulable interactively it is possible to generate more aesthetic but non interactive dot surfaces with the neon or ribbonjr commands also detailed in Appendix 6 There are two different types of dot surfaces available 1 A vdw or van der Waals surface uses the van der Waals radii of the atoms in the model MIDAS assigns a van der Waals radius to each atom according to its atom type as determined by the Protein Data Bank naming conventions e g if the first letter encountered in
141. dbrun command PdbrunSto6 s primary use is to convert saved PDBRUN files for renderers that require PDBRUN version 6 Another use is to get pdbrun invoked programs that output PDBRUN version 5 files to work with MidasPlus 2 1 Most pdbrun invoked programs do not output PDBRUN files Instead they either output a series of MIDAS commands e g rainbow or have no output e g conic A few however do output PDBRUN files which are then piped to other programs as input Neon for example outputs a PDBRUN file which is then piped to conic as input To make an old PDBRUN producing program work with MidasPlus 2 1 its alias should be changed from alias old program pdbrun old program to alias old program pdbrun pdbrun6to5 old program pdbrun5to6 Programs that do not produce PDBRUN output need only employ pdbrun6to5 to work with MidasPlus 2 1 Consult the pdbrun6to5 manual page for details SEE ALSO pdbrun6to5 1 midas 1 MidasPlus User s Guide AUTHOR Greg Couch UCSF Computer Graphics Laboratory APPENDIX 6 167 UCSF MidasPlus PDBRUN6TOS 1 PDBRUN6TOS 1 NAME pdbrun6to5 convert PDBRUN version 6 files to version 5 SYNOPSIS pdbrun6to5 o output filename input filename DESCRIPTION Pdbrun6to5 converts PDBRUN annotated PDB files as generated by MIDAS s pdbrun command from ver sion 6 to version 5 Its primary use is to make version 2 1 of MIDAS work with older pdbrun invoked pro grams The MI
142. description_file level M input_PDB_file output_PDB_file DESCRIPTION Uncryst reads a Protein Data Bank file and generates coordinates for subunits based on the crystallographic symmetry information obtained from the CRYST and SCALE records Uncryst assumes that the input PDB file contains atoms from a single subunit and creates a PDB file which contains multiple copies of the input atoms with each group transformed by a symmetry operator defined by the space group definition from the CRYST record The s argument specifies a file that contains the symmetry descriptions of crystallographic space groups The format of the file is given below If the s option is not specified then a default file see FILES sec tion will be consulted The I argument specifies the output level see below for explanation The default output level is zero The M argument specifies that each matrix used to transform the coordinates be printed In addition the determinants of the rows and columns of the rotational part of the matrix are also printed These numbers should all be unity deviation from unity results in skewed coordinates for the generated subunits 66 99 If the output PDB file argument is omitted or given as uncryst will write to standard output If the input PDB file argument is omitted or given as uncryst will read from standard input SYMMETRY DESCRIPTION The symmetry description file contains
143. display window and the right eye image is shown on the left hand side of the window The user must look crosseyed at the images to perceive the stereopsis effect Image size may fill the entire window in this mode Lefteye and righteye show the left and right view of a stereo image respectively This is useful for taking stereo slides since you can photograph each eye view individually If stereo convergence in sequential mode is poor try using the set command to adjust values for vpsep viewdist and eyesep especially vpsep The command stereo is equivalent to stereo off See also set 2 4 83 Stereoimg Usage stereoimg p renderer options The stereoimg command generates stereo pairs using MIDAS callable rendering programs e g rib bonjr neon etc Full details of the use of this command can be found in Appendix 6 of this document UCSF MidasPlus 55 UCSF MidasPlus 2 4 84 Stop Usage stop Stop terminates the current MIDAS session without saving any of the currently displayed models See also save 2 4 85 Surface Usage surface atom_specification Usage surface atom_specification Surface selectively displays solvent accessible surface points for models The syntax is the same as for the display command except that it applies to surface points rather than to bonds To prepare a solvent accessible surface for display see Solvent Accessible Surfaces in Part III of this manual The
144. ds fol lowed by the atomic coordinates in ATOM records and terminated with a TER record The first REMARK records must contain the compound name e g REMARK RHOIFOLIN The name of the compound RHOIFOLIN in this example must be present for viewdock to work properly subsequent REMARK records are optional and have no format restrictions The ATOM records for the com pound follow the REMARK records The output file produced by DOCK almost follows the PDB format however the last few fields in ATOM records are placed such that they cross PDB field boundaries MIDAS follows the PDB format strictly and will reject the erroneous records so the ATOM records need to be edited to remove the offending fields Finally the TER record ends a compound entry For each compound viewdock stores its name its residue sequence number the optional information from REMARK records and its discard state one of deleted entries which were discarded in a prior sessions marked entries which were discarded in the current session or undeleted undiscarded entries All this information is presented in an interface panel which consists of several parts a compound browser a MIDAS residue number field an information window a Discard Restore button and a menu bar browser names of marked compounds are noted by surrounding them with short dashes compound name sequence whereas names of deleted compounds are surrounded with long dashes
145. e MIDAS color including user defined colors see the colordef command or two colors and a mixture fraction separated by commas The mixture fraction is a number between zero and one that indicates the interpolation fraction along a color wheel between the two colors to use to get the actual color Zero corresponds to the first color while one corresponds to the second color In MIDAS the open obj modelnum command is used to open object files If a model number corresponding to an open molecule is used then the object will move in synchrony with that molecule Display and undisplay of an object is controlled with the objdisplay command and is independent of the display status of the corresponding molecule if any 3 10 Chemical Group Description Files The MIDAS addgrp command is used to add a new chemical group to a displayed molecular structure Many common chemical groups are supplied in the MIDAS groups directory see addgrp but it may be neces sary to create a group file to describe an uncommon chemical group Such a file would be placed in the user s personal group directory see addgrp for use If the user has some PDB file that contains the chemical group by far the easiest method to get the corresponding group file is to use the pdb2group 1 utility provided with the MidasPlus distribution see Appendix 6 Otherwise the group description file must be constructed by hand Information for doing so is provided below
146. e USER FILE record The data for non molecular graphics objects are also in this section bounded by USER OBJECT and USER ENDOBJ records The third section Annotation Trailers contains records specifying the angles and distances being explicitly monitored in the current view Throughout fields in PDB records that are not wide enough to hold their associated values are filled with asterisks instead Below the USER records found in each section are explained in detail The formats for these records in both the C and FORTRAN programming languages are presented at the end of this appendix Annotation Headers USER PDBRUN version Specifies the pdbrun format version used to annotate the file MidasPlus 2 1 uses version 6 MidasPlus 2 0 used version 5 There are utility programs for converting between these two versions if necessary See pdbrunSto6 1 and pdbrun6to5 1 in Appendix 6 of this manual USER EYEPOSxyz The viewer s position x y z for purposes of calculating what to display USER ATPOS xyz The location the viewer is assumed to be looking towards for determining line of sight USER WINDOW Mere Night bottom Yop Zhither Zyon View volume display bounds relative to the line of sight Except in stereo views the MIDAS view volume is symmetric about the line of sight x and y are both negative and equal in magnitude respectively to X ight and Yop which are both po
147. e a variety of striking effects and give detailed instructions on how each image was made If these demonstration images have been installed on your system they will be found in usr local midas demos images The README index file there has further information If the demonstration images have not been installed on your system you need to mount the distribution CD ROM and you will find the images in the CD ROM directory Midas 2 1 demos images SEE ALSO conic 1 midas 1 MidasPlus User s Manual FILES usr local midas resource neon dat default neon parameter file AUTHOR Thomas R Hynes Protein Engineering Department Genentech Inc and Department of Pharmaceutical Chemistry UCSF APPENDIX 6 152 UCSF MidasPlus NOESHOW 1 NOESHOW 1 NAME noeshow show AMBER INTERFACE format NMR derived constraints mardishow show MARDIGRAS format NMR derived constraints SUPPORT PROGRAMS sander2amber convert AMBER SANDER namelist style distance constraints to AMBER INTERFACE for mat xplor2amber convert X PLOR distance constraints to AMBER INTERFACE format xplor2tors convert X PLOR torsion angle information to AMBER style diana2amber convert DIANA distance constraints to AMBER INTERFACE format MIDAS COMMAND SYNTAX Command noeshow options constraint_file torsion_file or Command mardishow options constraint_file SHELL COMMAND SYNTAX sander2amber pdb_file sander_input_constraints gt refo
148. e display program midas tty terminal based version of MidasPlus display program mrotate generate script to bring model s into specific orientation neon generate a molecular model with solid stick bonds and shadows noeshow display NMR derived distance and torsion constraints pdb2group convert PDB file to addgrp style group description file pdb2site convert PDB file to dms site file pdbopen browse and or open available PDB files rainbow smoothly color molecule chain from red to blue ribbonjr generate ribbon representation of molecules run2ses convert PDBRUN format file to MIDAS session file stereoimg create conic neon or ribbon images in side by side stereo uncryst generate crystallographic symmetry units from CRYST records unmtrix expand MTRIX records in Protein Data Bank coordinate file viewdock facilitate use of DOCK generated bound ligand structures user contributed software see below Each program description contains a synopsis line indicating the correct usage of the command The usage includes the command name in boldface type followed by command line parameters Command line parameters enclosed in brackets are optional and the brackets should be omitted if you use such a parameter These command line parameters appear in 6699 boldface print indicating a flag The flag is usually a single character and is preceded by a character and is typed as is APPENDIX 6 102 UCSF MidasPlus italic print indicating a par
149. e model_file s DESCRIPTION MIME Midas is the interactive 3D display program for the MidasPlus molecular modeling system The program is designed to generate easily manipulated views of large molecules primarily proteins and nucleic acids Midas normally starts up in a window but if the fullscreen flag is used then midas will use the entire graphics display on start up It can be abbreviated full The nofork flag tells midas to not go into the background See the MIME section below for the most com mon usage If stereo will not be used then it may be advantageous to give the nostereo option This tells midas to look for a double buffered instead of a quad buffered graphics window thus saving screen memory for other applications This only affects systems that support nondistorted stereo in a window The script script option lets you specify a command script to be sourced at start up time The delegate delegate_name option treats standard input and output as a delegate with the given name If there is more than one filename specified on the UNIX command line midas opens the first file as model 0 the second as model 1 etc see open in the Command Reference Guide section of the MidasPlus User s Manual If only one file is given on the UNIX command line then midas will try to read it as a session file first and then open it as a model if it is not a session Midas also understands the various standard X applicat
150. e stereo image although stereo lefteye and stereo righteye are preferable since these commands generate a more technically accurate stereo image pair See also roll stereo wait 2 4 91 Update Usage Update transformed original filename Update changes the coordinates of a subset of atoms in a model The user must supply either the transformed or original keywords and a PDB filename containing atom records with new atom coordinates If PDB USER FILE record s are present in the file see Appendix 1 then the indicated models are updated otherwise the lowest numbered model is updated If PDB HELIX or SHEET records are present in the file they will take precedence over such records originally supplied with the model s If the keyword is transformed then the new coordinates are considered as having already been transformed by the current rotation and translation matrices If the keyword is original then the new coordi nates are treated as untransformed coordinates and the current rotation and translation matrices are applied to the new coordinates before they are integrated with the rest of the model 2 4 92 Vdw Usage vdw atom_specification Usage vdw atom_specification Vdw displays the van der Waals surface for the selected atoms The syntax is the same as for the display command except that it applies to surface points instead of bonds The vdw command may be interrupted by the ESC key Atoms whose vdw s
151. ear out the mark with mark See also makemark pdbrun 2 4 44 Match Usage match selected atom_specification The match command uses the least squares fit method to superimpose two models The atom_specification should contain an equal number of atoms from two different models The atoms are matched according to the order in which they are specified i e the first atom of the first model is matched to the first atom of the second model second atom to second atom etc The MIDAS com mand syntax allows much flexibility in specification i e atom specifications can use all the shorthands avail able for related atoms For example the user might match models and 2 thus match 1 3 C1 C2 P O2 2 3 Cl C2 P O02 MIDAS will transform the first model so that its atoms overlay those of the second model Specifying the selected option will make match transform not only the first model but all selected models as well using the same transformation that was applied to the first model The user should be aware that the order in which atoms are specified in a list does not necessarily force the order in the match For example match 1 3 C1 C2 P 02 2 3 C1 C2 P 02 is not specific as to the order of the atoms C1 C2 P and O2 In this case MIDAS will order the atoms as they occur in the residue connectivity for residue 3 If residue 3 of model 1 and residue 3 of model 2 are the same this is not a concern If they are different however
152. eator framebuffer and record it on the videodisk recordimage image file Place a SGI image file into the VideoCreator framebuffer and record it on the videodisk recordframe duration Record the contents of the VideoCreator framebuffer A duration of more than one frame may be given as a SMPTE time code stoprecord Leave record mode Turn the screen saver back on play start frame stop frame Play back the contents of the videodisk starting at the given start frame and ending at the optional stop frame stopplay Stop the playback location Report the current frame location on the videodisk in SMPTE timecode format loop start frame stop frame Continuously play back the frames between the given start frame and stop frame stoploop Stop the looping RECORD LOGGING The file tmp vlanunit log where unit is the unit number argument to videodisk contains one line for each completed recordxxx command Each line is composed of the date the location on the videodisk in SMPTE format and the record command that was completed setup screen image frame The log file is overwritten by the next recordsetup ENVIRONMENT VCOPTS command line flags for VideoCreator programs SEE ALSO expr smpte 1 vcvlancmd 1 vcpaste 1 vcsetmode 1 BUGS Depends on the VideoCreator Last time we checked when fieldmerge 1 was used to build frames with different images in each field the field order was field fieldO instead of the order listed
153. eb pages The Saving Screen Images and Converting Image Files to Other Formats sections above detail how to obtain TIFF and via conversion GIF files from MidasPlus screen images Journals usually accept photographs and the Screen Photography section later in Part III offers advice for photographing MidasPlus screen images Many types of documents including journal articles are prepared with word processing programs Word processors that accept images typically allow the inclusion of TIFF format files At times it may be desirable to use an Encapsulated PostScript image MIDAS with the copy file command and conic or neon with the f ps flag can all produce Encapsulated PostScript files directly TIFF and SGI image files can be converted to Encapsulated Postscript via the itops utility with the E command line flag A typical command issued from the UNIX command line to convert an image file to Encapsulated PostScript would be itops E saved_image gt EPS_file UCSF MidasPlus 81 UCSF MidasPlus 3 7 Making Videos Many MIDAS commands are useful for producing video tapes and movies and commands such as move rock roll and turn have optional parameters for the number of image update frames over which to carry out the command execution and the number of frames to wait before beginning execution There is some limited support for stop motion frame by frame video creatio
154. ects spheres but cannot cast shadows themselves In fact they can not even block first class objects first class objects show through Quads are typically used to construct large background areas that show the shadow of the scene as a whole For best results there are two important things to note First the default field of view for conic is quite narrow and if you do not see an expected shadow it may be because it is falling outside the field of view In such a case you may want to expand the field of view half angle using the fov keyword see above from the default 15 degrees to 25 or 30 degrees The second thing to note is that because of ambient light shadows will not be black If you desire black shadows turn off ambient lighting using the ambient keyword above quad_color r7 g1 b1 r2 g2 b2 r3 g3 b3 r4 g4 b4 APPENDIX 6 107 UCSF MidasPlus CONIC 1 CONIC 1 Define the vertex colors of following quads The interior color of the quad will be smoothly inter polated between the vertex colors If only one RGB triple is specified all vertices will have that color rcone x y zr g b dx dy dz angle Rcone is to cone as rpoint is to point rpointx yzrgb Define a point light source relative to the scene similar to point The x y z coordinate is relative to the center of the scene with lengths normalized such that the distance from the eye to the center of the scene is 1 Thus the option rpoint001111 would define a po
155. ecular Graphics volume 10 number 2 June 1992 R A Lewis et al Note that MIDAS first searches the directory usr local midasNib midas for command before examining the rest of the user s execution path This is useful to avoid name conflicts between MIDAS commands using the run pdbrun delegate mechanism and UNIX commands of the same name Finally it should also be noted that a delegate s state is not saved in MidasPlus session files If a ses sion is restored no delegates will be active See also pdbrun pickatom run system UCSF MidasPlus 29 UCSF MidasPlus 2 4 21 Delete Usage delete new_residue_type atom_specification Delete removes a branch of atoms from a residue All atoms from atom_specification to the end of the side chain are deleted from the residue Deleting from a main chain atom produces unpredictable results Because the structure of the residue changes with deletion a new_residue_type must be specified to differen tiate between the original and new residue types See also addgrp bond 2 4 22 Density Usage delegate start dens density mapfile mapfile2 The density delegate shows electron density contours at selected density levels from X PLOR map files Details of this delegate s usage can be found in Appendix 6 of this document 2 4 23 Devopt Usage devopt option argument Devopt sets device specific options Issuing a devopt command with no arguments will list the options a
156. ecule for collision checks The file consists of a series of lines such as the follow ing ASP 205 CA TYR 13 GLY 116 FRM HIS 178 TO The asterisk means all atoms of the residue and the FRM and TO mean all residues from 116 to 178 inclusive The sequence number may contain letters and if the PDB input file contains chain identifiers then those should be appended on the right of the sequence number Residue insertion codes if any should be placed between the sequence number and any chain identifier Residues contained in HETATM records should have an asterisk appended to the end of the resi due identifier The surface generated using the i flag is not always the same as the surface APPENDIX 6 116 UCSF MidasPlus DMS 1 DMS 1 generated by running the entire molecule and afterwards selecting out the desired atoms The first surface will not include reentrant surface lying between an atom in the i file and atoms not in the file The pdb2site 1 utility may be useful for generating site files Consult the pdb2site manual page for further details n Include the unit normals to the surface with each surface point record vV Produce more verbose output Dms will announce each computation phase as it is entered as well as a count of the atom types in the molecule and the number of computation requests handled by each host that participated in the dms calculation 0 The output is written to file This f
157. ed Because coordinates are multiplied by 100 and stored as integers coordinates must have absolute values smaller than 327 67 The flags may be in any order The meanings of the flags are described below a Include all atoms not just those in amino acid residues d Change the density of points on the surface Density is a factor affecting the density of points on the surface the default of 1 0 produces about 5 points per square angstrom Only values between 0 1 and 1 0 are permitted For large proteins a density of 0 5 is recommended e Calculate only the surface lying within the ellipsoid specified in file File consists of 5 lines which define an ellipsoid The five lines are the ellipsoid center line 1 an orthogonal matrix represent ing the orientation of the ellipsoid lines 2 4 and the lengths of the three semiaxes line 5 The normalized vectors of the semiaxes form the columns of the orthogonal matrix It is recom mended that you use a sphere so the matrix will be a unit matrix and all three lengths will just be the sphere radius g Write all the informative messages to file instead of the standard error output Genuine errors still go to the standard error output This file is not rewound at any time so messages from several runs may be accumulated i Calculate the molecular surface only for those residues and atoms specified in file but keeping the rest of the molecule for collision checks The file consists of a s
158. ed from residue a residue type standard Protein Data Bank abbreviation or residue sequence number or range of sequence numbers atom an atom name standard Protein Data Bank abbreviation The following examples illustrate the use of these symbols for referencing models residues and atoms Note that the lack of either a residue specifier or an atom specifier or both is interpreted to mean all units of the associated reference level 0 all atoms in all residues in model 0 13 5 0 all atoms of residue 50 in model 1 1 50 all atoms of HETATM residue 50 in model 1 0 12 CA alpha carbon of residue 12 in model 0 Note A summary of all special symbols described in this section appears in Appendix 3 of this document 2If MIDAS had to modify the file name to locate the PDB file see the documentation for the set molpath command in Part II then the modified name must be used The modified name can be shown with the set filenames command In the OpenGL version of MIDAS the modified name is also visible in the control panel UCSF MidasPlus 11 UCSF MidasPlus Groups of atoms or residues may be specified For example 0 12 CAG N alpha carbon of residue 12 in model 0 and nitrogen of residue 12 in model 0 0 12 CA N alpha carbon and nitrogen of residue 12 in model 0 1 LYS all lysine residues in model 1 3 45 83 range of residues 45 through 83 in model 3 No
159. ed property is used Data points whose value is below the given lower bound are not displayed bmax value Specifies the upper bound for the data values If this keyword is not used the maximum value for the specified property is used Data points whose value is above the given upper bound are not displayed min param Specifies the display parameter associated with the lower bound of the data values For the color command the value is any string corresponding to a MIDAS color for other commands the value is a floating point number max param Specifies the display parameter associated with the upper bound of the data values For the color command the value is any string corresponding to a MIDAS color for other commands the value is a floating point number state Report the current state associated with the display parameter If no property has been associated with the parameter the property field is reported as none The display parameter associated with a data point is linearly interpolated using the fol lowing formulae fraction data_value lower_bound upper_bound lower_bound parameter min_param fraction max_param min_param Note that min_param may be larger than max_param in which case the display parame ter is inversely proportional to the data value The ellipsoid axes lengths are computed in angstroms size is dimensionless and color is interpolated in hue saturation value HSV space by MIDAS For
160. elds in the short form used to display entries in the text list The Open button sends a command to MIDAS to open the selected entry The PDB entries displayed in the text list may be pruned using the entry inspector see below the Display All button adds all entries from the index file back into the text list so that another search for interesting entries may be done The entry inspector consists of a number of text fields and several buttons Each text field corresponding to a field in a PDB entry and when an entry is selected in the index browser displays the value of the field The Open button sends a command to MIDAS to open the entry with displayed ID code The Find Undo and Clear buttons are used to prune entries from the text list in the index browser The Find button searches through the list of entries in the text list and removes any whose fields do not match the values given in the inspector text fields For the Resolution and Zero fields the values are compared numerically a relational operator may precede the numeric value lt 2 means less than or equal to two and a miss ing operator implies equality For all other fields the values are treated as case independent regular expressions a field is defined to match the value if any part of the field string matches the regular expres sion see Regular Expression Examples below The Undo button will undo the effect of the previous Find Two Undo s in a row is t
161. electronic mail to midas ideas cgl ucsf edu or regular mail to MidasPlus Distribution Coordinator Computer Graphics Laboratory University of California at San Francisco San Francisco California 94143 0446 APPENDIX 6 103 UCSF MidasPlus Introduction 0 Part I Getting Started Displaying the Model ccc cccsstecuecscteessevvecscevesaseedevecteavacenteceuiesstecepnensnavercoses eds Part II MidasPlus User s Manual Table of Contents Manipulating the Model 0 0 ceeeeseeceneecseceeeceesecesaecececeaeeenaeceneeeeeeeneees On Line Help Tutorials 00066 Demonstration Images minine aaen an n aa a a E MidasPlus Web Resources ssccsssscescecsseeesceceececsecesaceneeesaeceneceueeeneeceeeeceeeeaeens Obtaining Standard PDB Files oo eee ec eecceeeeee cesses caeesaecaeesaecsecaeceesseeseensees Helpful Hints Command Reference Guide ccccccccccccessessccccecssssceceecssssessescesssssssseesesees Referencing Models Command Overview MIDAS Start Up Command Synopsis Commands Addaa Copy Delegate Delete Density Devopt Discern Display Residues and Atoms cccccccccccccesesesseesessesssssesessssrrseeseeees and Utilities Grouped by Function 000 eeeeeeeeeeeeee O0OD0O0 WOOD NN WWW WwW wWNYNNYNNYNNYNNNNNNNNNNNNNN PRR RR eK NNT TTOUOUAANANANDUNUA NAH HHP HPWNNNNRP KP DNF HK KF
162. elegate the user can issue the command delegate stop delegate_name Finally the command delegate list lists the names of all active delegates Implementor Perspective Delegate programs interact with MIDAS by issuing valid MIDAS commands and receiving as feedback the replies to those commands The delegate also receives any commands directed to it by the user APPENDIX 5 97 UCSF MidasPlus When a delegate is executed its standard input C standard I O library stdin or Unix file descriptor 0 and standard output stdout or descriptor 1 are connected to MIDAS Data sent to stdout will be interpreted by MIDAS Data received on stdin are either commands from the user via the delegate_name mechanism or replies from MIDAS commands which are normally displayed to the user The communications protocol between the delegate and MIDAS is very simple An event diagram of the pro tocol is shown in Figure 1 On start up the delegate sends lines of commands to MIDAS for execution For each line of command MIDAS sends back to the delegate all the reply lines followed by a line containing only the word SYNC When the delegate is finished with its initialization it informs MIDAS by sending a line containing only the word SYNC At this point the delegate should wait for user commands which will arrive on stdin via MIDAS When the delegate receives a user command it once again sends lines of commands to MIDAS using exactly the same synchr
163. elegate start g gd r filename The gd delegate allows the visualization of three dimensional energy maps as output by Peter Goodford s GRID program Details of this delegate s usage can be found in Appendix 6 of this document 2 4 32 Geterd Usage getcrd atom_specification The geterd command returns the untransformed x y and z coordinates for the atom specified The atom_specification must select one only atom The coordinates are returned in the command reply area at the bottom of the MIDAS window 2 4 33 Help Usage help topic filename The help command displays information on the selected topic If no topic is specified MIDAS displays a list of all available topics If instead of a topic a full pathname to a file i e with a leading is given the contents of that file are displayed This is primarily useful for delegate programs that wish to display help specific to the delegate 2 4 34 Intensity Usage intensity hither_value yon_value Intensity changes the value of the intensity at the hither and yon clipping planes The values range from 0 to 1 Default values are 1 for hither maximum intensity and 0 2 for yon minimum intensity Note that the location of the hither and yon clipping planes may be changed with the clip command or by manipu lating the sideview or sliders in the control panel For backwards compatibility it is legal to use intensity values in the range 0 255 which are then mapped to 0 1
164. els whose reference name matches a MIDAS atom specifier have starting coordinates that are the same as its atom other labels have starting coordinates at the origin by default but may be changed using the posi tion command The starting coordinates of all labels with reference names matching MIDAS atom specifiers are updated from MIDAS every time a command is processed by label3d The MIDAS object move draw commands for a label are constructed by adding the label starting coordinates and offset to the coordinates found in the character descriptions see open Consecu tive characters in a string are offset in the x dimension by the width of the left character plus a small inter character spacing no offsets are added in either the y or z dimension The move draw commands for all labels are recomputed every time a command is processed by label3d list label font List all labels or fonts offset x y z Change the starting position of the current label by adding an offset of x y z angstroms If z is not provided zero is used in its place This command is useful for repositioning the label when it hides or is hidden behind important atoms Repeated use of this command is not cumulative i e APPENDIX 6 136 UCSF MidasPlus LABEL3D 1 LABEL3D 1 FONTS the new offset overrides the old offset rather than being added to it open font_name directory Read character descriptions from directory directory and place them in a new font
165. ely in the crystallographic fractional unit cell Each formula is a simple arithmetic expression consisting of numbers x y and z Only the simple arithmetic operators are permitted Grouping using parentheses is not supported An additional restriction on the formulae is that they may only be linear com binations of x y and z Formulae that violate this restriction are silently ignored There can be no blank lines in a space group Lines beginning with a can be used to insert comments 29 APPENDIX 6 181 UCSF MidasPlus UNCRYST 1 SEE ALSO Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description International Tables for X Ray Crystallography Vol 1 Symmetry Groups FILES usr local midas resource uncryst sdf Default space group file AUTHOR Conrad Huang and Eric Pettersen Computer Graphics Laboratory University of California San Francisco APPENDIX 6 182 UNCRYST 1 UCSF MidasPlus UNMTRIX 1 UNMTRIX 1 NAME unmtrix expand MTRIX records in PDB files SYNOPSIS unmtrix i original_PDB_file o new_PDB_file m MTRIX_serial_id DESCRIPTION Unmtrix reads a Protein Data Bank file and generates coordinates for subunits specified by MTRIX records The i argument specifies the input PDB file If no input file is given unmtrix will read from standard input The o argument specified the outp
166. en though they are not such as in a backbone trace where amp carbons of a protein are shown as connected Atom and atom are atom serial numbers Annotation Trailers USER ANGLE atom atom atom atom value A USER ANGLE annotation will be issued for each angle being interactively monitored in MIDAS Atom 0 atom are atom serial numbers If atom is non zero it is a dihedral angle otherwise a simple bond angle The value is the angle in degrees USER DISTANCE atom atom value A USER DISTANCE annotation will be issued for each distance being interactively monitored in MIDAS Atom and atom are atom serial numbers The value is the distance in angstroms 3D Graphics Annotations These annotations appear between USER OBJECT and USER ENDOBJ records USER GFX BEGIN type USER GFX END The graphics BEGIN and END bound a graphics primitive Within a graphics primitive there can be any number of vertices see below and optional color changes Type is one of the following POINTS Each vertex represents a point MARKERS Markers are like points but they are represented differently Markers are used for singleton atoms whereas Color interpolation is done using the HLS color model because it provides superior interpolation results compared to an RGB color model HLS color interpolation is as follows H H f
167. entire file One record per embedded file USER COLOR Follows ATOM HETATM record Applies Precedes ATOM HETATM record Applies USER RADIUS only to that record to that record and any subsequent records until next USER COLOR RADIUS USER COLOR RGB triplet follows color specification RGB triplet precedes color specification USER CNAME MODEL ENDMDL Models demarcated with MODEL ENDMDL Models demarcated with USER FILE END USER FILE pairs pairs END USER OBJECT ee Model number indicated by surroundin USER FNDORT Model number indicated in record USER FILE END pair y g USER FONT Font size follows font name Font size precedes font name USER GFX TEXTPOS Non existent Indicates position of ensuing text label USER GFX LABEL Includes text label position Text label position indicated by preceding USER GFX TEXTPOS record Multiple con secutive USER GFX LABELs indicate con catenation GFX primitives Quads triangles polygons and normals not Quads triangles polygons and normals supported supported by ribbonjr APPENDIX 1 91 UCSF MidasPlus Appendix 2 PDB Atom Naming Conventions for Amino Acids Alanine CB Arginine NH1 Pa CB CG CD NE CZ NH2 Asparagine D1 LA CB CG NND2 Aspartic acid OD1 CB CG op2 Cysteine CB SG Glutamic acid OE1 P CB CG CD NN oE2 Glutamine OE1 CB CG CD NNNE2 Glycine X Histidine CB CG NDI CD2 CE1 Ne Hydroxyproline N
168. er it refers to the corresponding bond rotation If angle is specified the structure is rolled through that angle given in degrees for each frame If angle has a negative value the direction of the rotation is reversed Frames if specified indicates the number of image update frames over which the roll operation is carried out If frames is not specified the structure continues to roll until explicitly turned off with the command roll axis Note that two or three rolls may be active at the same time that is the user can roll the structure around two or three axes at the same time Each must be turned off explicitly Wait_frames if specified indicates the number of frames to wait before beginning the roll This is use ful for making videos For example roll x 2 90 30 rolls the model 180 degrees over 90 image updates i e 2 degrees on each frame update after waiting 30 image update cycles before beginning MIDAS continues to process commands while the requested motion is in progress To have command processing pause until the motion is finished use the wait command The default values for axis and angle if omitted are y and 3 respectively If roll does not work it is likely you have failed to select the target models See also freeze select turn wait 2 4 69 Rotation Usage rotation rotation_number atom atom2 atom3 atom4 Usage rotation rotation_number Rotation activates a bond rotation All rotations are
169. erate the appropriate file Include this file in the command line esp i dfr dms o dfr esp q chrgs a dfr UCSF MidasPlus 66 UCSF MidasPlus where chrgs is the name of the charges file The q flag and charges file must precede the name of the PDB file in the command line Note that the electrostatic surface potential computed by esp depends crucially on the charge data in the charges file so users should verify the data given in this file is correct for their particu lar application The esp program has several other options which are described in the esp manual page see Appendix 6 of this document 3 3 Protein Data Bank Format MidasPlus uses the Protein Data Bank PDB format as a standard for all coordinate text files The Pro tein Data Bank at Brookhaven National Laboratory BNL is a clearing house for macromolecular coordinate data and distribution CD ROMs are written in a standardized format specified by BNL A complete and concise description of the format is given in the document Protein Data Bank Atomic Coordinate Entry Format Description which is published and distributed by Brookhaven National Laboratory A newsletter is also published on a periodic basis by BNL MidasPlus supports version of the PDB format Version 2 records and fields are ignored by MidasPlus programs but this should not impact modeling with MIDAS since records fields added in version 2 do not contain any information needed by MIDAS I
170. eries of lines such as the follow ing ASP 205 CA TYR 13 GLY 116 FRM HIS 178 TO The asterisk means all atoms of the residue and the FRM and TO mean all residues from 116 to 178 inclusive These records are read with a FORTRAN a3 1x a4 1x a3 format statement and the residue name sequence number and atom name if specified must match those of the input file exactly The residue name must be left justified and the sequence number must be APPENDIX 6 146 UCSF MidasPlus MS 1 MS 1 right justified The sequence number may contain letters Up to one hundred such records may be used The e and i flags are compatible The surface generated using the i flag is not always the same as the surface generated by running the entire molecule and afterwards selecting out the desired atoms The first surface will not include reentrant surface lying between an atom in the i file and atoms not in the file The QCPE version of ms does not have this bug s Use the supplied file argument to specify the atomic radii The format of the file is an atomic symbol followed by its radius one per line usr local midas resource connect tpl uses this for mat n Include the unit normals to the surface with each surface point record 0 The output is written to file This flag is not optional r Only residues numbered b through e inclusive are used in the calculation This is quite different from the
171. es You need not mark one very small set of atoms and one larger set you could mark approximately equally sized sets of atoms as long as the set size isn t too large perhaps a few dozen atoms each For example if you were working with a nucleic acid structure and marked all H1 s with both noemark1 and noe mark2 and then used a cutoff of about 5 angstroms the resulting helical chain of H H lines would show where the structure had fairly even distances as well as where there were breaks in the structure The h option was designed to be used with no distance constraint file and is the only option that allows the distance constraint file to be omitted from the command line Nonetheless you can specify a distance constraint file and it will be shown normally Note that since the marking mechanism is normally used to restrict constraint display any marks used to delimit H H interactions will also restrict displayed con straints Tips on usage Displaying multiple constraint sets There are times that it is desirable to display several different constraint files separately For example if you ve divided your constraints into positive constraints distances determined from a cross peak the atoms must be at most a certain distance apart and negative constraints distances determined from the absence of a cross peak the atoms must be at least a certain distance apart then you might like to show these sets
172. essing and holding the left and middle mouse buttons simultaneously results in z translation of the selected model s More mouse based interactions are possible via the control panel located to the right of the main win dow In the control panel appear controls for manipulating the selection state of models the viewing parame ters and some general purpose sliders The sideview shows a stylized representation of the molecule s as viewed from the side Also represented are the viewer s eyepoint the box at the junction of the convergent lines and the hither and yon clipping planes the left and right vertical lines respectively A typical sideview area is shown in Figure 1 UCSF MidasPlus 6 UCSF MidasPlus movable eye abstract molecule movable hither plane movable yon plane Figure 1 Sideview The eyepoint and clipping planes can be moved by positioning the mouse over them depressing the left button and dragging the item In addition on non NexXT systems dragging a clipping plane with the left and middle mouse buttons depressed moves both planes apart or together thickness while dragging a plane with only the middle button depressed will move both planes in synchrony sectioning Moving the eyepoint changes the apparent size scale of the image Holding down the Shift key will halve the rate of any motion controlled by the sideview control panel including sliders as well as translations not rotations of the models in
173. eter with Tkinter tk and tcl included and libraries must be installed Point your favorite web browser at http www python org for information about obtaining the latest release of Python SEE ALSO midas 1 python 1 AUTHOR Conrad Huang Computer Graphics Laboratory UCSF APPENDIX 6 187 UCSF MidasPlus
174. evices are altered for scaling and rotation functions Value is a positive or negative integer which reflects the relative change in speed The absolute range is 2 to 14 with default value of 10 Note that in the OpenGL version of MIDAS holding down the Shift key will halve the rate of speed of all motions controlled by the sideview control panel as well as translations but not rotations of models in the main window 2 4 82 Stereo Usage stereo off sequential walleye crosseye lefteye righteye Stereo specifies how images are displayed Off indicates a monocular image Sequential indicates a time sequential stereographic image of the type that is utilized by Crystal Eyes stereo systems Note that sequential requires special hardware to work properly and that not all workstations may support this hardware only SGI and DEC Alpha workstations support hardware stereo Walleye indicates side by side stereo pairs having positive horizontal parallax That is the left eye image is shown on the left hand side of the display window and the right eye image is shown on the right hand side of the window This is the clas sic method of generating stereo image pairs The sizes of the images are constrained to avoid overlap and can be changed with the walleye_scale variable see the set command Crosseye indicates side by side stereo pairs having negative horizontal parallax That is the left eye image is shown on the right hand side of the
175. f sheet color red color green would return all atoms that are red or green that are also in a B sheet 2 1 4 Zone Specifiers Zone specifiers are used to select atoms and residues that are within a given distance of the referenced atom s z lt and zr lt specify all residues within the given distance from the referenced atoms za lt specifies all atoms within the given distance z gt zr gt and za gt yield the sets complementary to their lt counter parts For example 1 za lt 10 29 selects all atoms within 10 angstroms of model 1 2 1 5 Temperature Factors and Electrostatic Potentials Atoms may be selected by temperature factor and surface points by electrostatic potential using the lt and gt symbols Electrostatic potential selection requires the symbol e gt or e lt to select poten tials above or below a specified value respectively Temperature factor selection requires the symbol b gt or b lt to select factors above or below a specified value respectively These symbols follow the entire atom specification and must have a preceding blank For example 1 HIS b gt 25 0 all atoms in histidine residues in model 1 which have temperature factors exceeding 25 0 1 e gt 10 e lt 20 0 all surface points in model 1 with potentials between 10 and 20 kcal mole per elementary charge Note that electrostatic potentials only apply
176. f 9 3 6A1 6A1 3 X F9 3 ATPOS ATPOS 9 3f 9 3f 9 3f 6A1 5A1 X 3 X F9 3 WINDOW WINDOW 9 3f 9 3f 9 3f 9 3f 9 3 9 3 6A1 6A1 6 X F9 3 FOCUS FOCUS 9 3f 6A1 5A1 2X F9 3 VIEWPORT VIEWPORT 9 3f 9 3f 9 3f 9 3f 6A1 8A1 3 X F9 3 BGCOLOR BGCOLOR 5 3f 5 3f 5 3 6A1 7A1 3 X F5 3 Per Molecule Annotations FILEt FILE 34d 56s 6A1 4A1 X 14 X 56A1 MARKNAME AARKNAME 57s 6A1 8A1 X 57A1 MARK ARK 57s 6A1 4A1 X 57A1 CNAME CNAME 5 3f 5 3f 5 3f 38s 6A1 5A1 3 X F5 3 X 38A 1 COLOR COLOR 5 3f 5 3f 5 3f 38s 6A1 5A1 3 X F5 3 X 38A 1 RADIUS RADIUS 7 3f 6A1 6A1 X F7 3 OBJECT OBJECT 6A1 6A1 ENDOBJ ENDOBJ 6A1 6A1 CHAIN CHAIN 6d 6d 6A1 5A1 2 X 16 Annotation Trailers ANGLE ANGLE 6d 6d 6d 6d 9 3f 6A1 5A1 4 X 16 X F9 3 DISTANCE DISTANCE 6d 6d 9 3f 6A1 8A1 2 X 16 X F9 3 3D Graphics Annotations GFX BEGIN GFX BEGIN 32s 6A1 9A1 32A1 GFX END GFX END 6A1 7Al GFX COLOR GFX COLOR 5 3f 5 3f 5 3f 38s 6A1 9A1 3 X F5 3 X 38A 1 GFX NORMAL GFX NORMAL 39 3f 9 3f 9 3f 6A1 10A1 3 X F9 3 GFX VERTEX GFX VERTEX 9 3f 9 3f 9 3f 6A1 10A1 3 X F9 3 GFX FONT GFX FONT 3d 53s 6A1 8A1 X 13 X 53A1 GFX TEXTPOS GFX TEXTPOS 9 3f 9 3f 9 3f 6A1 9A1 3 X F9 3 GFX LABEL GFX LABEL 3 56s 6A1 9A1 X 56A1 APPENDIX 1 90 UCSF MidasPlus Summary of Changes from PDBRUN Version 5 to Version 6 Record Type Version 5 Version 6 USER PDBRUN 3 6 MASTER One record for
177. f this delegate s usage can be found in Appendix 6 of this document 2 4 25 Display Usage display atom_specification Usage display atom_specification Display selectively displays the atoms of a model The atom_specification may be any combination of molecules residues and atoms for the currently open models To display only selected portions of a model use display to remove the unwanted atoms and labels The display label vdw and surface commands together allow any combination of bonds labels and atom surfaces to be displayed See also chain show label surface vdw 2 4 26 Distance Usage distance distance_number atom atom2 Usage distance distance_number Distance dynamically calculates and displays distances in angstroms between specified atoms A dot ted line is drawn between each pair of atoms for which a distance calculation is active The user may assign a distance_number between 0 and 15 inclusive to each active distance calculation If distance_number is not given one will be assigned for you The distance calculation may be deactivated using distance distance_number Atoml and atom2 may be any two atoms in the displayed models specified in standard MIDAS atom selection syntax UCSF MidasPlus 32 UCSF MidasPlus Examples distance 1 1 12 CA 0 47 CA assign distance 1 distance 0 1 remove distances 0 and 1 See also watch 2 4 27 Echo Usage echo text Echo places all of the text ar
178. g contains an a or A the atoms will be drawn as filled circles If the fill_type string contains a b or B the bonds will be drawn as filled sticks EXAMPLES From MIDAS the command to print a bs figure with a surrounding frame would be pdbrun conect bs f lpr Pprintername The command to save an Encapsulated PostScript bs image to a file would be pdbrun conect bs e gt savefilename BUGS Bs requires that USER records specifying EYEPOS and WINDOW be present in the input file These records are automatically supplied by midas 1 but are not simple to compute manually SEE ALSO midas 1 AUTHORS Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 104 UCSF MidasPlus CONIC 1 CONIC 1 NAME conic generate CPK style molecular models with shadows SYNOPSIS conic p f output format s a mode o output file x pixels wide y pixels high c config file e shell command t v 1 A C F S scale_factor W PDB file DESCRIPTION Conic reads a Protein Data Bank file and generates a Corey Pauling Koltun style image of the molecule If no PDB file is specified standard input is used There can be an arbitrary number of light sources Specu lar highlights diffuse reflections and shadows are all computed properly Capturing Screen Images in Part III of the MidasPlus manual discusses saving converting a
179. g program BUGS Stereoimg assumes that the size of the screen is 1280 by 1024 AUTHORS Conrad Huang Eric Pettersen UCSF Computer Graphics Laboratory APPENDIX 6 178 UCSF MidasPlus STEREOPS2ILLUSTRATOR 1 STEREOPS2ILLUSTRATOR 1 NAME stereops2illustrator convert a stereo Midas copy file PostScript to Adobe Illustrator format SYNOPSIS stereops2illustrator lt stereo copy file gt Illustrator file DESCRIPTION Stereops2illustrator reads in a PostScript file generated by the MIDAS copy command when displaying an image in stereo and converts it to an Adobe Illustrator format file for inclusion in desktop publishing docu ments SEE ALSO ps2illustrator 1 midas 1 BUGS Depends on the csplit and nawk programs that might not be available on all platforms AUTHOR Scott Dixon SmithKline Beecham Pharmaceuticals APPENDIX 6 179 UCSF MidasPlus TIFFPAIR 1 TIFFPAIR 1 NAME tiffpair assemble a pair of TIFF images side by side SYNOPSIS tiffpair outimage leftimage rightimage DESCRIPTION Tiffpair reads a pair of TIFF image files and places them side by side The height of the two images must be the same Tiffpair is used by stereoimg 1 to compose stereo TIFFs from left and right eye images SEE ALSO stereoimg 1 assemble 1SGI APPENDIX 6 180 UCSF MidasPlus UNCRYST 1 UNCRYST 1 NAME uncryst generate atomic coordinates from crystallographic symmetry SYNOPSIS uncryst s symmetry_
180. gument into the MIDAS reply buffer visible at the bottom of the graphics window Echo may be used by MIDAS scripts to send messages back to the user 2 4 28 Fix Usage fix rotation_number The fix command removes a previously activated torsional bond rotation and leaves the structure as currently displayed It is necessary to fix a rotation before giving a save command if the current position of the rotation is to be reflected in the saved PDB file of the model with the active rotation 2 4 29 Fixreverse Usage fixreverse rotation_number Fixreverse fixes the named bond rotation and activates the reverse bond rotation using the same rotation_number This command insures that the model will not move relative to other displayed models as is often the case when the reverse command is used Warning In the case of multiple bond rotations ifthe set of atoms rotated by a given bond rotation includes the pivotal atom of another bond rotation and if the set of atoms rotated by this second rotation includes the pivotal atom of the first then MIDAS will not allow such rotations In executing fixreverse reversing the bond rotation may cause such a conflict and be disallowed Reversing bond rotations must be done in an appropriate order such that intermediate combinations are legal see rotation 2 4 30 Freeze Usage freeze Freeze stops all motion on the screen See also rock roll UCSF MidasPlus 33 UCSF MidasPlus 2 4 31 Gd Usage d
181. he backbone to render as helices and sheets The MIDAS ksdssp command can be used to generate HELIX and SHEET records if they are absent UCSF MidasPlus 68 UCSF MidasPlus Protein Data Bank Format Record Columns Data Justifi Data Type cation Type ATOM 1 4 ATOM left character 7 11 Atom serial number right integer 13 16 Atom name left character 17 Alternate location indicator character 18 20 Residue name right character 22 Chain identifier character 23 26 Residue sequence number right integer 27 Code for insertions of residues character 31 38 X orthogonal A coordinate right floating 39 46 Y orthogonal A coordinate right floating 47 54 Z orthogonal A coordinate right floating 55 60 Occupancy right floating 61 66 Temperature factor right floating TER 1 3 TER character 7 11 Serial number optional right integer 18 20 Residue name optional right character 22 Chain identifier optional character 23 26 Residue sequence number optional right integer 27 Code for insertions of residues optional character HETATM 1 6 HETATM 7 66 same as ATOM records SSBOND 1 6 SSBOND character 8 10 Sequence number optional right integer 12 14 Residue name CYS right character 16 Chain identifier character 18 21 Residue sequence number right integer 26 28 Residue name CYS right character 30 Chain identifier character 32 35 Residue sequence number right integer CONECT 1 6 CON
182. he same as doing nothing The Clear button will clear all the text fields Because an empty value in a text field matches anything Clear is useful if the subsequent Find only searches on one or two fields The Help button brings up a window displaying these instructions REGULAR EXPRESSION EXAMPLES Pdbopen uses case independent egrep 1 style regular expressions The simplest regular expression is a string with no magic characters For example a value of serine will match the field HYDROLASE SERINE PROTEINASE because the field contains the string serine Magic char acters i e are used to construct more complex regular expressions such as rd na which will match all fields containing either the string rna or dna Finally the following expression matches A T and T A transitions in the Compound field for DNA CATGUPJAP T CATGUP CATGUP TP A CATGUP SEE ALSO egrep 1 APPENDIX 6 165 UCSF MidasPlus PDBOPEN 1 PDBOPEN 1 AUTHOR Conrad Huang Computer Graphics Laboratory UCSF APPENDIX 6 166 UCSF MidasPlus PDBRUNSTO6 1 PDBRUNSTO6 1 NAME pdbrun5to6 convert PDBRUN version 5 files to version 6 SYNOPSIS pdbrunSto6 o output filename input filename DESCRIPTION PdbrunS5Sto6 converts PDBRUN version 5 or less annotated PDB files to version 6 Version 5 files were generated by version 2 0 and earlier of MIDAS s p
183. hese parameters are useful for controlling the rate of motion and are helpful when constructing MIDAS command scripts and making videos MIDAS continues to process commands while the requested motion is in progress To have command pro cessing pause until the motion is finished use the wait command If the move command does not work it is likely you have failed to select the target models See also select wait UCSF MidasPlus 38 UCSF MidasPlus 2 4 49 Mrotate Usage delegate start mr mrotate The mrotate delegate is used to interpolate smoothly between different model positionings The inter polation can be shown directly in MIDAS or saved as MIDAS commands to a text file Details of this delegate s usage can be found in Appendix 6 of this document 2 4 50 Neon Usage neon options The neon command produces a three dimensional representation of the displayed molecule s with appropriate shadows The molecule s can be depicted as space filling spheres balls and sticks sticks or tubes The current orientation and coloring is retained This image is not interactive and takes anywhere from a minute to several minutes to produce After the image is displayed on an SGI clicking the left mouse button returns to MidasPlus There are many options which are detailed fully in the neon manual page included in Appendix 6 of this document The neon command is actually an alias that executes the pdbrun command and sends data to the neo
184. his page such as the on line tutorials discussed in section 1 4 One particularly impor tant link points to a page discussing known problems in the current MidasPlus release This page not only details all currently known bugs but includes workarounds and or fixes if available There is also a delegate for viewing molecular dynamics trajectories available on the web The delegate was written by David Konerding and is called Midasmovie Information about the latest version of Midasmo vie can be found at http picasso ucsf edu dek movie html 1 6 Obtaining Standard PDB Files If your host is connected to the Internet it is possible to obtain PDB files either via the World Wide Web or via anonymous ftp To fetch files via the web point your favorite web browser at http www pdb bnl gov and follow the Searching and Browsing the PDB link To fetch files via anonymous ftp ftp to the host ftp pdb bnl gov 130 199 146 1 For detailed instructions on how to use ftp type man ftp at your shell prompt When you connect use the login name anonymous Any password will be accepted though it is usual to give your normal Internet e mail address as the password e g joe cgl ucsf edu Upon logging in you will receive a detailed informational message about usage of the server as well as available data files If you lack Internet access or want a full PDB distribution but have limited bandwidth to the Internet you can ge
185. icture is on the bright side you can leave out the left most setting while if it is dark you can leave off the right most setting if you are running out of or conserving film Film is usually cheaper than the time it takes to redo pictures however 2 For those pictures with many possible settings such as space filling with a black background it is not neces sary to try each setting It really depends on the brightness of your image The middle settings five of your choice will do The brighter images will not need the left most settings while the darker images will not need the right most settings 3 Solid image pictures such as space filling pictures ribbons and slides with backgrounds may show some of the screen refresh lines These pictures need all five exposures for this reason 4 When using the labeling program ilabel see Appendix 6 it is usually best not to use solid white labels Change the color of your labels to be for example slightly blue White labels will usually be too bright to pho tograph well Try to make your labels no brighter than the brightest thing in your picture 5 To use ASA 100 film double exposure time at the appropriate fstop or use the same times listed but one smaller fstop e g instead of using fstop 4 0 for 1 2 second use fstop 4 0 for 1 second or fstop 2 8 for 1 2 second see a d below a when using ASA 100 film Fstop 2 8 but times must be doubled UCSF MidasPl
186. ific sequence to form the molecule Each residue is made up of atoms organized according to the coordinates and connectivity information This scheme reflects nature s organization of biomolecules amino acid chains make up protein molecules and nucleotide chains make up DNA molecules MIDAS allows the user to display multiple models molecules simultaneously These molecules are assigned model numbers by the user with the open command or a default by MIDAS Each molecule consists of one or more residues each of which has a unique associated residue number according to its location in the residue sequence The atoms which make up the residue each have associated atom names which are unique within any single residue Thus any displayed atom may be uniquely described by its model number residue number and atom name The residue and atom names are determined at the time the input file is read in and generally match the standard Brookhaven Protein Data Bank PDB residue and atom names The principal exception is that resi due numbers in HETATM records have an asterisk appended since residue numbers in HETATM records frequently duplicate those in ATOM records The symbols for these reference levels are defined as follows Atom Specification Symbols Symbol Reference Level Definition model number a number assigned to the displayed model by the user via the open command or the file name that the model was open
187. ill be handled by the mrotate delegate while other commands will be pro cessed by MIDAS Taking snapshots of orientations To save an orientation as a potential endpoint of interpolation later use the command mr snapshot sl The s1 in the above command is the name that is assigned to the orientation the name will be used in inter polation commands later To save another orientation move the model around using the mouse and issue the command mr snapshot s2 Interpolating between orientations To interpolate from orientation s1 to s2 use the commands reset sl mr interp sl s2 0 The reset command puts the model back into orientation s1 The interp command makes mrotate generate a series of MIDAS commands which will transform model 0 from orientation s1 to orientation s2 Note that model 0 must be the only model selected and that it must already be in orientation s1 when the command is given To save the generated MIDAS commands in file com use the command mr store com sl s2 0 Finishing up To terminate the mrotate delegate use the command mr stop All saved snapshots will of course be lost COMMANDS When mrotate is acting as a delegate for MIDAS as shown in the DESCRIPTION section the user can give it commands by typing mr mrotate_command in the MIDAS command window The list of commands is given below in alphabetical order interp from to n Generate the command to interpolate model n from orientation from to orientation to
188. int light source that coincided with the eye whereas rpoint020111 would define a point light source directly above the center of the scene twice as far above the scene as the distance from the center of the scene to the eye rquad x yl zl x2 y2 z2 x3 y3 z3 Rquad is to quad as rpoint is to point rspot x y z r g b dx dy dz power Rspot is to spot as rpoint is to point size xy Sets the image size The default image size is 1280x1024 If conic is invoked from within MIDAS then the default image size will be the same as the MIDAS window size spot x y zr g b dx dy dz power Define a spotlight The absolute Cartesian coordinates of the light source are x y z The color of the light is given by r g b The Cartesian direction of the spotlight is given by dx dy dz The intensity of the spotlight drops off as the angle between the spotlight direction and the pixel direc tion the rate of decrease is the cosine of the angle raised to the powerth power Power must be an even integer odd integers will be incremented silently COLORING THE MOLECULE Conic uses two sources of atom radius and coloring information If neither source of information yields a radius and color for an atom then the atom is ignored The first source is embedded in the input to conic which is an extended Protein Data Bank format The format is identical to standard PDB format except that ATOM and HETATM records may be preceded by USER records whose text field contains
189. intf SYNC n void fflush stdout We simply echo back any commands to MIDAS If we are in verbose mode we notify the user before and after each command a while fgets buf sizeof buf stdin NULL if verbose send_command echo Delegate executing s buf send_command buf if verbose send_command echo Delegate done n void printf SYNC n void fflush stdout exit 0 send_command K Send a command to MIDAS and wait until the ii synchronizing string comes back uf static int send_command char fmt va_list args char buf BUFSIZ va_start args fmt void vfprintf stdout fmt args if record_fp NULL fputs gt record_fp vfprintf record_fp fmt args va_end args void fflush stdout Make sure buffered data get sent Keep reading until we see a line containing only SYNC which denotes end of MIDAS replies Afi while fgets buf sizeof buf stdin NULL APPENDIX 5 100 UCSF MidasPlus if record_fp NULL fprintf record_fp lt s buf if strcmp buf SYNC n 0 break return APPENDIX 5 101 UCSF MidasPlus Appendix 6 MidasPlus Program Suite MidasPlus has several utilities for preparing surface files building templates and correcting common PDB file problems These utilities are typically run directly from the UNIX shell and not from the MIDAS command prompt In addition the re
190. ion file simple color by type images may be generated from raw PDB files The default atom information file contains the following lines 1 8 1 8 reas 1 85 1 0 1 9 12 35 1 8 95 lg 1 8 64 1 28 1 38 C EXAMPLES NQ WHWOAMVTTAUHOA zZ Gy El 0 O O 0 O O GO O O Ou Ee 5 oa aun uo 0 5 0 0 O OO t 0 m T OTO T O O O O H ae 29 The demonstration images included on the MidasPlus distribution CD show how to achieve a variety of striking effects and give detailed instructions on how each image was made If these demonstration images have been installed on your system they will be found in usr local midas demos images The README index file there has further information If the demonstration images have not been installed on your system you need to mount the distribution CD ROM and you will find the images in the CD ROM directory Midas 2 1 demos images BUGS Light intensity does not attenuate with distance SEE ALSO imgview 1 midas 1 FILES usr local midas resource conic atinfo default atom information file AUTHORS Eric F Pettersen Conrad Huang Gregory S Couch UCSF Computer Graphics Laboratory APPENDIX 6 109 UCSF MidasPlus DENSITY 1 DENSITY 1 NAME density MidasPlus delegate for displaying formatted X PLOR electron density data MIDAS COMMAND SYNTAX Command delegate start dens density mapfile mapfile2 DE
191. ion method is usually used with name being arrow and name2 being strand or helix PDB USER RECORDS In addition to the USER records that MIDAS uses ribbonjr also interprets several of its own FLIP XSEC TION and NORIBBON The FLIP record specifies a residue whose orientation should not be computed in the standard way Ribbonjr orients a residue by defining both a direction and a normal vector The APPENDIX 6 175 UCSF MidasPlus RIBBONJR 1 RIBBONJR 1 direction is defined by the vector from the guide atom of the previous residue to the guide atom of the next residue The normal vector is defined as perpendicular to the direction and in the peptide plane defined by the previous residue and the current one the normal vector is also constrained to be less than 90 degrees from the normal vector of the previous residue If the current residue is FLIPped however its normal vec tor is replaced by its opposite vector The XSECTION record specifies the cross section type for a range of residues For further information about cross section types refer to the preceding description of the x command line flag and the CROSS SECTION FILE section of this manual page The NORIBBON record specifies a range of residues which should not have a ribbon representation i e they will be drawn as balls and sticks The alignment of the residue information in these USER records are exactly the same as those on a HELIX record Examples of these USER records
192. ion options See the OPTIONS section of the X 1 manual page for a list of possible options Details of midas commands and their syntax can be found in part II of the MidasPlus User s Manual Midas can be used as a MIME viewer for web browsers by adding the line chemical x pdb midas nofork s to your HOME mailcap See mailcap 4 This will also work with MIME capable mail programs such as MediaMail 1 ENVIRONMENT MIDASRC Give an alternate location for the startup file The default location is usr local midas resource midas midas rc MIDAS_COPY Use an alternate program instead of Ipr h to output to a printer from the midas copy command MODELS Give an additional directory in which to search for residue templates these define the connectivity of residues in PDB files GROUPS Give a list colon separated of directories in which to search for chemical groups user s groups in addition to the system groups See the addgrp command for more information SHELL The UNIX shell midas will use to run programs specified with the delegate pdbrun run and sys tem commands SEE ALSO MidasPlus User s Manual netscape 1 MediaMail 1 mailcap 4 X 1 AUTHORS Conrad Huang Greg Couch and Thomas Ferrin UCSF Computer Graphics Laboratory Paul Bash contributed vdw style surfaces and the addaa addgrp swapaa and swapna commands APPENDIX 6 141 UCSF MidasPlus MIDAS 1 MIDAS 1 Countless other contribut
193. ions however you need to run midas noexec with your options appended so that you can see what those options correspond to when used with the back end program again ignoring the appended noexec The options differ between the two back ends due to the way the X window system used in conjunction with OpenGL handles command line options Of course this only tells you what options to use with the normally selected back end If you actually want to execute the other back end the midas noexecother will show how to run the other back end program with your desired command line arguments Executing the back end program directly also allows you to control the user interface used since the interfaces differ in some regards between the two versions UCSF MidasPlus 86 UCSF MidasPlus Appendix 1 Pdbrun Format USER Records A PDBRUN file has three principal sections The first section Annotation Headers has global modeling information The second section Per Molecule Annotations has molecular data for each model Each model s data starts with a USER FILE record and is terminated with an END record The serial numbers in ATOM HETATM and TER records are incremented continuously from one model to the next Due to field widths this imposes a limit of 99999 atoms in a scene Any PDB records present in the model s original source file and not normally inter preted by MIDAS e g REMARKS are preserved and placed just after th
194. ions from a cast of hundreds APPENDIX 6 142 UCSF MidasPlus MIDAS TTY 1 MIDAS TTY 1 NAME midas tty terminal based version of MidasPlus display program SYNOPSIS midas tty b s script R num_rows C num_columns session_file model_file s file DESCRIPTION Midas tty is a version of MIDAS that runs on any ASCII terminal Midas tty does everything that the MIDAS interactive display program does except generate a three dimensional image of the molecular model In particular it accepts all normal MIDAS commands e g open chain label distance copy save This is useful for editing an annotated PDB file or setting up session files without accessing the graphics display on a workstation If either standard input or standard output is redirected i e is not a terminal then midas tty runs in a line oriented batch mode Thus it can be called from within a shell script for mass processing of MIDAS ses sions OPTIONS The b option puts midas tty into a batch mode regardless of whether standard input or output is redirected The s script option lets you specify a command script to be sourced at start up time The R and C options allow you to change the aspect ratio of the midas tty window by changing the number of rows and columns See the BUGS section below SEE ALSO midas 1 MidasPlus User s Manual AUTHOR Greg Couch UCSF Computer Graphics Laboratory BUGS Interactive d
195. isco supported by NIH P41 RR 01081 The article which describes the MIDAS MidasPlus system and should be included in your references is T E Ferrin C C Huang L E Jarvis and R Langridge The MIDAS display system J Mol Graphics 6 13 27 1988 If you make use of conic images in your publication neon is a preprocessor for conic you should also include the following reference C C Huang E F Pettersen T E Klein T E Ferrin and R Langridge Conic A fast render er for space filling molecules with shadows J Mol Graphics 9 230 236 1991 Similarly images of van der Waals surfaces can be referenced with P A Bash N Pattabiraman C C Huang T E Ferrin and R Langridge Van der Waals Sur faces in Molecular Modeling Implementation with Real Time Computer Graphics Science 222 1325 1327 1983 We would also appreciate receiving two reprints of any publications resulting from your work with MidasPlus Manual Organization The MidasPlus User s Manual is divided into four main sections Part I entitled Getting Started is a short chapter designed to get new users going quickly and also provides pointers on where to learn more Part II Com mand Reference Guide provides a detailed description of the MIDAS command language and the concise syntax and example usage of each of the many MIDAS commands New users should be sure to consult the Command Synop
196. isible strand also sheet helix mark and color If a property name is pre ceded by a it means the atom must not have that property The visible property is true if an atom actu ally appears on the screen The strand and helix properties are true for atoms mentioned in PDB SHEET and HELIX records respectively The color and mark properties must be followed by an equals sign and then respectively either a color designation see the color command for details or a mark name see the mark command The following specifier selects all atoms named CA which appear on the screen are not labeled and are not green or red ca visible label color green color red When several properties are listed in one atom specifier MIDAS returns only those atoms that have all the listed properties For example n sheet color green would specify green nitrogens in B sheets To specify atoms that are green or that are in B sheets a some what more verbose syntax is required n sheet n color green This latter technique can be employed whenever specifying atoms having one of several properties The one exception to the multiple property behavior described above is for color properties Since atoms cannot have multiple colors simultaneously the default behavior for specifiers involving multiple color properties is to return atoms that have any of the specified colors So for example an atom specifier o
197. issing it is placed 1 01 angstroms from N along the bisector of 1 the vector opposite the bisector of C N CA and 2 the vector opposite the C O vector from the previous amino acid COMMAND ARGUMENTS c energy_cutoff The default energy cutoff for defining hydrogen bonds as recommended by Kabsch and Sander is 0 5 kcal mol A good H bond has about 3 kcal mol binding energy This option allows the user to change the cutoff h minimum_helix_length Normally HELIX records for helices of length three residues or greater are generated This option allows the user to change the minimum helix length s minimum_strand_length Normally SHEET records for strands of length three residues or greater are generated This option allows the user to change the minimum strand length Reducing the minimum strand length to 1 is not recommended as there are bridges in many structures that confuse the algorithm for defining sheets S summary_file Normally ksdssp silently discards all the hydrogen bonding information after generating the HELIX and SHEET records This option makes ksdssp print the information to a file The nota tion is similar to that used by Kabsch and Sander but is in a vertical instead of horizontal format PDB_file The input Protein Data Bank PDB file may contain any legal PDB records Only ATOM records will be used All others are silently discarded If no PDB_file argument is given the data is read from
198. istances angles are not shown in batch mode The aspect ratio of the terminal emulation window affects the size and orientation of hardcopy images gen erated with the copy command Use the R num_rows and C num_columns command line options to change the aspect ratio APPENDIX 6 143 UCSF MidasPlus MROTATE 1 MROTATE 1 NAME mrotate MidasPlus delegate for interpolating between orientations MIDAS COMMAND SYNTAX Command delegate start mr mrotate DESCRIPTION Mrotate is a MidasPlus delegate that generates MIDAS commands that transform models from one orienta tion to another The standard way that mrotate is invoked is for the user to start a MIDAS session and issue the MIDAS command delegate start mr mrotate which runs mrotate and tells MIDAS to pass commands beginning with mr through to mrotate for further processing The complete set of commands that mrotate can handle are described in the COMMANDS sec tion of this manual page EXAMPLE A few typical uses of mrotate are demonstrated in this section It is assumed throughout this section that the standard PDB file alc a lactalbumin has been opened for display in MIDAS as model 0 and is the molecule of interest for transformation purposes Setting up The first thing is to start the mrotate delegate with the command delegate start mr mrotate You should receive a reply indicating the delegate started normally After issuing the above command all commands prefaced with mr w
199. itplanes lt 24 dithering makes the images look better The effect is more dramatic when the linewidth is greater than 1 zbuffer on off Use zbuffer to resolve occlusion If you turn this off and leave smooth and antialias_points on MIDAS will act like a vector graphics display Miscellaneous memlock on off If MIDAS is setuid root then it can lock all of its data into memory so it won t be paged out by competing processes This significantly enhances MIDAS performance on systems where large memory background processes are running Also to the best of our knowledge there are no security holes opened by enabling this option Since MIDAS must be setuid root for this option to work your system administrator has to explicitly enable this during MidasPlus installion UCSF MidasPlus 31 UCSF MidasPlus GL related smooth on off Same as OpenGL version antialias_points on off Same as OpenGL version colormap on off Use a colormap for antialiasing lines Limits the number of colors you can have 22 maximum but is much faster on ancient SGI s ucsf_stereo on off Setting this option on indicates that the computer monitor needs to be switched into stereo video mode by hand See also set 2 4 24 Discern Usage delegate start disc discern The discern delegate allows the visualization of arbitrary multidimensional data by using shape and color in additional to the Cartesian coordinate dimensions Details o
200. ity of spheres drawn to create sticks tubes dashes and objects A value of 3 is good for most work 4 is recommended for final full screen images so that individual spheres are not resolved and 5 is best for closeups of a small number of residues Increasing the number slows the calcula tion Though the setting 5 is sufficient for almost all situations occasionally when working on a highly scaled up view or with very thin cylinders a higher setting is required Neon permits set tings up to 11 Note that each setting above 5 uses double the number of spheres of the next lower setting Therefore to minimize wait time always use the lowest setting that provides a satisfac tory image Dash flag Set to 1 to draw lines between between atoms connected by the distance command in Midas The type of line is under control of dash parameters listed below Object flag Set to 1 to include Midas graphics objects See Non Molecular Graphics Objects in Part III of the MidasPlus User s Manual for details on graphics objects CPK Flag Set to to get the same space filling representation of atoms obtained with conic with the addition of depthcuing coloring by temperature factor and the inclusion of graphics objects when the corresponding parameters are set Stick thickness Radius in angstroms of sticks connecting atoms Tube thickness Radius in angstroms of tubes connecting O carbons Dash thickness Radius in angstroms of dashed lines
201. k ticks to pause after a fade has completed before proceeding to the next fade or exiting The number of clock ticks per second is defined by the variable CLK_TCK in file lt limits h gt The default value of pause is zero The e argument specifies a shell command that is exe cuted at the end of each frame This is useful if one wished to record individual frame images e g saving to videodisk with the videodisk 1 program SEE ALSO videodisk 1 AUTHOR Conrad Huang Computer Graphics Laboratory University of California San Francisco APPENDIX 6 123 UCSF MidasPlus FIXATNAME 1 FIXATNAME 1 NAME fixatname correct AMBER pseudo PDB files so they are in standard PDB format SYNOPSIS fixatname file DESCRIPTION Versions of AMBER prior to version 3 0 revision A produced PDB files that had atom names aligned in the wrong columns see MidasPlus User s Manual Part III Protein Data Bank Format for details of PDB for mat Fixatname corrects this misalignment AMBER PDB files have their atom names left adjusted in columns 13 16 of each line Fixatname left adjusts the atom name in columns 14 16 with the former con tents of column 16 being placed in column 13 This results in atom names that conform to the PDB stan dard with the rather infrequent exception of atom names with a two character atomic symbol such as iron FE Such cases can be corrected by hand after processing by fixatname Fixatname reads from standar
202. kness units frames wait_frames Usage thickness The thickness command changes the distance between the hither and yon clipping planes by the specified number of angstrom units A positive unit value increases the distance between the clipping planes whereas a negative value decreases it This results in displaying an increased or decreased cross section of the current model s Frames moves the clipping planes in the specified manner for the specified number of image update frames Wait_frames if specified indicates the number of frames to wait before beginning the move thick ness will halt an ongoing thickness operation Frames and wait_frames default to 1 and 0 respectively These parameters are useful for controlling the rate of clipping and are helpful when constructing MIDAS command scripts and making videos MIDAS continues to process commands while the requested motion is in progress To have command processing pause until the motion is finished use the wait command Thickness without the units parameter will report the distance in angstroms between the clipping planes UCSF MidasPlus 57 UCSF MidasPlus See also section clip wait 2 4 90 Turn Usage turn axis angle frames wait_frames Usage turn axis Turn functions the same as roll except that the default values for the angle and number of frames are 3 degrees and 1 frame respectively Thus the command turn y will generate an approximate left ey
203. l not print The S option sets all of the above options that are appropriate for slides a page type of 35mm 24 bit RGB binary PostScript gamma of 1 0 and automatic scaling and rotation The L option lets one specify an ilabel 1 label file that will be scaled and rotated to match the image SEE ALSO ilabel 1 gamma 6 snapshot 1 Graphics Library User s Guide 4Dgifts iristools DIAGNOSTICS The program refuses to generate output if the image won t fit on the page BUGS The a and r options are almost always desired The options are separate because some older color PostScript printers are much slower when images are rotated The image libraries do not allow piping images from one program to another Does not do any color correction Autoscaling fits the page size rather than the imageable area AUTHOR Greg Couch UCSF Computer Graphics Laboratory APPENDIX 6 132 UCSF MidasPlus KSDSSP 1 KSDSSP 1 NAME ksdssp generate HELIX and SHEET records from protein coordinates SYNOPSIS ksdssp c cutoff h length s length S file PDB_file output_file DESCRIPTION Ksdssp is an implementation of the Kabsch and Sander algorithm for defining secondary structure of pro teins Ksdssp reads a Protein Data Bank format file containing coordinates of the backbone atoms N CA C O and optionally H of a protein and generates HELIX and SHEET records If an amide hydrogen is m
204. la tive positions This behavior can be overridden if desired with the command devopt move_windows off After a few seconds delay MIDAS should be ready for command line input at the Command prompt The control panel on the right side is described in detail below under Manipulating the Model Bernstein F C The Protein Data Bank a Computer Archive J Mol Biol 112 535 542 1977 2Information about obtaining standard PDB files can be found in the Obtaining Standard PDB files section of Part I of this manual 3As described under VDW Surfaces in Part III of this manual 4As described under Solvent Accessible Surfaces in Part M 5 As described under Non Molecular Graphics Objects in Part III Note that the directory usr local midas bin must be on your execution path for the midas command to be found See section 2 3 Midas Start Up for further details 7The interface for the OpenGL version of MIDAS is described here On some older SGI systems MIDAS uses the older IRIS GL graphics li brary for performance reasons IRIS GL MIDAS presents a slightly different interface All aspects of the described OpenGL interface apply except for the following IRIS GL MIDAS uses only one window The command and reply areas are embedded in the lower left part of the window and the control panel is embedded in the lower right The control panel initially shows only the side vie
205. lag is not optional w Change the water probe radius from the default radius of 1 4 angstroms This parameter must be between 1 0 and 201 0 The output consists of a series of atom and surface point records with the same format for the first six fields Each atom is followed by the surface points if any which belong to it These first six fields are in the following format residue name sequence number atom name x coordinate y coordinate z coordi nate For an atom record the seventh field is A For a surface point record the seventh field begins with an S followed by a C R or S according to whether the point is part of contact reentrant or saddle surface saddle is a type of reentrant surface where the probe is in contact with exactly two atoms This is followed a digit used for depicting different density levels The eighth field is the molecu lar surface area associated with the point in square angstroms If the n flag is specified the next three fields are the unit normal vector pointing outward from the surface Informative messages and errors are written to the standard error output unless a g file is specified The chemical elements and radii that the program handles are detailed in the table below The program gets these values from the file usr local nidas resource dms radii If there is a file in the current directory called radii then dms will u
206. layed then in order for the ribbonjr command to show the correct secondary struc ture the model must have been opened from a PDB file that contained correct HELIX and SHEET records If such records were not present it is possible to have MIDAS compute the secondary structure information T UCSF MidasPlus 45 UCSF MidasPlus with the ksdssp command Ribbonjr needs no additional information to correctly display a nucleotide struc ture By default ribbonjr shows all displayed atoms not just the ribbon The a option will limit display to the ribbon only If it is desirable to show a few key sidechains but not all sidechains display can be res tricted to backbone atoms in MIDAS with the command chain mainchain and then the desired sidechains can be shown with the display command before running ribbonjr When ribbonjr is invoked from MIDAS MIDAS actually executes a front end program that in turn exe cutes the actual ribbonjr program This makes it easier to use the inventor and midas formats of ribbonjr since the front end captures the ribbonjr output in a temporary file and displays the file in ivview or MIDAS itself as appropriate If it is necessary to invoke ribbonjr directly for instance if you want to capture the out put into a permanent file then one must circumvent the front end and invoke the ribbonjr program itself This can be done with the command pdbrun surface usr local midas bin ribbonjr
207. le must be ordered such that in the case of overlapping atom names longest names appear before shorter ones For example if the file contains the radius for both B and BR BR must appear before Protein Data Bank File Record Formats r residue i infile c radiifile y BUGS B in the file SEE ALSO midas 1 AUTHOR Laurie Jarvis UCSF Computer Graphics Laboratory APPENDIX 6 130 UCSF MidasPlus ILABEL 1 ILABEL 1 NAME ilabel label an Silicon Graphics image with arbitrary text SYNOPSIS ilabel f i Jabels_in_file o labels_out_file image_file DESCRIPTION ilabel displays the given Silicon Graphics image_file and lets the user put labels over the image The Sili con Graphics image file may be generated by scrsave 1 imgsnap 1 or some other program such as conic 1L that uses the Silicon Graphics Image Library The labels are drawn using the Silicon Graphics GL Font Manager which supports many fonts in arbitrary sizes Labels may be saved to a file for reuse via the o flag The stored attributes of labels include color vertical and horizontal justification font size and position relative to the image The saved label files may be displayed again using the i flag There may be several i files but at most one o file The output file is created when the user selects Exit from the pop up menu If the file already exists the user is asked whether the file should be overwritte
208. lider Functions Keyword Function translation model translation rotation model and bond rotation clipping clipping planes scaling changes size of selected models section moves hither and yon planes in the same direction at the same rate thickness moves hither and yon planes in the opposing directions at the same rate nothing for canceling slider assignment The direction if applicable may be any of Slider Directions Direction Designation Applicability x the x axis translation rotation y the y axis translation rotation Z the z axis translation rotation h hither plane clipping section thickness y yon plane clipping section thickness 0 15 rotation number rotation Note that if direction is an integer the corresponding intramolecular bond rotation is assigned to the slider Direction is required for the functions translation rotation and clipping The default device assignments are located in usr local midas resource midas midas rc and are listed in Appendix 4 of this document The user may find it convenient to make additional automatic assignments by constructing a midasrc file in his or her home directory and or present working directory Each time MIDAS is executed any midasrc files in the user s home directory and the current working directory are executed before user commands are processed The assign command without any arguments report
209. lied with all supported platforms of the MidasPlus distribution However if you wish to obtain the most recent perl version the perl distribution can be anonymously ftp ed from jpl devvax jpl nasa gov 137 79 113 100 and most likely will be found in the pub per 4 0 subdirectory there The model numbers specified on the rainbow command line cannot be preceded by hash marks as they are in most other MIDAS commands because the rainbow command is passed through a shell interpreter the standard shell treats hash marks and anything following hash marks as comments and strips them AUTHOR Eric Pettersen UCSF Computer Graphics Laboratory APPENDIX 6 170 UCSF MidasPlus RIBBONJR 1 RIBBONJR 1 NAME ribbonjr generate ribbon representation of proteins or nucleic acids SYNOPSIS ribbonjr options PDB file output file DESCRIPTION Ribbonjr reads a Protein Data Bank file and generates a ribbon representation of the molecule The ribbon position and orientation are controlled by two atoms the guide atom and the twist atom For amino acids the guide atom is the a carbon and the twist atom is the carbonyl oxygen This choice of atoms makes the ribbon run approximately parallel to the peptide plane For nucleotides the guide atom is C5 and the twist atom is C1 This choice makes DNA ribbons approximately perpendicular to the helical axis The PDB file may carry extra atom information such as color and radius in the same fa
210. ling to program can easily implement their own flavors of delegates and need not wait for MIDAS developers to implement desired new features In addition delegates can use information sources other than MIDAS Thus they can potentially inject some much needed chemistry information into MIDAS User Perspective At MIDAS start up there are no active delegate programs To make use of a delegate program during a MIDAS modeling session the user issues a delegate start command to request that MIDAS start the delegate pro gram One of the parameters of the delegate start command is an arbitrary string used as a name to refer to that delegate during the remainder of the MIDAS session MIDAS command lines that start with that string will be given to the delegate program for processing less the initial delegate name string Delegates are controlled from MIDAS using the delegate command which supports three operations start stop and list New delegates are invoked with the command delegate start delegate_name command options where delegate_name is the name that the user will use to refer to the started delegate process and command is the Unix command to execute the delegate program Associated command line options if any can be given as options Once a delegate is running the user can send commands to it by prefixing the command with the name of the delegate i e delegate_name delegate_command arguments To terminate an active d
211. lways ignore such records Unmtrix will only operate on MTRIX records with a blank seventh column an example set of which is shown below MTRIX1 1 91000 41511 00700 429 790 1REI 128 MTRIX2 1 41396 91000 02598 29878 IREI 129 MTRIX3 1 01700 02136 1 00000 33 14600 1REI 130 SEE ALSO Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description AUTHOR Conrad Huang Computer Graphics Laboratory University of California San Francisco APPENDIX 6 183 UCSF MidasPlus VIDEODISK 1 VIDEODISK 1 NAME videodisk control a V LAN videodisk SYNOPSIS videodisk u unit v vcopts command args DESCRIPTION Videodisk is a C shell script that controls a V LAN interfaced videodisk As distributed it is dependent on the VideoCreator hardware and software from SGI although the V LAN commands used should work with any videodisk recorder The u option sets the V LAN device unit number defaults to unit 1 The v option sets command line flags for the various VideoCreator programs used The VideoCreator command line flags can also be set with the VCOPTS environment variable Frames arguments to com mands are given in the SMTPE timecode format HH MM SS FF see expr smpte 1 for details on SMPTE time codes The commands are recordsetup Set the videodisk up for recording Turn off the screen saver Initialize log file see below recordscreen Place a SGI screen image into the VideoCr
212. matic carbons and nitrogens will have van der Waals radii that are somewhat too big Note that only amino acid and nucleic acid residues will be included unless a is also specified Dms can be set up to run on multiple machines simultaneously for increased performance By default it only runs on the local host The UCSF MidasPlus Installation Guide that came with the MidasPlus CD ROM contains instructions on how to configure dms to use multiple machines If it is desired to simply visualize a small molecular surface from within MIDAS it may be easier to use the makems 1 delegate rather than run dms directly Consult the makems manual page for further details OPTIONS The flags may be in any order The meanings of the flags are described below a Include all atoms not just those in amino acid and nucleic acid residues d Change the density of points on the surface Density is a factor affecting the density of points on the surface the default of 1 0 produces about 5 points per square angstrom Only values between 0 1 and 10 0 are permitted For large proteins a density of 0 5 is recommended g Write all the informative messages to file instead of the standard error output Genuine errors still go to the standard error output This file is not rewound at any time so messages from several runs may be accumulated i Calculate the molecular surface only for those residues and atoms specified in file but keeping the rest of the mol
213. ments The following is a list of the default options aliases and device assignments made by MidasPlus at the start of each MidasPlus session These default assignments are stored in usr local midas resource midas midas rc The user may replace these defaults with an alternate file defined by the UNIX environment variable MIDASRC If this variable is set to a legal source file name it is executed instead of the MidasPlus default file This is especially use ful for making video tapes as the user may not want extraneous text appearing on the screen at the beginning of the session APPENDIX 4 The default assignments are assign 0 section assign thickness assign 2 scaling slider 3 left open for user assignment assign 3 assign 4 rot 0 assign 5 rot 1 assign 6 rot 2 assign 7 rot 3 colordef white 1 1 1 colordef green 0 1 0 colordef cyan 0 1 1 colordef blue 0 0 1 colordef magenta 1 0 1 colordef red 100 colordef yellow 1 10 colordef black 0 0 0 colordef gray 5 5 5 colordef grey gray alias model alias molecule alias residue alias atom alias sidechain cb alias mainchain n ca c o alias close open alias conic pdbrun usr local midas bin conic alias ksdssp pdbrun ksdssp alias mardishow pdbrun noobj mardishow alias neon preneon usr local midas bin conic alias noeshow pdbrun noobj noeshow alias pdbopen delegate start pdbopen pdbopen alias preneon pdbrun conect
214. model assist viewing of sets of ligands identified by DOCK program change current working directory pop MIDAS window to front of other screen windows push MIDAS window behind other screen windows terminate the current MIDAS session execute a UNIX shell command PDB File Enhancement Correction correct nucleotide pseudo PDB files to conform to PDB standard correct AMBER pseudo PDB files so they are in standard PDB format generate Protein Data Bank HELIX and SHEET records expand CRYST records in PDB file to generate symmetric subunits expand MTRIX records in PDB coordinate file generate script that brings model s into specific orientation read a command file record all executed MidasPlus commands in a file temporarily suspend all input processing read and execute a command file change coordinates of a model from a PDB file suspend input processing until model has stopped moving specify an action involving delegate program s display text in reply area display contents of a text file on the screen reserve name for future mark command associate a name with a group of atoms copy transformation matrix from one model to another output a transformation matrix to a file set a transformation matrix from a file pipe PDB file describing current models to UNIX command abort a pickatom request used by delegates to request that the user pick an atom execute a shell command and send output to MIDAS change coordinates of a model from a P
215. n Consult the videodisk 1 manual page in Appendix 6 for further details MIDAS videos are produced from scripts or command files which can be created by the user with a text editor or recorded during a MIDAS session using the record command Using command scripts minimizes the disk space required for files To review a script save a session run the script and do a load to return to the saved session s state To stop MIDAS in the middle of a script you may have to press the ESC key multiple times 3 8 Screen Photography The following table is useful as a guideline for taking photographs of Midas screen images Exposure Times in Seconds Using ASA 200 Slide Film for Midas Pictures Fstop 2 8 a Fstop 4 0 b Fstop 5 6 c Fstop 8 0 d 1 1 2 14 8 1 12 1 4 18 1 12 14 1 8 1 12 14 18 ribbon black bkg X xX X X X ribbon titles black bkg X X X X X X X X ribbon color bkg X X X X X spacefill black bkg X X X X xX X X spacefill color bkg X X X xX X spacefill titles color bkg X X X X X sticks linewidth 3 color bkg X X X X X dot surface sticks X X X X X dot surf sticks titles X X X X X most stick pictures xX X X xX X Please note the following 1 Most of the above pictures have five possible settings For the safest results at least four settings should be used If your p
216. n unless the f flag was specified in which case no question is asked You can also save labels before exiting by choosing Save Labels off the pop up menu If you do this you will be prompted for a file name whether or not you specified o on the command line You can save a new image with the labels embedded in it by choosing Save Image from the pop up menu You will be prompted for a file name Note that if you intend to use the itops 1 utility to print the image it is better to save the labels in a separate file rather than embedded in the image since the quality of the labels will then be limited by the resolution of the printer rather than the resolution of the image Labeled images can be converted to printable PostScript files with the itops 1 utility provided with the MidasPlus distribution It is necessary to use the L flag of itops in order to have the labels placed on the image To add a new label simply click the left mouse button which should make a triangular cursor appear and type in the label Labels containing multiple lines may be created by typing either RETURN or LINEFEED at the appropriate place The left button is also used to select other labels so that they may be edited The middle button is used to select and move labels The right button displays a menu which contains options to show and hide the defaults panel see below redraw the images and labels save the current labels in a file save the current image turn
217. n and conic programs See also conic ribbonjr pdbrun 2 4 51 Noeshow Usage noeshow options constraint_file torsion_file The noeshow command allows the display of NMR derived constraints on a model structure in MIDAS Full details of the use of this command can be found in Appendix 6 of this document 2 4 52 Objdisplay Usage objdisplay atom_specification Usage objdisplay atom_specification Usage objdisplay model_number model_range Usage objdisplay model_number model_range Objdisplay displays one or more entire non molecule graphics objects see open for a description of graphics objects If the argument to objdisplay is an atom specification then the object s with model numbers corresponding to the specified atoms will be displayed Otherwise the argument s to objdisplay should be one or more model numbers or ranges of the form separated by spaces Note that the model_number should be an integer without a preceding symbol Examples UCSF MidasPlus 39 UCSF MidasPlus objdisplay 1 displays the object associated with model 1 objdisplay 1 5 8 displays the objects associated with models 1 and 5 through 8 objdisplay sheet undisplay all objects associated with models with beta sheets See also display open 2 4 53 Open Usage open original model surface ms object model_number filename surface_filename Usage open close model surface ms object model_n
218. n identifiers recog nition of uncommon atom types etc See the dms 1L manual page for further details DESCRIPTION Ms calculates the molecular surface of a molecule The molecular surface resembles the van der Waals surface of a molecule except that crevices between atoms are smoothed over and interstices too small to accommodate the probe are eliminated The surface includes cavities in the interior of the molecule even if they are not accessible to a solvent molecule coming from the outside The molecular surface calculated is that defined by F M Richards 1977 Ann Rev Biophys Bioeng According to Richards definition the molecular surface consists of two parts contact surface and reentrant surface The contact surface is made up of those parts of the molecular van der Waals surface that can actually be in contact with the surface of the probe The reentrant surface is defined by the interior facing part of the probe when it is simultaneously in contact with more than one atom File is an input file of coordinates The input file must be in the Protein Data Bank format The first letter or first two letters of the atom name is used to determine the element type By default implicit hydrogens are included for carbon nitrogen and oxygen atoms thus aromatic carbons and nitrogens will have van der Waals radii that are somewhat too big Note that only amino acid residues will be included unless a is also specifi
219. n italics faceted edged segmented path name xl yl r1 gi bl x2 y2 r2 g2 b2 xN yN rN gN bN faceted edged segmented spline kind count name xl yl r1 gi bl x2 y2 r2 g2 b2 xN yN rN gN bN interpolate namel name2 point namel name2 The first form describes a cross section using a connected closed path The name of the cross section type is name and the list of coordinates are supplied in x and y Name must start with an alphabetic character and can only contain alphanumeric characters _ underscore and period Each coordinate also optionally has a color whose value is specified by r g and b associated with it for use with xsection color scheme see the c flag The last coordinate of a cross section is automatically connected to the first coordinate by ribbonjr The second form describes a cross section using a series of spline control points The type of spline is given by kind which may be one of bspline bezier hermite or cardinal The number of intermediate points generated on the spline is given by count The name coordinates and colors are the same as in the path specification Both cross section specifications may be prefixed by one of three keywords faceted edged or seg mented A faceted ribbon will not be smooth along its length As it curves there will be edges across its width to accommodate the curvature An edged ribb
220. n of this document Opening a font makes it the current font so after the above commands are executed the current font is greek Making a label To make an example label which is associated with a specific atom use the command 11l label 0 41 CD1 Label text This would display the string Label text in greek near atom CD1 of residue 41 of model 0 Changing label attributes As mentioned above the current font is greek so to change the label text to roman issue the command use r The text initially starts with its lower left corner near the anchor atom To change the justification so that the center of the right edge of the label is near the atom use the command justify right center APPENDIX 6 134 UCSF MidasPlus LABEL3D 1 LABEL3D 1 If the label were too close to the structure it could be moved away with the command 1l offset 1 0 which would move the label angstrom to the left positive x moves right positive y moves up positive z optional moves closer The label could then be made a little smaller with the command If instead mand scale 0 9 you wanted to make all labels that use the current font to be smaller you would use the com scalefont 0 9 Finally to color the label light blue the following two commands could be used the first of which is a standard MIDAS command colordef lblue 0 0 0 7 1 0 1 color lblue Making
221. n the ribbonjr manual page included in Appendix 6 of this document In addition to ribbon depictions of protein structures ribbonjr can display ribbon representations of nucleotide structures optionally using stylized representations of nucleotide sugars and bases with the P flag Ribbonjr has three principal display modes selected with the f flag screen inventor and midas In screen mode the default ribbonjr displays a static ribbon drawing in a separate window Clicking the left mouse button in the window will dismiss it In inventor mode SGI only ribbonjr will invoke the ivview 1 program part of the IRIS Inventor program suite to display a ribbon representation of the molecule This representation can be rotated by the user in real time This window can be dismissed by selecting Quit from the File pulldown menu at the upper left of the ivview window Note that IRIS Inventor must be installed on your system for this mode to be useful if you are uncertain if Inventor is installed check to see if usr sbin ivview exists In midas mode a wireframe representation is generated and then displayed in MIDAS itself as a graph ics object in the lowest available model number The representation can be removed with the open object model_num command Consult Non Molecule Graphics Objects in Part III of this manual for further information on MIDAS graphics objects If a protein is disp
222. n this section a shortened description of the PDB format is presented that is sufficient for use in creating MIDAS input The complete PDB file structure contains a wealth of information including source journal citations and identification of substructures such as disulfide bonds helices beta sheets and active sites Since the entire Protein Data Bank entry contains much more information on a macromolecule than is needed for model build ing knowledge of a subset of the format is sufficient for MIDAS users Users should bear in mind however that adhering strictly to the format specifications is key to successful model building The modeling programs are unforgiving about incorrect input formats and much time and frustration can be saved by diligence in data preparation 3 3 1 Description Protein Data Bank format is a character oriented format which consists of lines of information in a file One file generally contains enough information to characterize a single molecule or model Each line of information in the file is called a record There are usually several different types of records present in the same file such as ATOM records which contain coordinate values for atoms SSBOND records which contain disulfide linkage information and TER records which signal the end of a chain of residues These records are arranged in a specific sequence to characterize the molecule UCSF MidasPlus 67 UCSF MidasPlus Protein Data Bank Rec
223. named font_name The newly opened font becomes the current font If directory is not an absolute path i e it does not start with a then the system font directory will be searched for directory Fonts available in the system font directory are described in the FONTS section of this document The character descriptions are stored in files whose names are either single lettered or begin with O and consist of all numeric digits Files with single letter names contain descriptions for the corresponding letters files with names composed of all numeric digits contain descriptions for the characters with the corresponding octal ASCII values Character descriptions are simply move and draw commands in MIDAS object file format For example m000 d010 position x y z Set the starting coordinates of the current label to be x y z in angstroms If z is not provided zero is used in its place Note that this command has no effect if the current label s reference name matches a MIDAS atom specifier as the label coordinates will be updated automatically save filename Write out a series of commands to file filename When this file is processed by the source com mand see below the same fonts and labels that existed when the save command was executed will be created scale sx sy Scale the current label by sx in the x dimension and sy in the y dimension If sy is missing it is set equal to sx scalefont sx sy Scale the cu
224. nd 20 kcal mole per elementary charge amp intersection Finds the set of atoms that appear in both atom specifiers on left and right e g 1 amp 2 1 zr lt 10 gives all residues in model one that are within 10 angstroms of residue one in model two command separator separates multiple commands on a single line RETURN return accept the line LINEFEED linefeed accept the line RUBOUT backspace erase the character before the cursor CTRL H backspace erase the character before the cursor CTRL U line kill erase the whole line CTRL W word kill erase the word before the cursor CTRL D delete erase the character under the cursor CTRL K erase to end of line CTRL P history retrieve previous command CTRL N history retrieve following command CTRL A go to beginning of line CTRL E go to the end of line CTRL B move back a single character CTRL F move forward a single character CTRL L move cursor one word left CTRL R move cursor one word right CTRL G insert next character without interpretation ESC break break after the completion of the current command see source command Note Control characters are typed by holding down the CTRL key on the keyboard and typing the corresponding alphabetic character For example to type CTRL H hold down the key marked CTRL while at the same time striking the H key APPENDIX 3 94 UCSF MidasPlus Appendix 4 Default Options Aliases and Device Assign
225. nd bonds using PostScript The output of bs may be sent directly to a PostScript printer Alternatively bs can generate Encapsulated PostScript files that may be incorporated into documents Bs interprets not only the standard PDB format records but also USER records of the appropriate for mat Any USER record that begins with the words EYEPOS WINDOW CHAIN COLOR or RADIUS is interpreted specially For details of this format see the pdbrun format description in the Midas User s Manual COMMAND LINE FLAGS The command line flags interpreted by bs are b ball_fraction Set the radius of the rendered circle to be ball_fraction of the radius of the atom The default value is 0 25 e Generate Encapsulated PostScript Normally the image is automatically scaled to fit an 8 5x11 page with one inch borders When this flag is given the image is scaled to fit in a 3 inch square f Put a frame around the displayed image m margin Set the margin between the image and its bounding box This margin is only present when the e flag is absent The margin is given in PostScript units i e 72 units per inch and is 2 by default s stick_fraction Set the radius of the rendered stick to be stick_fraction of the radius of the rendered circles The default value is 0 5 Stick_fraction must be between 0 0 and 1 0 exclusive F fill_type Normally the circles and sticks drawn by bs are figure outlines If the fill_type strin
226. nd described below close font_name Close the font named font_name If any label is currently displayed using the specified font label3d reports the error and the font is not closed color midas_color_name Make the current label be drawn using color midas_color_name which must already be defined in MIDAS justify left center right top center bottom Set the justification mode of the current label If the vertical justification is not specified the current vertical justification is retained Labels are initially justified left bottom label label_ref display_value Make the label whose reference name is abel_ref the current label If no such label exists create such a label If display_value is supplied make that the value shown for the label If not and the label did not previously exist make label_ref the display value The label reference name is a any sequence of characters that does not include or The brackets are reserved for referencing different components of a multi font label For example name 1 refers to the second component of the multi font label name the index is zero based To create a multi font label see the append command above A newly created label is displayed in the current color or white if no color has been set using the current font To change these defaults use the color and use commands The lower left hand comer of the label is considered its starting point Lab
227. nd printing conic images COMMAND LINE FLAGS The command line flags interpreted by conic are p Use preview mode Set the image size to 645x484 and antialias mode to none see below s Invoke imgview 1 on the computed image file SGI or TIFF image formats This flag is only meaningful when used in conjunction with the o flag or the output configuration file option a mode Set the antialias mode Mode is the same as the argument to the antialias option in the configuration file see below o file Store the computed image in file in the selected image format see the f flag The default save format is TIFF The image is not displayed unless the s flag is also specified x size Set the horizontal image size to size pixels y size Set the vertical image size to size pixels e shell command Execute the shell command when the image has finished drawing and exit when the command is done c file Use file as the conic configuration file f output format Use the given output format if possible The supported output formats are screen sgi ps and tiff which are on the screen SGI image file Encapsulated PostScript file and TIFF file formats respec tively The default format is tiff if the o flag see above is specified and screen otherwise Also if you use the ps format see the H option t Make the background color transparent This only works when writing output to SGI and TIFF image files
228. nderscores This command is most useful on the NeXT where one might color the active site with the colorpanel color and then rename it to a different name to save it See also color colordef 2 4 18 Conic Usage conic options The conic command produces a space filling rendering of the displayed molecule s The current orientation and coloring is retained Each atom is depicted as a sphere of the appropriate radius with realistic highlighting and shadowing effects This image is not interactive and takes anywhere from a few seconds to a few minutes to produce Clicking the left button returns to MIDAS There are many options which are detailed fully in the conic manual page included in Appendix 6 of this document The conic command is actually an alias that executes the pdbrun command and sends data to the conic program See also ribbon pdbrun UCSF MidasPlus 28 UCSF MidasPlus 2 4 19 Copy Usage copy date box flat bg background color intensity 0 1 printer printer file file title title al The copy command sends a PostScript description of the current picture to a printer or disk file The optional keyword date puts today s date in the lower left hand corner of the copy The optional keyword box draws a heavy border around the copy The flat option forces all vectors line segments to be the same thickness thereby disabling the pseudo depthcuing effect created with variable width lines The background opti
229. nential averaging of pseudo atoms See the x flag for more info e lowbound Change the lower energy penalty threshold where torsion colors change from green to yellow to lowbound Default is 1 0 APPENDIX 6 157 UCSF MidasPlus NOESHOW 1 NOESHOW 1 E hibound Change the upper energy penalty threshold where torsion colors change from yellow to red to hibound Default is 4 0 f file Store violated constraints in a file named file sorted by magnitude of violation See also the n flag F Don t quit on encountering the first error continue to report errors This is useful when debug ging problems using noeshow which is discussed in the next section h cutoff Show hydrogen hydrogen interactions that are no more than cutoff angstroms apart See the Showing possible H H interactions section for a description of this option If this option is specified the constraint file command line argument can be omitted l Label atoms involved in unsatisfied constraints For pseudo atoms only the atom that the con straint is drawn to the closest is labeled L Expect LEaP nomenclature for atom names LEaP is a module provided with AMBER If you don t know what LEaP is you don t care about this flag n Used in conjunction with the f flag show signs as well as magnitudes of violated constraints vV Show only badly violated distance constraints V Show only badly violated torsion constraints
230. number and atom specification separated by spaces Chain identifiers if present in the PDB file should be appended to the residue number Residue insertion codes if any should be placed between the residue number and any chain identifier Residues in HETATM records should have a appended to them An atom specification can be an atom name any atom in the named resi due or FRM followed on the next line by TO used in pairs to denote residue ranges Note that atom names should correspond exactly to the name given to the same atom by MIDAS As an example a file appearing as ASN 15 FRM LYS 21 LO HIS 123 aj GLU 141 CB GLU 141 CG selects residues 15 through 21 inclusive residue 123 the selects all the atoms of the residue and atoms CB and CG of residue 141 The surface is calculated only for these specified atoms and residues Using pdb2site Usually the selected portion of the model is an active site The user may determine which atoms are of interest by one of two methods 2a display the model and choose the atoms visually 2b display the model and choose the atoms within a given radius of a ligand use the zone specifiers in the atom specification syntax Once you have displayed only those atoms you want surfaced you could then use the pdb2site util ity to generate a site file via the MIDAS command pdbrun pdb2site o site 3
231. oeshow For MARDIGRAS input format constraints the coloring scheme is simple if the distance is less than 5 angstroms then the constraint is colored green if between 5 and 6 angstroms yellow and greater than 6 angstroms red Mardishow does not support restricting constraint display either through the marking mechanism of noeshow or by undisplaying parts of the molecule Bad things will happen if you try Pseudo atom constraints are measured to the heavy atom connected to the hydrogens rather than involving any kind of averaging Mardishow is designed to work with a single model structure rather than an ensemble The only way to use mardishow in conjunction with an ensemble is to display one structure of the ensemble at a time Mardishow supports a subset of the flags of noeshow namely a f F l and n In addition it has the following flags d amount When displaying MARDIGRAS output format constraints make the outside bounds of the energy well amount angstroms from the inner bounds which are given in the constraint file s Enable stereospecific constraints If a constraint names a hydrogen involved in a rotamer and this option is given then the constraint will be measured and drawn to that hydrogen Otherwise the constraint will go to the connected heavy atom FORMAT EXAMPLES AMBER INTERFACE format restraint at1l 2 HA at2 2 HN v1 2 664 r2 3 164 r3 3 252 r4 3 75
232. of lines of the form new atom_name xX y Z The atom names should be in uppercase letters and need not be unique The Cartesian coordinates specified by these lines are generally ignored by most programs and may be set to 0 0 0 if they are not conveniently available The third part of file group file is a separator and is a single line read internal coordinates for new group The fourth and final part of the group file is the connectivity and relative position description and is a series of lines of the form mode atoml atom2 atom3 atom4 bond_length bond_angle dihedral_angle The mode field of the line is a single character either or and is generally ignored Each of the four atom fields may be either a number or n3 n2 or n1 If itis a number it refers to an atom in the group The atoms listed in the group are numbered sequentially with the first atom being 0 If the atom field is one of the special strings it refers to an atom in the molecule to which the group will be attached Atom 0 is always attached to atom n3 The bond length is the distance between atoml and atom2 The bond angle is the angle formed by atoml1 atom2 and atom3 with atom2 as the vertex The dihedral angle is the angle formed by all four atoms with atom2 and atom3 as the internal vertices An example of a group file for 4 hydroxy phenol follows 4 OH phenyl new C 0 000 0 000 0 000 new C 0 000 0 000 0 000 new C 0 000 0 000 0 000 new C 0 000 0 000 0 000 new O
233. ommand color green 0 H amp 1 N za lt 2 5 e On the SGI and DEC Alpha you can push any window including the MIDAS window behind other windows by positioning the mouse cursor over the window and typing ALT F3 Similarly you can pull a window to UCSF MidasPlus 9 UCSF MidasPlus the front by putting the mouse cursor over it and typing ALT F1 This is very convenient if you need to get to your shell windows frequently while using MIDAS e On the SGI only there is program called cedit that is quite handy for determining what red green blue values to use to get a desired color To start it type cedit or possibly usr sbin cedit Cedit displays three sliders one each for red green and blue By moving the level indicators up and down you can mix in various amounts of red green and blue into the composite color displayed in the rectangle on the right side of the cedit window The number values below the slider bars vary from 0 to 255 so you need to divide by 255 to get the 0 1 range expected by MidasPlus commands or utilities that use RGB values Error Recovery e If your models have been moved so that they are no longer visible on the display the window command should make them visible again e It is prudent to save session files see save command periodically during long modeling sessions to avoid having one command inadvertently wipe out a carefully set up view However if you have not saved a ses sion it i
234. ompleted dms output file can be quite large so be sure adequate disk space is available 5 To display the surface invoke the midas display program Open the PDB file first using the open command as described in the Command Reference Guide section of this document Then using the same model number open the surface file For example open 1 dfr open surface 1 dfr dms opens PDB file dfr as model 1 and associates the surface dfr dms with it This may be shortened to open 1 dfr dfr dms To display the surface use the surface command surface 1 3 2 3 Electrostatic Potential Molecular Surfaces Users who wish to display electrostatic potential molecular surfaces should run the dms program as described above with an additional flag n This flag generates surface normals in the dms output file The dms output file may be used to generate the electrostatic potential of the surface using the program esp Esp requires a dms file and a PDB file as input Assuming the dms file name is dfr dms and the PDB file name is dfr the command to calculate electrostatic potential is esp i dfr dms o dfr esp a dfr The program generates an annotated dms surface file which in this example is named dfr esp The atomic charges for the various residue types are held in the system file usr local midas resource charges esp The user may substitute his or her own file of charges if desired Use the system file as a format guide to gen
235. ompound state in a file called PDB_file info which may be used by future viewdock sessions The Exit menu allows the user to choose whether com pound state is saved and whether to terminate the associated MIDAS session List Select which compounds are displayed in the compound browser based on their discard states Mode Select the operating mode Midas Select what is displayed in MIDAS Show Undeleted will show all undeleted compounds while Show Displayed will show all compounds that appear in the browser Rewrite Create a PDB file that only contains undeleted compounds The new file is created by removing lines from the input PDB file i e not DOCK s extended PDB file MIDAS INTERACTIONS Viewdock uses the following command to invoke MIDAS usr local midas bin midas d dock This default behavior may be overridden by setting the environment variable VIEWDOCK_MIDAS to the appropriate MIDAS invocation command Viewdock may also be invoked as a delegate from a running MIDAS session When viewdock detects that neither its standard input nor its standard output are files it assumes that it was invoked through the MidasPlus delegate mechanism and acts accordingly So the command delegate start viewdock usr local midas bin viewdock PDB_file will start an instance of viewdock for PDB_file Multiple instances of viewdock may run simultaneously IMPLEMENTATION NOTES Viewdock is implemented as a Python script so the Python interpr
236. on sets the background copy color without changing what is shown on the screen Similarly the intensity option controls the color intensity of the copy background without affecting the screen background If the printer keyword is given the copy is sent to printer If the file keyword is given the Postscript is saved in file If neither is given the copy is sent to the default system printer If the title keyword is given the entire rest of the line is taken to be the title for the picture Therefore if title is specified it must be the last thing in the copy command If no title is given you will be prompted for the title If no title is desired simply hit RETURN at the prompt The title is centered at the bottom of the picture See also bs 2 4 20 Delegate Usage delegate list Usage delegate start name command command_options Usage delegate stop name The list subcommand lists all the active delegates The start and stop subcommands start and terminate a delegate of the given name respectively The delegate mechanism allows other programs to extend the interactive capabilities of MidasPlus The delegate mechanism is discussed in detail in Appendix 5 of this manual Note that the discern 1 utility described in Appendix 6 of this document is a MIDAS delegate For a detailed description of an application developed using delegates see Automated Site Directed Drug Design Using Molecular Lattices in the Journal of Mol
237. on will not be smooth around its circumference there will be edges along its length A segmented ribbon will combine the features of a faceted and edged rib bon It would seem more descriptively natural to interchange the the faceted and segmented keywords but unfortunately due to backwards compatibility issues the keywords are as described Three types of cross sections must be defined in a cross section file helix strand and turn Ribbonjr also uses the cross section type arrow for creating arrows at the end of strands if it is defined When ribbonjr reads in the PDB file it automatically assigns residue cross section types based on secondary structure The user may override these cross section type assignments by supplying XSECTION USER records in the PDB file see below The third form in the grammar specifies how cross section type changes from name to name2 should take place Normally when the cross section type changes the ribbon abruptly changes from one type to the other If interpolate is specified however the cross section linearly changes from name to name2 This is useful for presenting a smooth transition between different cross section types such as from strand to turn Note that namel and name2 cross section types must have the same number of coordinates in their specifications If point is specified the cross section is linearly interpolated from type name to type turn and then abruptly changes to type name2 This transit
238. onds Line 6 is such a line These lines are typically introduced with a instead of a though will still work 3 11 Web Browsing PDB Files with Midas If you browse web sites that offer PDB files you may want to have MIDAS invoked to view the PDB files of interest The procedure for doing so is fairly simple In your home directory edit your mailcap file or create one if none exists Add the following line to the file chemical x pdb midas nofork s This will also cause MIME capable mail reading programs such as SGI s MediaMail 1 to use MIDAS to display PDB files If you make PDB files available via the web you have to ensure that your web server marks such files with the chemical x pdb MIME content type You may need to contact your webmaster to set this up Con versely if a site you are browsing fails to mark its PDB files with the chemical x pdb content type then despite the mailcap setup above MIDAS will not be invoked to display the PDB file UCSF MidasPlus 84 UCSF MidasPlus 3 12 Performance Issues with Midas By default MIDAS is configured to use the best combination of aesthetic and performance options for common modeling situations On platforms with certain graphics hardware or for certain modeling sessions e g very large systems you may wish to vary from these default options to obtain improved performance This section details various performance
239. onization as on start up Between the time it forwards a user command to the delegate and the time it receives the terminating SYNC message from the delegate MIDAS will not accept any input from the user Thus a buggy delegate can cause MIDAS to appear to hang until the delegate exits When the delegate receives an end of file indication on stdin it should terminate gracefully without trying to communicate with MIDAS as stdout may already been closed Conversely MIDAS detects when a delegate closes stdout and removes the delegate from the list of active delegates This might be necessary if the delegate detects an error and wishes to exit or if the delegate wants to perform a long calculation and needs no futher interaction with the user While waiting for a user command a delegate may spontaneously generate MIDAS commands This is useful for programs that need to run for a substantial period of time before yielding results and can let the user manipulate the model while the computation occurs These delegates can send the SYNC message before entering background MidasPlus Delegate Invoke delegate with delegate start Initialization lt Line of MidasPlus commands MidasPlus replies gt SYNC SYNC Time User command to delegate gt lt Line of MidasPlus commands MidasPlus replies gt SYNC SYNC Terminates delegate with delegate stop diad stdin clo
240. op up list at the top of this panel section has two choices all and individually Choosing all will select all models this is useful for global adjustment of the modeling session Choosing individually will revert to the selec tions before all was chosen On NeXT systems the bottom control panel section simply contains an array of buttons with model numbers as labels which can be used to toggle the selection status of the corresponding model One button is labeled with All and can be used to toggle between selecting all models and selecting individual models similar to the pop up list described above For all systems when there are more open models than selection devices you will need to use the select command instead of the mouse to select and deselect them On non NeXT systems each section of the control panel has a checkbox next to its title Initially each checkbox is selected Deselecting a checkbox will cause that section of the control panel to collapse and display only the title Reselecting the checkbox will re expand the corresponding control panel section Finally the Session menu can be used for opening models or sessions and saving sessions On non NeXT systems it is located at the top of the main window On NeXT systems it is an item of the main MIDAS menu The appropriate sub menus are Open for opening sessions
241. or PDB residues and template residues These can be summarized as 1 All atoms within a single residue must have unique names For example residue VAL may have only one atom named CA Other residues may also have a CA atom but not more than one CA may appear in VAL 2 Residue names are a maximum of three characters long and uniquely identify the residue type Thus all residues of a given name in a file will be the same type of residue and have the same structure For example residue SER has a certain connectivity specified in the template for SER Each occurrence of a serine residue in the Protein Data Bank file will conform to this pattern of connec tivity If there is a mismatch between the atoms in a PDB file residue and that residue s template then atoms found in the PDB file and not the template will be connected using simple distance based cri teria whereas atoms in the template but not the PDB file will simply be omitted 3 3 3 Common Errors in PDB Format Files If a data file fails to produce a model or produces an incorrect model in MIDAS it is sometimes difficult to determine where in the hundreds of lines of data the mistake occurred This section enumerates some of the most common errors found in PDB files 3 3 4 Program Generated PDB Files Spurious Long Bonds A couple of common errors in program generated PDB files result in MIDAS di
242. ord Types Recognized by MIDAS Record Type Data Provided by Record ATOM atomic coordinate record containing the x y z orthogonal angstrom coordinates for the given atom HETATM atomic coordinate record containing x y z coordinates for atoms of nonstandard residues These record types are used by BNL to distin guish standard residues such a amino acids and nucleic acids from nonstandard groups such as inhibitors substrates and saccharides The only functional difference with ATOM records is that HETATM residues are by default not connected to other residues Note that water residues should be in HETATM records SSBOND defines disulfide bond linkages between amino acid residues Notice that the templates as described thus far allow only for linkage to the next residue in the chain and to the previous residue in the chain SSBOND records are special case links which are handled separately in MIDAS and bond rotations about these links are not allowed TER indicates the end of a chain of residues For example a hemoglobin molecule consists of four subunit chains which are not connected TER indicates the end of a chain and prevents a connection line to the next chain This record type is also used to prevent connection of substrates to other displayed parts of the model CONECT gives explicit connectivity of atoms HELIX indicates the location and type right handed alpha etc of helices One record per helix SHEET indic
243. ough to abel3d for further pro cessing The complete set of commands that abel3d can handle are described in the COMMANDS section of this manual page EXAMPLE A few typical uses of abel3d are demonstrated in this section It is assumed throughout this section that the standard PDB file alc a lactalbumin has been opened for display in MIDAS and is the molecule of interest for labeling purposes For purposes of clarity Jabel3d command names will be shown in full though shortened forms of the command names are accepted by label3d The acceptable short form of the command name will be emboldened for emphasis Setting up for labeling The first thing is to start the Jabel3d delegate with the command delegate start 11 label3d You should receive a reply indicating the delegate started normally After issuing the above command all commands prefaced with 11 will be handled by the label3d delegate while other commands will be pro cessed by MIDAS If the reply states that the delegate failed to start properly it may be that label3d had been invoked earlier in the session but not stopped with the abel3d command stop see finishing labeling below Typing makemark label will allow the delegate to be started normally Next the fonts that will be used must be opened This example will be using two fonts which would be opened with the commands ll open r roman c open g greek c The available fonts are described fully in the FONTS sectio
244. ource midas midas rc and usr local midas resource midas rc dev hostname respectively Note that the hostname portion of the latter filename should be replaced with the name of the machine that the file applies to as returned by the UNIX hostname command The order of execution of start up files proceeds as follows 1 The general system start up file OR the file specified by the user s environment variable MIDASRC See Appendix 4 of this document 2 The midasrc in the user s home directory 3 The midasrc in the user s present working directory 4 UCSF MidasPlus 14 UCSF MidasPlus 4 At this point any command line session file or PDB files are opened 5 The host specific start up file 6 Any script file s specified with the s command line option Start up files are conveniently used for assigning sliders as well as defining aliases and setting display options see the assign alias and set commands Any legal MIDAS command however may be included in a start up file MIDAS normally starts up in a window with a standard title resize borders etc On a non NeXT system use the f command line option to get a full screen window with no border If you always want full screen behavior when running MIDAS you can put the following line in your cshrc file alias midas midas f 2 4 Command Synopsis 66 99 MIDAS commands may be grouped together on one line using the ch
245. ow 2 4 73 Scale Usage scale factor frames wait_frames Usage scale Scale increases the size of the displayed view by the specified scaling factor The scaling factor must be positive a scaling factor less than one will decrease the size of the displayed view Note that this com mand does not modify the model coordinates Frames scales the models in the specified manner for the specified number of image update frames Wait_frames if specified indicates the number of frames to wait before beginning the scaling scale will halt an ongoing scale Frames and wait_frames default to 1 and 0 respectively These parameters are useful for controlling the rate of scaling and are helpful when constructing MIDAS command scripts and making videos MIDAS continues to process commands while the requested motion is in progress To have command processing pause until the motion is finished use the wait command See also wait 2 4 74 Section Usage section units frames wait_frames Usage section Section moves the hither and yon clipping planes the specified number of angstrom units This has the effect of displaying a different cross section of the displayed model s A positive number of units displays a cross section closer to the user whereas a negative number displays a cross section farther away from the user Frames moves the clipping planes in the specified manner for the specified number of image update frames Wait
246. pdbrun command which sends the current transformed coordinates of molecules to a user specified program and treats the output of that program as MIDAS commands pdbrun is most useful for one shot type computations such as alternative rendering conic or coloring atoms according to sequence position rainbow For computations that require information at several different times during a single MIDAS session however pdbrun is too inefficient The solution is a mechanism that allows designated programs called delegates to communicate with MIDAS while executing in parallel For example there is a delegate called mrotate supplied with the MidasPlus distribution that supports two commands snapshot and interpolate Users can use the snapshot command to save molecule positions at selected points during a session and the interpolate command to smoothly interpolate between two saved positions While it would be possible to add the snapshot and interpolate commands directly to MIDAS this approach requires one to have both an understanding of the internal program structure and permission to change source files Writing the rotation delegate required no modifications to MIDAS and once the matrix arithmetic was solved took less that a day to implement Less than 300 lines of new code including comments were written The delegate facility provides an alternative to modifying MIDAS every time additional functionality is desired Users who are wil
247. pears after the first labeled atom in the residue Examples label 3 label everything in model 3 label 2 HIS label all histidine residues in model 2 label 2 40 unlabel the 40th residue in model 2 See also rlabel label3d 2 4 37 Label3d Usage delegate start label3d The label3d delegate allows the placement of text labels at arbitrary three dimensional coordinates in the modeling scene Such labels can be imaged by neon and ribbonjr Details of this delegate s usage can be found in Appendix 6 of this document See also label 2 4 38 Link Usage link residue Usage link residue This command is obsolete and is provided for backwards compatibility with old MIDAS command scripts Use bond instead See also bond UCSF MidasPlus 35 UCSF MidasPlus 2 4 39 Load Usage load session_name Load restores the state of a saved modeling session see the save command The current modeling session will be replaced with the saved session However since delegate states are not saved in session files any active delegates will remain active See also open save 2 4 40 Longbond Usage pdbrun conect longbond 1 bondlength r bond_ratio The longbond command is used to break excessively long bonds Such bonds frequently result when opening PDB files that lack proper TER or HETATM records Details of this command s usage can be found in Appendix 6 of this document 2 4 41 Makemark Usage makemark name
248. position Red green and blue are floating point values between 0 and 1 inclusive USER COLOR red green blue color specification This annotation sets the color of the following ATOM or HETATM record If a color is not given for an atom then it inherits the value of the previous USER COLOR record The color specification is either a single color name see USER CNAME record above or a comma separated triplet of color name color name inter polation factor where interpolation factor is a floating point value between 1 and 1 inclusive and the absolute value indicates the proportion of hue lightness and saturation HLS components of the two named colors The red green blue triplet is redundant because the values are already implied by color specification but are provided as a convenience so that programs reading pdbrun files need not provide code to interpret the color specification themselves USER RADIUS radius This annotation sets the van der Waals radius in angstroms of the following ATOM or HETATM record If a radius is not given for an atom then it inherits the value of the previous USER RADIUS record USER OBJECT USER ENDOBJ These annotations denote the start and end of a user defined graphics object specification see 3D Graphics Annotations below USER CHAIN atom atom This annotation indicates a pseudo bond A USER CHAIN annotation is used to denote that two atoms should be depicted as if they were bonded ev
249. quently specified light sources By default a light source only shines on a point if there are no intervening spheres If the noshadow flag is specified however all points are considered to be lit The shadow flag will undo the effects of a noshadow flag for subsequent light sources The noshadow flag is generally used if the scene is very complex and having shadows makes the resulting image difficult to interpret This problem may also be miti gated by using multiple light sources matprop kd ks power Define default material properties Kd is the diffuse reflection coefficient Ks is the specular reflection coefficient Power controls how sharply defined a specular light is and must be a posi tive even integer The higher the value of power the smaller the specular reflection area The default values are 0 5 0 25 and 8 respectively Kd and ks must be in the range 0 1 and power must be 2 or higher output file Store the computed image in file in the selected image format see the f and o options above pointxyzrgb Define a point light source The arguments are the same as those for the light option except that x y z defines the light position rather than direction quad x7 y1 z1 x2 y2 z2 x3 y3 z3 Define a quadrilateral actually a parallelogram in the image Since the quad is a parallelogram only three vertices are necessary to define it Quads are second class objects They can be in shadow from first class obj
250. r interactive use in Inventor format this number should probably be set lower t Make the background color transparent This works with the tiff format to add an alpha channel to the file so the resulting image can be composited onto other backgrounds This option depends on OpenGL support for destination alpha and consequently does not work on all systems x filename Read cross section information from filename in addition to the default system file Cross section specifications in file filename will override those from the system file If there is no file named filename in the current directory ribbonjr will search for the file in the system directory The cross section file format is described in the CROSS SECTION FILE section below Several cross section files are provided in the ribbonjr system directory They are xs default the default when no cross section file is specified it produces a ribbon with an elongated ellipsoid cross section that is smooth along the ribbon s width and length xs rayshade a cross section file appropriate for use when generating output that will then be used in a ray tracer program such as pov or rayshade The polygonal sections used to render the ribbon are much more finely subdivided than normal xs rect a rectangular cross section with sharp edges Produces a ribbon with flat faces and sides xs ribbed a novelty cross section file Uses an elongated ellipsoi
251. reneon gt output_file DESCRIPTION Neon works with the MidasPlus package to create solid stick or ball and stick representations of molecular models The currently displayed atoms their orientation position and colors are taken from the interactive display of midas 1 using the pdbrun Midas command and are sent to neon Neon processes the informa tion under the control of parameters set in the neon dat file in the current directory and the output is sent to the Midas utility conic 1 to create the final image See conic 1 for a detailed description of its command line options Neon has three parameters for the depiction of a simplified backbone a smooth tube connecting amp Q carbons an intermediate bent tube and a straight tube with straight segments con necting amp carbons Neon has two parameters which create a smooth gradient of color over the the model based on the temperature factors of the atoms Dashed or solid lines can be drawn between atoms joined by the distance command in midas to illustrate hydrogen bonds and other interactions Neon handles Midas objects allowing arrows and lines to be displayed It is also possible to combine neon and conic rendering styles or differing types of neon rendering styles See the PRENEON section and the EXAMPLES Capturing Screen Images in Part III of the MidasPlus manual discusses saving converting and printing neon images EXAMPLE OF THE NEON DAT CONTROL FILE
252. ribbonjr f tiff other options savefile Note that the final dash in the above command before savefile is space separated from both the preceding options and from savefile Also note that ribbonjr will still render the image to the screen because it uses the graphics subsystem for computing the image Conic neon Neon is a preprocessor which uses conic as a back end for final rendering Neon passes any com mand line arguments it gets to conic therefore the method for saving image files is identical for neon and conic The remainder of this description will refer to conic but is applicable to both Conic can save to Encapsulated PostScript SGI image file on SGIs only and TIFF formats by specifying the _f command line flag along with the argument ps sgi or tiff respectively The command flag o savefile must also be specified If you use the ps format you may also want to supply the H flag hex encode data instead of using binary data since many printers don t accept binary PostScript Note that unlike ribbonjr if conic is given the o savefile option it won t also display the image unless the s flag is given as well 3 6 2 Converting Image Files to Other Formats The itops 1 utility provided with MidasPlus and documented in Appendix 6 can convert both TIFF and SGI image files to optionally Encapsulated PostScript Encapsulated PostScript can be include
253. ribed in the DESCRIPTION section above i e skip step D Do not fix type 1 problems described in the DESCRIPTION section above i e skip step B PDB_file The input Protein Data Bank PDB file may contain any legal PDB records Only ATOM records will be used All others are silently discarded If no PDB_file argument is given or is the data is read from standard input output_file LIMITATIONS The output of dnacheck is a set of PDB format records If no output_file argument is given or is the records are written to standard output Only DNA structures are handled RNA structures are not If someone were to develop RNA blueprints and test them with the C option we would be willing to redistribute them on the MidasPlus web site SEE ALSO UCSF MidasPlus User s Manual AUTHORS Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 120 UCSF MidasPlus ESP 1 NAME ESP 1 esp calculate electrostatic potential SYNOPSIS esp i dms_file 0 esp_file q file a pdb_file r n c cutoff e epsilon p len v w DESCRIPTION Esp calculates the electrostatic potential of a solvent accessible surface and stores it in an annotated ms sur face file This information can then be used by MIDAS to selectively color molecular surfaces based on electrostatic potential Esp prints out a summary of the conditions used to calculate the potential
254. rmatted_constraints diana2amber v viol_add pdb_file diana_low_bounds diana_high_bounds gt reformatted_constraints xplor2amber c chain_ID v viol_add pdb_file xplor_constraints gt reformatted_constraints xplor2tors options xplor_torsion_output gt reformatted_torsion_file DESCRIPTION USAGE Noeshow and mardishow are programs for displaying NMR derived constraints on model structures in MIDAS Noeshow can display distance constraints in AMBER INTERFACE format and via format conver sion programs constraints in X PLOR DIANA MARDIGRAS output or AMBER SANDER namelist for mats Mardishow can display constraints in MARDIGRAS input or output formats Noeshow s functional ity is generally a superset of that provided with mardishow and mardishow is provided principally for its ability to display MARDIGRAS input format constraints If a conversion program for MARDIGRAS input format is developed mardishow may be withdrawn Noeshow can also show torsion angle constraints if given the restraint analysis output from the SANDER AMBER module The conversion program xplor2tors can be used to convert X PLOR torsion angle infor mation to a form usable by noeshow Finally noeshow can be used to indicate all hydrogens within a given cutoff distance of one or more desig nated hydrogens This capability can be used with or without an accompanying set of distance constraints Distance constraint preparation If your distan
255. roceedings IBM Scientific Computing Symposium on Computer Aided Experimentation 1965 2C Levinthal Scientific American 214 6 42 52 1966 3R Langridge Federation Proceedings of the American Society of Experimental Biology 33 2322 2328 1974 4T E Ferrin and R Langridge Computer Graphics 13 320 331 1980 5D M Ritchie and K Thompson Communications of the ACM 17 7 1974 UNIX is a registered trademark of Unix Systems Laboratory 6R Langridge T E Ferrin I D Kuntz M L Connolly Science 211 661 666 1981 TT E Ferrin C C Huang L E Jarvis and R Langridge J Mol Graphics 2 55 1984 ST E Ferrin C C Huang L E Jarvis and R Langridge J Mol Graphics 6 13 27 1988 9T E Ferrin C C Huang L E Jarvis and R Langridge J Mol Graphics 6 2 12 1988 functions to MidasPlus without modification of the MIDAS source code The MidasPlus delegate facility makes it significantly easier for new or specialized features to be added without requiring knowledge of the internals of a large and sophisticated interactive graphics program such as MIDAS The first delegate program Builder was a module for performing site directed drug design using a molecular lattice approach 0 Many additional MidasPlus delegates have now also been developed see table below It is especially noteworthy that several of these Midas Plus delegates have been designed and implemented by graduate students and postdoctoral fellow
256. rovides no coordinates Thus only if the user provides a coordinate value for the atom OXT will MIDAS draw OXT If OXT does not appear in the template however providing coordinates for OXT is not sufficient for adding the addi tional atom since the associated connectivity information must also be provided In other words an atom must be included in the template in order to appear in the MIDAS model 5 Note that none of the hydrogen atoms contained within a real glycine amino acid are included in the above template specification Historically hydrogen atom coordinates have not been included in pro tein and nucleic acid structures because of the limited resolution provided by x ray crystallography techniques For structures where hydrogen atom information is available appropriately named atoms e g HA 1HG1 can be added to the residue definitions and thus incorporated into the template file in the same manner as other atoms in the template Most commonly used templates have already been constructed and reside in a library accessible to MIDAS usr local midas resource midas models The naming conventions used in these templates are those specified by the Brookhaven Protein Data Bank and include amino acids nucleic acids and many prosthetic groups Thus for the most part the residues needed to build a molecular model are already available For any exceptions however the user must either rely on the distance based connectivity algorithm or
257. rrent font by sx in the x dimension and sy in the y dimension If sy is missing it is set equal to sx source filename Read commands from file filename and execute them stop Terminate abel3d Note that this command should be used instead of the MIDAS delegate stop command so that label3d can issue some necessary cleanup commands to MIDAS before exiting Also note that this command will remove all labels unlabel abel_ref Destroy the label named label_ref If label_ref is omitted the current label is destroyed update Update is a do nothing command that may be used when model positions have changed and the position or orientation of labels need to be updated use font_name Make the current label be displayed using font font_name The font data provided with abel3d was derived from the public domain distribution of the Hershey Fonts APPENDIX 6 137 UCSF MidasPlus LABEL3D 1 LABEL3D 1 A variety of font faces font sizes and levels of detail are provided The font faces are Name Description roman Roman greek Greek italic Italic script Script cursive cyril Cyrillic gothgr Gothic German gothgb Gothic English gothit Gothic Italian The font sizes and level of detail are Name Description p Plain very small no lower case letters s Simplex plain normal size no serifs d Duplex normal size no serifs doubled lines c Complex normal size serifs doubled lines t Triplex normal size serifs
258. rted for use with noeshow Again this is output information and again an example is provided in the Constraint formats section The X PLOR output information can be converted to the AMBER format with the xplor2tors program the procedure for which is shown in the SHELL COMMAND SYNTAX section above X PLOR torsion constraints are expressed as a desired angle and an allowable range about that angle Xplor2tors has two options to control the transition from satisfied green to slightly violated yellow to badly violated red The a degrees option con trols how close to the edge of the range an angle can be before it is shown as slightly violated default 5 degrees The A degrees option controls how far beyond the edge of the range an angle can be before it is shown as badly violated default 10 degrees APPENDIX 6 154 UCSF MidasPlus NOESHOW 1 NOESHOW 1 Basic usage This section will discuss how to use noeshow to display NMR constraints in MIDAS Mardishow is used in a very similar manner and any differences will be discussed in the Mardishow section below Noeshow is run from within MIDAS so the first step is to display the model structure or structures in MIDAS Once you ve done that invoke noeshow as shown in the MIDAS COMMAND SYNTAX section above The parts of the command enclosed in brackets are optional and can be omitted Noeshow will read the file s you specify
259. rwise enhanced in programs such as Adobe Photoshop or SGI Showcase On SGI workstations images saved in SGI image format can be manipulated with standard IRIX image tools to achieve a variety of effects If these tools were installed on your system then man imagetools will describe them If they were not installed i e man imagetools responds with No manual entry found UCSF MidasPlus 79 UCSF MidasPlus for imagetools and you wish to install them consult the next section Converting Image Formats for installation information Also the ilabel 1 program documented in Appendix 6 can be used to add text labels to SGI image files In generating an image you intend to save it is frequently desirable to obtain the highest quality image possible at the expense of increased rendering time You should check the documentation for the rendering command you are using for options that can be used for increased quality For example the ribbonjr r option and the conic and neon a option will produce higher quality images than standard We discuss in turn how to save images from MIDAS ribbonjr conic and neon Methods for convert ing saved images to other formats are covered in the Converting Image Formats section which follows MIDAS The copy file command will save an Encapsulated PostScript file of the current modeling display In some situations it may be desirable
260. s Appendix 5 describes the details of the MidasPlus delegate facility Also since the MidasPlus distribution is supplied as docu mented source code users wishing to develop new delegate modules are free to use any of the existing delegates as a training tool and starting point for their own developments MidasPlus Delegates Name Author s Function Builder D Roe Graduate student Assemble lead compounds Conic Huang Pettersen Couch and Ferrin Generate shadowed CPK style molecular images Density C Schafmeister Graduate student Display X PLOR electron density contour maps Discern C Bayly Postdoc and C Huang Visualize multidimensional data Gd H De Winter REGA Contour GRID output prepare GRID input GDE M Young Graduate student Interface to Genetics Data Environment program Ksdssp C Huang Define protein secondary structure Label3d C Huang and J Newdoll Create three dimensional labels for images Makems S Newmyer Graduate student Create solvent accessible surfaces within MIDAS MidasMenu Huang Morris Genentech and Ferrin Graphical user interface front end for MidasPlus Midasmovie D Konerding Graduate student Animate trajectory of structures Neon T Hynes Genentech Generate models with solid stick bonds and shadows Noeshow E Pettersen and S Farr Jones Postdoc Display NOE constraints Qpackt L Gregoret Graduate student Protein structure analysis and modeling Rainbow E Pettersen Color protein backbone
261. s all current assignments assign removes an assignment Example assign 0 clipping h See also brotation select rotation 2 4 7 Bond Usage bond atom atom2 Usage bond atom atom2 The bond command tells MIDAS that atom and atom2 are bonded Atom and atom2 must be in the same model bond breaks an existing bond between two atoms UCSF MidasPlus 23 UCSF MidasPlus 2 4 8 Brotation Usage brotation rotation_number atom atom2 atom3 atom4 Usage brotation rotation_number Brotation produces a backwards rotation i e the portion of the molecule which remains fixed in a rotation command is rotated in the brotation command and vice versa Aside from that the brotation com mand is identical to the rotation command See rotation for an explanation of the syntax and behavior of brotation See also rotation reverse fix fixreverse 2 4 9 Bs Usage pdbrun conect bs options Bs generates a ball and stick PostScript description of the scene currently displayed by MIDAS The generated PostScript can be saved into a file for later use or sent directly to a printer Bs PostScript can be saved to a file with a command such as pdbrun conect bs options gt savefile Bs PostScript can be sent to a printer with a command such as pdbrun conect bs options lpr Pprintername A more detailed description of bs along with a list of available options can be found in Appendix 6 of this document
262. s allows the label3d delegate to issue some cleanup commands to MIDAS before stopping Unless these cleanup commands are executed a new label3d delegate cannot be started Note that the stop command will remove all current labels MIDAS cannot restore delegates to the state they were in when a MIDAS session is saved If it is necessary to save a session involving a label3d delegate the delegate s state will have to be recorded with the label3d save command and restored in the restarted session with the source command Both these commands are described in detail in the COMMANDS section of this manual page APPENDIX 6 135 UCSF MidasPlus LABEL3D 1 LABEL3D 1 COMMANDS When label3d is acting as a delegate for MIDAS as shown in the DESCRIPTION section the user can give it commands by typing ll Jabel_command in the MIDAS command window The list of commands is given below in alphabetical order Note that the command names can be shortened to the minimum number of characters need to distinguish the command from other Jabel3d commands For example append could be shortened to a or scalefont could be shor tened to scalef append value Append the string value to the current label This creates a multi font label and makes the newly appended part the current label Subsequent commands such as color and use will only affect the new addition To make some intermediate part of a multi font label become the current label use the label comma
263. s asked to surface a particular model the requested model will be surfaced as if the other models did not exist The standard way that makems is invoked is for the user to start a MIDAS session and issue the MIDAS command delegate start ms makems which runs makems and tells MIDAS to pass commands beginning with ms through to makems for further processing Any text sent to makems is interpreted as an atom specification to be surfaced Makems will compute the surface by invoking dms 1 with default dms settings and then display the computed surface in MIDAS Any surface previously computed by makems will be closed first EXAMPLES Some simple examples the examples assume that makems was invoked as shown in the SYNTAX section above ms CYS Surface all cysteine residues Surface the entire molecule ms color green Surface all atoms currently colored green BUGS As mentioned in the DESCRIPTION section makems only surfaces one model If the atom specification given to makems spans multiple models the lowest numbered one will be surfaced AUTHOR Dr Sherri Newmyer The Scripps Research Institute 10550 North Torrey Pines Road La Jolla California 92037 newmyer scripps edu APPENDIX 6 140 UCSF MidasPlus MIDAS 1 MIDAS 1 NAME midas MidasPlus molecular interactive display program SYNOPSIS midas X options fullscreen nofork nostereo script script delegate delegate_name session_fil
264. s based on sequence position Ribbonjr C Huang Depict protein secondary structure Stereoimg E Pettersen and C Huang Create space filling stereo image pairs Viewdock C Huang Assist analysis of DOCK output Future Development Plans MidasPlus is a powerful tool for its target problem domain of molecular visualization Nonetheless as noted above its original design dates to 1980 and significant advances in programming and visualization techniques have occurred since then In order to take best advantage of these advances we are designing and implementing a new molecular visualization package code named Chimera to succeed MidasPlus We anticipate Chimera building on the strengths of MidasPlus e g atom selection syntax extensibility while incorporating new features such as e Integrated menu and command line interfaces e A fully programmable object oriented command language 2 with complete access to molecular data e Interactive solid representations of molecules e Advanced graphics techniques such as texture mapping transparency and volume visualization e Support for web publishing import export VRML e Closer integration with other UCSF packages e g Sparky DOCK AMBER e Increased portability 10R L Lewis D C Roe C C Huang T E Ferrin R Langridge and I D Kuntz J Mol Graphics 10 66 78 1992 Computer Graphics Laboratory staff unless otherwise noted Not currently included in
265. s command prompts the program for the current values of color_spec contour_level and file_name contour model_number at level color color_spec Starts the contouring procedure and displays the computed contours as model model_number at contour level level using color color_spec If model_number is absent the lowest available model number will be used If the specified model_number already exists no contours will be drawn Level and color_spec can also be specified using the level and color commands see above GRIDIN CREATION COMMANDS These commands deal with the creation of a GRID input file define_grid extent show model_number Define_grid calculates the size of a box encompassing all atoms displayed in the viewing win dow If the additional parameter extent is given then the box size is increased along all sides by 2 extent angstroms The default value for extent is 0 If the optional keywords show model_number are given then the grid boundaries will be displayed as model model_number If model_number is not supplied in conjunction with the keyword show the lowest available model number will be used to display the box boundaries makegrid file_name This command writes a template input file for GRID called file_name If no explicit file_name is provided by the user it defaults to grid in Makegrid can only be executed after having defined a grid with define_grid The following commands set specifi
266. s may be used The sup ported types are bspline hermite bezier and cardinal The default spline type is bspline See the E flag above for more information about helical representation S red green blue Set the strand color in color scheme structure The default strand color is 0 1 0 Use of this flag implicitly sets color scheme to structure see the c flag T red green blue Set the turn color in color scheme structure The default turn color is 0 0 1 Use of this flag implicitly sets color scheme to structure see the c flag W Force MIDAS to wait until ribbonjr has exited before continuing Z debug level Specify the debug level The output is probably somewhat cryptic CROSS SECTION FILE The Jane Richardson type ribbon representation uses different shapes for different secondary structure types For example turns are commonly represented as thin tubes and helices and strands are represented as wide ribbons In this case the cross section of a turn is a small circle and those of helices and strands are elongated ovals Ribbonjr reads the standard cross section descriptions from a default file but the user may override them by supplying his own cross section file see the x command line flag APPENDIX 6 174 UCSF MidasPlus RIBBONJR 1 RIBBONJR 1 The grammar for cross section and interface descriptions is shown below optional elements are sur rounded by square brackets and user selected values are i
267. s sometimes possible to recover by careful use of the record command By default MidasPlus records all your typed commands in a temporary file which is removed when MidasPlus is stopped You can use this file to bring back the display that you had before the mistake less any mouse movements of the models To do this run the command record filename to save the temporary file to a file called filename use your favorite editor to remove the record command at the end of the file as well as any other commands you don t want then start a new MidasPlus session and in it run read filename to restore your work Miscellaneous Tips e The midas tty program can be used to run MidasPlus commands in batch mode or to capture MidasPlus replies into a file This can be useful if you have a repetitive non interactive task making the same amino acid substitution into dozens of molecules for example or need information presented in replies such as RMS deviations from a match command Midas tty is fully described in Appendix 6 of this manual UCSF MidasPlus 10 UCSF MidasPlus Part II Command Reference Guide 2 1 Referencing Models Residues and Atoms 2 1 1 Models Residues and Atoms MIDAS uses a hierarchical command syntax developed in 1980 by the UCSF Computer Graphics Laboratory for referencing models residues and atoms In each MIDAS model molecules are made up of residues The residues are chained together in a spec
268. s the neighboring hydrogens that should be considered for the cutoff marked with noemark2 Then noeshow would be run with the h cutoff option to specify the cutoff distance Noeshow will draw a pink line between each pair of hydrogens satisfying the cutoff criterion and will show the corresponding distance at the midway point of the line Since noeshow is implemented as a perl script it is not very fast at numerical calculations It is therefore best if you limit the marked sets of atoms to the smallest sets that still have all the atoms of interest For example let s say you have marked one or more hydrogens with noemark1 and you intend to run noeshow with a cutoff distance of 5 angstroms You could simply not mark any atoms with noemark2 in which case noeshow would have to calculate the distance from every hydrogen marked with noe mark1 to every other hydrogen in the molecule It would speed things up considerably to use noe mark2 to mark only those atoms that could possibly satisfy the cutoff with a command such as APPENDIX 6 156 UCSF MidasPlus NOESHOW 1 NOESHOW 1 mark noemark2 mark noemark1 za lt 5 1 which marks all atoms within 5 1 angstoms of the atoms in noemark1 with the mark noemark2 this is one of the more advanced uses of atom specifiers you may want to look at Referencing Models Resi dues and Atoms in the MidasPlus manual for further information particularly the section Atom Proper ti
269. s to sliders change center of rotation stop all motion translate selected models rock a structure about the x y or z axis roll a structure or bond rotation about the x y or z axis select models for move rock roll or turn commands set molecule s effective center of mass set the control speed of sliders and spaceball rotate a structure about the x y or z axis monitor bond or dihedral angle visualize multidimensional data monitor atom distances return lt x y z gt coordinates for an atom label atoms and residues ribbon representation of secondary structure enable residue labeling specify center of image chain specified atoms together move clipping planes color bonds labels and surfaces display specified molecules residues atoms set depth cue intensity at hither and yon clipping planes create arbitrary labels with depth when viewed in stereo display specified non molecule graphics object save restore the current model orientations on from a stack rainbow color atom chains from red to blue reset all models to original orientations display using ribbon representation save a model s current orientation apply a scaling factor to all models change displayed image s cross section set options especially fullscreen halfbond and linewidth display specified atoms and no others specify whether to use stereo and in what manner change thickness of the displayed image cross section
270. se that file instead So in order to add uncommon elements or use different radii one should copy the default file and modify it The file format is documented in the file itself Element Radius H 1 20 C 1 90 N 1 50 O 1 40 F 1 35 P 1 90 S 1 85 Cl 1 8 Fe 0 64 Cu 1 28 Zn 1 38 Br 1 95 I 2 15 Other 1 90 SEE ALSO pdb2site 1 The UCSF MidasPlus Installation Guide AUTHOR Conrad Huang University of California San Francisco FILES usr local midas resource dms radii default atomic radii APPENDIX 6 117 UCSF MidasPlus DMS 1 DMS 1 DIAGNOSTICS Many and varied Be sure to examine the g file before you leave a background job running overnight APPENDIX 6 118 UCSF MidasPlus DNACHECK 1 DNACHECK 1 NAME dnacheck regenerate DNA files to match Protein Data Bank specifications SYNOPSIS dnacheck c file h r A C directory D C I PDB_file output_file DESCRIPTION Dnacheck reads a Protein Data Bank PDB file containing DNA atomic coordinates and creates a file that matches the Protein Data Bank format for nucleotides Dnacheck corrects three types of problems 1 Residue and atom name mapping PDB specifies a set of residue and atom names for nucleotides Frequently data files not from PDB use slightly different naming conventions Dnacheck knows about some of these conventions and will convert names to the PDB standard set 2 AMBER output AM
271. separately at first and then together To do this you would run noeshow once for each constraint set you want displayed Noeshow will open each successive graphics object in a different model number the lowest available at the time You can then undisplay specific graphics objects with the objdisplay modelnum command objdisplay modelnum will of course redisplay them while close modelnum will dispose of them per manently Showing only torsion restraints Showing torsion constraints with no distance constraints may seem problematic at first since noeshow requires an argument specifying a file of distance constraints However this is simple to get around by specifying a distance constraint file that is empty On UNIX systems such as the SGI there is a special system file that is always guaranteed to be empty dev null There fore invoking noeshow as noeshow options dev nul11 torsion_file would display only the torsion constraints in torsion_file Options Many default behaviors of noeshow can be modified by command line option flags The options supported by noeshow are a Show all constraints including satisfied constraints A Show all torsions including satisfied torsions c For multi atom pseudo atoms measure constraint to geometric centers of atoms rather than doing exponential averaging See also the D and x flags D Don t divide by number of atoms when doing expo
272. ser Plane may be either hither or yon Frames moves the clipping plane in the specified manner for the specified number of image update frames Wait_frames if specified indicates the number of frames to wait before beginning the move clip will halt an ongoing clip Frames and wait_frames default to 1 and 0 respectively These parameters are useful for controlling the rate of clipping and are helpful when constructing MIDAS command scripts and making videos MIDAS continues to process commands while the requested motion is in progress To have command processing pause until the motion is finished use the wait command Clip can be invoked without the units parameter in which case it will report the distance to the clip ping plane from the eye point See also intensity section thickness wait 2 4 14 Cofr Usage cofr atom_specification view Usage cofr When invoked without any arguments the cofr command reports the current center of rotation If given an atom_specification the cofr command sets the center of the bounding box of the given atom s as the center of subsequent rotations If the view keyword is given instead the center of rotation is set to be the center of the current view cofr causes MIDAS to use its default center of rotation which is the center of mass of the selected models instead of any previous user specified one See also setcom UCSF MidasPlus 25 UCSF MidasPlus 2 4
273. ses delegate exits Figure 1 Event diagram of delegate communications protocol APPENDIX 5 98 UCSF MidasPlus computation mode and then spontaneously generate MIDAS commands once the calculation completes The only drawback to using background computation is that the user may try to send more commands to the delegate result ing in a race condition where the user command may be interpreted as a reply to a MIDAS command Implementors of this type of delegate should clearly document which user commands use background computation modes and possibly warn the user at run time that further input is not advisable A delegate can request that the user pick an atom by sending the pickatom command to MIDAS The delegate should be prepared to handle the situation where the user aborts the pick with the pickabort command Both com mands are documented fully in Part II of this manual Note that the discern 1 utility described in Appendix 6 is a MidasPlus delegate and its source code is supplied with the MidasPlus source distributions Translating MIDAS atom specifiers into corresponding PDB records can be very difficult in some cases To assist delegates in expanding atom specifiers MIDAS has a mark command in order to associate a name with atoms corresponding to an atom specifier The delegate can first mark the user specified atoms and then use the pdbrun command with the mark name option to obtain PDB records corresponding to the mark See the
274. set surface 2 4 54 Pdb2site Usage pdbrun pdb2site o site_file Pdb2site is a simple way to generate a site file for use in conjunction with the dms 1 command for computing molecular surfaces Details of pdb2site s usage can be found in Appendix 6 of this document 2 4 55 Pdbopen Usage pdbopen options The pdbopen command launches a pair of windows for browsing a PDB distribution hierarchy for PDB files of interest Naturally this is only useful if a PDB distribution is available on your system Full details of the use of this command can be found in Appendix 6 of this document UCSF MidasPlus 41 UCSF MidasPlus 2 4 56 Pdbrun Usage pdbrun all conect nouser noobj surface mark name command cmd_args Pdbrun causes command and cmd_args to be passed to the user s preferred UNIX shell for execution A set of concatenated PDB files describing the current models hereinafter referred to as a PDBRUN file is also passed as standard input to command Normal shell metacharacters notably output redirection can be used Errors are ignored and any shell output is interpreted as MIDAS commands and executed For instance pdbrun cat gt file would result in a PDBRUN file describing the current models to be saved to a file named file see also the save and write commands MIDAS has no way of directly restoring state from a saved PDBRUN file but see the run2ses 1 command in Appendix 6 Note that M
275. set record clears the command memory and prevents sub sequent commands from being remembered This will save some time and disk space since the commands are remembered in a temporary disk file To save the remembered commands to a permanent file use the record command Controls whether a circle defining the transition between x y versus z rotation is shown when MidasPlus is in virtual trackball manipulation mode Displays the Command and Reply text lines on the bottom of the display screen This option can be turned off using unset text when taking photographs MIDAS prints confirmation messages after each successful command If verbose is unset these messages will not appear UCSF MidasPlus 51 UCSF MidasPlus Set Unset Value Options Keyword Function bg_color Sets the MIDAS background color Value can be any color name as described in detail under colordef eyesep The separation between the centers of the viewer s eyes in inches This information is necessary to compute the projections for stereo viewing It is rarely necessary to change the default setting for most adults but it might be necessary for children viewing stereo font Allows atom labels to be in any font style The value is a font name e g Helvetica The default font on the SGI is raster A list of acceptable font names can be found in usr local midas resource midas xpsfontmap the first column fontsize Allows atom
276. sfied and not within 5 degrees of violated Note that X PLOR torsion coloring can be adjusted with options to the xplor2tors conversion script By default noeshow will not display the satisfied torsion angle constraints The A option flag will cause them to be displayed as well Restricting display By default noeshow displays all the violated constraints present in the constraint file At times this may be more information than is desired There are several methods of restricting the displayed constraints to those of interest detailed below In the early stages of structure refinement it may be desirable to show only the badly violated constraints if you are uncertain about all the cross peak assignments for example Giving noeshow the v option will restrict the display to only badly violated constraints i e those colored red or blue The simplest way to restrict constraint display to specific areas of the structure is to undisplay the parts of the structure where you don t want constraints shown Noeshow will not show constraints where one or both ends would be on an undisplayed part of the structure To get this effect you have to undisplay the undesired regions before running noeshow You could then redisplay the whole structure after having gen erated the constraints of interest Undisplaying parts of the structure after running noeshow has no effect on displayed constraints APPENDIX 6 155 UCSF MidasPlus NOESHOW 1 N
277. shion described in the conic 1 manual page under section Coloring the Molecule The color of the ribbon is the same as the color of the guide atoms If no PDB file is specified or is provided as the PDB file name then stan dard input is used PDB files generated by some programs may not conform to the PDB standard The utility dnacheck 1 pro vided with the MidasPlus distribution corrects many of the common problems found in such files Consult the dnacheck manual page for further details Also for proteins ribbonjr requires the information con tained in HELIX and SHEET PDB records in order to correctly display secondary structure If a PDB file lacks such records the ksdssp 1 utility can be used to generate the records The ksdssp manual page con tains further details Unless their display is explicitly suppressed with the a command line option non mainchain atoms and bonds are shown as balls and sticks Mainchain atoms are not individually depicted unless they are con nected to a displayed non mainchain atom The mainchain atoms for amino acids are N CA C and O The mainchain atoms for nucleotides are P O1P O2P O3P C5 O5 O3 and C3 The bonds are derived either from CONECT records if they exist in the PDB file or from drawing templates found in MIDAS template directories The ribbon representation from ribbonjr may be in one of several formats midas inventor rayshade pov screen and tiff
278. sidue are of type HETATM instead of ATOM Normally dnacheck retains the record type of atoms from the input file This option is most useful when there are many unconnected residues such as waters which are of type ATOM in the input file but should actually be of type HETATM Renumber the sequence number of residues Normally dnacheck retains the sequence number insertion code and chain identifier of residues from the input file This option makes dnacheck renumber the residues making all insertion codes the space character Hetero residues are given consecutive sequence numbers starting from 1 with chain identifiers set to the space character Non hetero residues are split into chains with residues in each chain given consecutive sequence numbers starting from 1 If there is only one chain in the file the chain identifier is set to the space character otherwise the chain identifiers are set to consecutive alphabetic characters start ing with A Do not fix type 2 problems described in the DESCRIPTION section above i e skip step C C directory D I Set the default directory where dnacheck searches for configuration files and blueprints Nor mally dnacheck looks for configurations files and blueprints first in the current directory then in the default directory usr local midas resource dnacheck Even with this option set dnacheck will still search the current directory first Do not fix type 3 problems desc
279. sis subsection in Part II as it provides a list of all available MIDAS commands grouped together by function Differences in the way MidasPlus acts on various workstations are explicitly noted throughout the manual Part II Advanced Concepts discusses a variety of topics including important details in MIDAS input file format displaying molecular surfaces computing electrostatic potential surfaces and adding hydrogen atoms Beginning users may skip Part III on first reading but should be aware that the input data used by MIDAS is critical to a pro ductive modeling session hence careful reading of this section is essential if you are using a data file that has a nonstandard format Finally the appendices describe additional details such as atom naming conventions special characters and symbols used by MIDAS default options aliases and device assignments and the MidasPlus delegate mechanism Especially noteworthy is Appendix 6 MidasPlus Program Suite which describes many ancillary programs that are part of the overall MidasPlus package The MidasPlus delegates listed above are described in detail in Appendix 6 as well as a wealth of stand alone programs intended to complement the functionality pro vided by MIDAS Lastly there is a full descriptive index at the end of the manual which may be of use in locating particular topics of interest Recent changes to the MidasPlus User s Manual are now indicated with a
280. sitive z yon clipping planes respectively USER FOCUS focal length Distance from viewer to focal plane along line of sight Used primarily when making stereo projections The focal length is typically between the hither and yon distances If the focal length is zero then an orthographic projection is used rather than a perspective projection USER VIEWPORTx x min max Y min Ymax Extent of the MIDAS window in screen coordinates USER BGCOLOR red green blue Color of the MIDAS background given as amounts of red green and blue each in the range 0 to 1 hither 224 Z on are positive distances from the viewer to the hither and ither yon Per Molecule Annotations USER FILE model filename Each embedded PDB file or graphics object file is identified by the original filename that the molecular or graphics data was fetched from and by its model number USER MARKNAME name This record notes a mark name in use in the MIDAS session see the makemark command That mark name may be then used in subsequent USER MARK records USER MARK name This annotation marks the following ATOM or HETATM record with the given name Unlike the USER COLOR and USER RADIUS records which see marks are not inherited by subsequent records A single atom may have multiple marks APPENDIX 1 87 UCSF MidasPlus USER CNAME red green blue color name This annotation defines a named color and its com
281. so available on the World Wide Web at http www cgl ucsf edu home glasfeld tutorial intro html The tutorial available only via the Web was developed by Dr Bryan Jones at the Biomolecular Structure Center of the University of Washington for the benefit of users there We have slightly modified the tutorial to make it generically applicable to any MidasPlus installation It is a more condensed introduction to MidasPlus functionality than the Glasfeld tutorial The URL is http www cgl ucsf edu home meng tut t html UCSF MidasPlus 8 UCSF MidasPlus 1 4 1 Demonstration Images There are demonstration images provided with the MidasPlus distribution These images show various uses of the rendering programs available with MidasPlus Each image is accompanied by a general descrip tion of how it was prepared If the demos were installed on your system they are optional then the sample images will be found in usr local midas demos images The file README INDEX in the images directory contains information on the contents of the directory If the demos were not installed on your system they can either be installed consult the MidasPlus Ins tallation Guide for details or viewed directly from the MidasPlus CD ROM once mounted On the CD ROM the images directory is Midas 21 demos images 1 5 MidasPlus Web Resources The main MidasPlus web page is located at http www cgl ucsf edu midasplus html Much useful infor mation is linked to from t
282. some subroutines might be useful to you as is Source code for the entire MidasPlus distribution including all delegates is pro vided on the installation CD If you need to access that source code you will have to ask your system adminis trator if he she has installed the MidasPlus sources and if so in what location e There have been several additions to the MIDAS command language specifically to support delegate operations A list of commands related to delegate support can be found in the table of commands grouped by function near the beginning of section 2 4 Specifically the groupings Auxiliary Program Support and Script Support are of interest An example of a delegate that simply echoes user input follows include lt stdio h gt include lt stdarg h gt ifndef TRUE define TRUE 1 define FALSE 0 endif FILE record_fp Sample MidasPlus delegate ef main int ac char av register int cj int verbose FALSE char buf BUFSIZ extern int optind APPENDIX 5 99 UCSF MidasPlus extern char optarg static int send_command char Process command line arguments while c getopt ac av vr EOF switch c case v verbose TRUE break case r record_fp fopen optarg w if record_fp NULL setbuf record_fp char NULL break First we sync with MIDAS which is expecting us to notify it of proper start up EF void pr
283. splaying very long bonds between residues that should be disconnected To address this problem the Jongbond program has been developed Longbond can be run from within MIDAS to break bonds of excessive length Consult the longbond manual page in Appendix 6 for details If you are writing a program that generates PDB files and long bonds appear you may be interested in the common errors that cause them so that your program can be corrected One such error is the omission of TER cards at the end of molecule chains According to the PDB standard TER cards mark the end of molecule chains and MIDAS depends on them in order to determine when to connect adjacent residues You should insert them in your PDB file if they are missing Consult section 3 4 1 for details of TER card format Alternatively you could mark all chains with differing chain IDs MIDAS will not connect adjacent residues if they have differing chain IDs A second common cause of long bonds is improper use of ATOM records when HETATM records should be used HETATM records should be employed for isolated compounds that do not form chains such as H O or hemoglobin MIDAS then knows not to connect adjacent residue numbers Many programs generate files that fail to employ HETATM records appropriately Make sure that the first six columns of the ATOM record are changed to HETATM so that the remaining columns stay aligned correctly Incorrect Secondar
284. standard input output_file The output of ksdssp is a set of PDB HELIX and SHEET records If no output_file argument is given the records are written to standard output SEE ALSO Wolfgang Kabsch and Christian Sander Dictionary of Protein Secondary Structure Pattern Recognition of Hydrogen Bonded and Geometrical Features Biopolymers 22 2577 2637 1983 AUTHORS Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 133 UCSF MidasPlus LABEL3D 1 LABEL3D 1 NAME label3d Midas delegate for displaying 3 D labels MIDAS COMMAND SYNTAX Command delegate start Il label3d DESCRIPTION Label3d is a MidasPlus delegate that generates MIDAS object files which contain character labels com posed of move and draw commands The built in MIDAS atom labels are fixed size characters which appear left to right across the display Because the character labels that Jabel3d generates are MIDAS objects they may be translated rotated and scaled in three dimensions in the same manner as molecules An additional benefit of being MIDAS objects is that these character labels may be shown by ribbonjr 1 and neon 1 Label3d is a program designed to run in conjunction with MIDAS using the MidasPlus delegate mechan ism The standard way that abel3d is invoked is for the user to start a MIDAS session and issue the MIDAS command delegate start ll label3d which runs label3d and tells MIDAS to pass commands beginning with Il thr
285. support began with the formation of the Computer Graphics Labora tory at Princeton University in 1969 under the leadership of Prof Robert Langridge and resulted in a number of pioneering developments including CAAPS Computer Aided Analysis of Protein Structure In 1976 Langridge moved this NIH research resource to UCSF A new graphics package was designed to operate under the UNIX gt operating system and a new molecular graphics system MMS was also designed initially in collaboration with the group under Prof J Kraut at U C San Diego This evolved into a system MIDS which was good enough to accom modate the new developments in color graphics and made possible the display of interactive surfaces The MIDS system was used by numerous visitors to our laboratory in the late 1970 s In 1980 we decided to redesign the system completely making use of the lessons learned over the previous 15 years The result the original MIDAS system emphasized highly interactive display and manipulation with a data structure designed for very fast access to large and complex molecules such as proteins and nucleic acids The system was originally developed on the UNIX operating system for use with an Evans and Sutherland Picture Sys tem 2 display however between 1982 and 1989 MIDAS was ported to a variety of graphics display engines PS2 MPS PS300 family and Silicon Graphics IRIS family and operating systems BSD UNIX System V UNIX and VM
286. t III of this manual A group name must contain only alphanumeric characters Note that adding a group creates a new residue which is colored white and has no labels The tempera ture factor for the new residue is set to the highest currently found in the model See also delete 5The user s groups directory location can be overridden by setting the GROUPS environment variable to a directory or a colon separated list of directories If the GROUPS environment variable is not set and HOME groups does not exist then the current directory will be searched instead UCSF MidasPlus 21 UCSF MidasPlus 2 4 3 Alias Usage alias name wordlist Usage alias name Alias assigns to name the specified wordlist All subsequent appearances of the space delimited name will be substituted with the wordlist If the name is preceded with a then the substitution will only occur at the beginning of a command This is useful for aliasing a long command to a short name without worrying about that same short name inadvertently being used and expanded in the middle of other commands The wordlist may contain multiple commands separated by semicolons in which case the wordlist must be embedded in double quotes like this alias name command1 command2 The alias command without any arguments reports all current aliases The alias command with name only reports the alias for that name alias name deletes the alias for
287. t in the PDB file 2 1 2 Wildcard Symbols The global wildcard symbol matches all atoms in a residue or all residues in a model It stands alone as a symbol i e it cannot be used to match parts of names or sequences such as G or A To do that use the wildcard character For example color red c means to color all atoms whose names begin with the letter c This works for residue names too but not residue sequence numbers The single character wildcard symbol is used to select atom names and residue names whose names follow pat terns cannot be used to match sequence numbers For example 1 12 all atoms in residue 12 of model 1 0 1 2 50 CA all alpha carbon atoms in residues 50 to the end of models 0 1 and 2 2 G all three character residue names which begin with the letter G in model 2 0 H H H all hydrogen atoms with one two or three letter names in model 0 The percent symbol may be used to specify every nth item where n is an integer For example 1 5 selects every fifth residue in model 1 1 HIS 4 selects the fourth atom of each HIS residue 3This is due to the fact that is a legal character in such names UCSF MidasPlus 12 UCSF MidasPlus 2 1 3 Atom Properties Atom properties are specified with the operator The currently supported properties include display label vdw surface v
288. t inappropriate if e A large surface is to be computed which may take several minutes or hours e Dms must be run with non default settings e g dot density probe radius etc UCSF MidasPlus 64 UCSF MidasPlus e Dms non surface output is of interest e g total surface area information e The generated surface file must be retained for later use makems automatically deletes it The second approach involves invoking dms from the UNIX command line with the appropriate PDB and site specification files and taking the resultant surface opening it and its associated PDB file in MIDAS and then displaying the surface with the surface command The procedure for running makems is covered in detail in the makems manual page in Appendix 6 of this manual The procedure for running dms from the UNIX command line is discussed below 3 2 2 1 Running Dms Directly 1 Begin with a PDB file which has been displayed and is known to be correct 2 The surface may be calculated for the entire model or specific sections To select specific sections a file must be prepared containing the residues and or atoms of interest Either the file may be prepared by hand if the atoms residues of interest are already known or the pdb2site utility run from within MIDAS can be used to generate the file Both approaches are described below Preparing a Site File by Hand The format for the site file is a series of lines containing the residue name residue
289. t information on obtaining copies of coordinates from the data bank by writing to Protein Data Bank Chemistry Department Building 555 Brookhaven National Laboratory Upton New York 11973 USA Alternatively contact can be made by e mail to orders pdb pdb bnl gov or phone 516 344 5752 or fax 516 344 1376 1 7 Helpful Hints In perusing a manual of this length it is easy to overlook some useful techniques for making common modeling tasks easier This section presents a few techniques that seem to be missed frequently Shortcuts e It is usually much easier to pick a desired atom off the display see section 2 1 7 Atom Picking than to type in its atom specifier Previously typed commands can be retrieved with Control P and edited if necessary see Appendix 3 Special Characters and Symbols Used in Midas Frequently typed commands and command arguments can be shortened by using aliases see the alias com mand Also Midas will accept abbreviated command names as described in section 2 4 Command Synopsis It is useful to become acquainted with the full power of atom specifiers section 2 1 they have been extended significantly in recent releases For example you can color yellow all beta sheet residues within 5 angstroms of a helix with the command color yellow sheet amp helix z lt 5 or color green all hydrogens in model 0 within 2 5 angstroms of nitrogens in model 1 with the c
290. ta file should be changed ATO dS HIS 1 49 169 26 701 10 917 1 00 16 00 ATO 2 CA HIS 1 50 197 25 578 10 784 1 00 16 00 ATO 3 CB HIS 1 51 312 26 048 9 843 1 00 16 00 ATO 4 CD2 HIS 1 51 797 26 043 7 286 1 00 16 00 ATO 5 CE1 HIS 49 691 26 152 6 454 1 00 17 00 ATO 6 CG HIS 50 958 26 068 8 340 1 00 16 00 ATOM 7 N HIS 49 668 24 248 10 436 1 00 25 00 ATOM 8 ND1 HIS 49 636 26 144 7 860 1 00 16 00 ATO 9 NE2 HIS 51 046 26 090 6 098 1 00 17 00 ATO 10 O HIS 1 48 241 26 524 11 749 1 00 16 00 ATO Lis SER 5 47 713 29 006 10 110 1 00 15 00 ATO 12 CA SER 5 49 138 29 147 10 620 1 00 15 00 ATO 13 CB SER 5 49 875 29 930 9 569 1 00 16 00 ATO 14 N SER 5 49 788 27 850 10 784 1 00 16 00 ATOM 15 10 SER 5 46 740 29 251 10 864 1 00 15 00 ATO 16 OG SER 5 49 145 31 057 9 176 1 00 19 00 ATO LF C GLN 3 45 406 27 172 8 963 1 00 14 00 ATO 18 CA GIN 3 46 287 28 193 8 308 1 00 14 00 Common Typos Another common error often arises in the data entry process Sometimes the letter l may be errone ously substituted for the number 1 This error has different repercussions depending upon what data field the error occurs in If the letter l appears in the residue number MIDAS does not complain but then the letter l rather than the number 1 must be used in all subsequent references to that residue This can be very confusing especially when all the other residues in the model
291. tem menu On a two button mouse like the NeXT s the original system menu functionality of the right button is lost and the right button acts just like the middle button on a three button mouse On the NeXT the right mouse button will not function unless the Menu Button has been enabled via the Preferences application Depressing and holding the left button controls model rotation While the button is held down a dashed blue circle is displayed on the screen Moving the mouse outside the circle results in model rotation about the z axis The area inside the circle is a virtual trackball when the mouse is within this area it grabs the trackball and rotates it The model rotates as if it were inside the trackball Once com fortable with this interaction method display of the dashed circle can be suppressed if desired by typing set showsphere The icon used for the mouse cursor changes when the left mouse button is depressed and also changes dependent on whether or not the mouse is inside or outside the trackball circle regardless of whether or not the actual circle is displayed Thus the mouse icon can be effectively used as a visual feedback clue to indicate the type of rotational motion currently in effect Depressing and holding the middle mouse button allows dragging the model s left right and up down In other words the middle button controls global translation of the selected model s Depr
292. that name 2 4 4 Align Usage align atom atom2 Align positions the model s containing the specified atoms such that the two atoms lie along the z axis at the center of the screen Atom2 is positioned in the front and atom is in the back See also reset push pop savepos window 2 4 5 Angle Usage angle angle_number atom1 atom2 atom3 atom4 Usage angle angle_number Angle monitors the angle in degrees between the three specified atoms If four atoms are specified the dihedral angle is monitored The atoms need not be connected and no diagnostic is given if the atoms are not connected Up to 16 angles 0 15 may be monitored simultaneously If the angle number is not specified MIDAS will assign one for you angle angle_number will remove the indicated angle monitor 2 4 6 Assign Usage assign slider_number function direction Usage assign slider_number Assign is used to activate control panel sliders Each slider s number is displayed just to the left or right of the slider itself on the control panel Usually only one slider may be assigned to any one function and reassignment of a function cancels the previous assignment This default action of canceling a previous assignment can be disabled via the unset reassign command see set unset UCSF MidasPlus 22 UCSF MidasPlus Function may be any of the following key words or the first two letters of the appropriate key word S
293. the main MIDAS window The Assignments area of the control panel contains a series of pseudo devices referred to as sliders for controlling various modeling interactions Each slider is numbered and may be assigned a function such as model rotation or translation clipping plane manipulation or bond rotation adjustment Some sliders are pre assigned with functions but can be reassigned as needed See the assign command in Part II for further details On non NexXT systems sliders are implemented as a series of four buttons for fast double arrow and slow sin gle arrow motion in the left right or near far directions Holding down the left mouse button over a slider button will cause motion appropriate to the slider label to occur continuously On NeXT systems sliders are represented with a grabbable bar that can be pulled to the left or right to control the rate of motion and that will snap back when released The bottom section of the control panel contains controls related to model selection On non NeXT sys tems this area contains a list of open models containing both the model number and file name from which the model was opened Highlighted models are selected for motion and will respond to textual motion commands as well as mouse directed movement Un highlighted unselected models will not Clicking on a model label will toggle the selection status When a new model is opened it is automatically selected The p
294. the mouse cursor on and off and quit The default display attributes for labels are as follows font Times Roman size 14 color white justification bottom left All these values may be changed via the defaults panel which is shown when the user selects the Show Defaults option from the right button menu When the mouse cursor is over the defaults panel the left mouse button is used to select the justification mode and label color the font size may be changed by typ ing the size and then RETURN no cursor is shown and new fonts may be selected from the right button menu Also colors may be selected from anywhere on the screen If the mouse button is depressed over the color selection area the mouse may be moved anywhere and a color will not be selected until the but ton is released SEE ALSO BUGS conic itops label3d snapshot Cannot display arrows AUTHOR Conrad Huang UCSF Computer Graphics Laboratory APPENDIX 6 131 UCSF MidasPlus ITOPS 1 ITOPS 1 NAME itops convert a SGI or TIFF image file to Color PostScript SYNOPSIS itops a b bits per color g gamma factor i 1 p page type q r s scale factor z 8 E S L label file image file DESCRIPTION itops converts an SGI RGB format or TIFF format image file to Color PostScript The output appears on standard output and would normally be piped directly to the pr 1 or Jp 1 command OPTIONS The I option lists
295. then the order is not specific and the models may not be superimposed in the way the user would expect Ordering may be forced by using the designation match 1 3 C1 C2 P O2 2 3 Cl C2 P 02 The RMS error value from the least squares fit is returned in the command reply area at the bottom of the MIDAS window The RMS error is only for those atoms named in the match command line since the models being matched may or may not have identical numbers of atoms 2 4 45 Matrixcopy Matrixget Matrixset Usage matrixcopy from_model to_model Usage matrixget filename Usage matrixset filename Matrixcopy makes the 4x4 transformation matrix of model to_model the same as that of model from_model UCSF MidasPlus 37 UCSF MidasPlus Matrixget prints the current 4x4 transformation matrices to a file named filename Matrixset reads matrices from the file named filename and sets the current transformation matrices using the same file format as matrixget See also cofr getcrd 2 4 46 Midasmovie Midasmovie is a delegate for displaying molecular dynamics trajectories written by David Konerding Midasmovie is not provided with the MidasPlus distribution but is available free via the web You can find information about the installation and use of midasmovie by pointing your favorite web browser at http picasso ucsf edu dek movie html 2 4 47 Midaspush Midaspop Usage midaspush Usage midaspop Midaspush pushes the MIDAS display windo
296. tice in the above example that the two atoms CA and N may be delimited by either a comma or the symbol In either case the preceding most recent molecule and residue information applies to the named atoms Using the notation specifies an ordering of the atoms and causes MIDAS to work on the named atoms in that order Using commas specifies a group of atoms in no particular order which allows MIDAS to work on them in whatever order is most efficient Thus in specifications where the order of the atoms is significant e g the match command the notation should be used For models and residues the same conventions are followed with replaced by or respectively For example for atoms on different residues but the same model 1 12 14 CA alpha carbons in residue 12 and residue 14 1 12 14 CA all atoms in residue 12 and alpha carbon in residue 14 1 12 20 CA 14 N alpha carbons in residues 12 through 20 and nitrogen in residue 14 LYS CA alpha carbons in all lysine residues In the example above the first statement gives two residues which make up a single residue specification Therefore the carbon atoms in both residues are selected In the second example the entire residue 12 and only the carbon in residue 14 are selected The residue sequence number has to be followed by the residue insertion code and the chain identifier in that order if they are presen
297. tion of the models is not changed If the image has drifted off the screen this is an excellent way of making it visible again If given an atom_specification as an argument window will recalculate the view to enclose just those atoms instead of all of the models See also align center push pop reset savepos UCSF MidasPlus 60 UCSF MidasPlus 2 4 98 Write Usage write surface relative n model_number filename relative n This command causes the specified model to be written out as a PDB file Current bond rotations must be fixed before the write if they are to be reflected in the written file The relative option specifies that the atomic coordinates written out are relative to the untransformed atomic coordinates of model n otherwise the coordinates are written as currently transformed This option may be specified in either of two places in the command line see usage above If a filename is not given then the file that the model was opened from will be overwritten If the surface option is given then the model s surface is written instead The surface is written in the format used by the dms program see Appendix 6 Note that the relative option is not supported for sur faces See also fix pdbrun save UCSF MidasPlus 61 UCSF MidasPlus This page intentionally left blank UCSF MidasPlus 62 UCSF MidasPlus Part III Advanced Concepts This section describes some additional features of MID
298. to save a bitmap image of the MIDAS screen to a file e g for image labeling We are aware of methods for bitmap grabbing only on SGI and NeXT systems On an SGI system the snapshot program can be used to capture all or part of the screen into an SGI image file Consult the snapshot manual page man snapshot for details Snapshot can be invoked from the UNIX command line or from within MIDAS with system snapshot On a NeXT system Grab app can be used to capture the contents of the MIDAS window into a TIFF file If you do not want the control panel in your MIDAS image the command set control will cause it to be undisplayed Similarly the command set text will cause the MIDAS command line and reply area to not be shown Ribbonjr Ribbonjr is capable of saving to a wide variety of formats Many of these formats e g inventor pov rayshade are simply input files for other renderers The only format which is really an image is tiff In order to save to TIFF you must give the command line option f tiff and append the name of a save file to the end of the ribbonjr command An additional complication is that when invoked from MIDAS the ribbonjr command actually runs a front end script that in turn runs the ribbonjr program This is so that the output of the midas and inventor formats can be captured and immediately displayed In order to use tiffformat you must circumvent the front end pdbrun surface usr local midas bin
299. to surface points and are calculated and incorporated into surface files by the esp utility program see Appendix 6 of this document for details 2 1 6 Atom Intersections Intersections of groups of atoms are handled with the amp operator For example one may want all atoms in model which are within 10 angstroms of model 0 UCSF MidasPlus 13 UCSF MidasPlus 1 amp 0 z lt 10 2 1 7 Atom Picking Atom picking allows a user to select atoms one at a time using the mouse instead of typing in the atom names on the keyboard This is useful for identifying atoms whose names are not known and for non typists An atom can be picked by pointing the cursor at it and then clicking the left or middle mouse button while the ALT SGI or Alternate NeXT or DEC Alpha key is depressed On non NexXT systems the cursor will change shape into a picking arrow while the picking key is being held down When the pick is made the corresponding atom specifier will be inserted in front of the command line cursor When picking atoms it may be necessary to rotate the molecule so that the desired atom is not obscured by other atoms or so that neighbor atoms are not picked by mistake The command may be edited at any point using the editing commands detailed in Appendix 3 The command is executed when the user hits the RETURN key 2 2 Command Overview MIDAS commands allow the user a variety of modes of execution The user may 1 T
300. tom and residue labels makemark destroy mark name mark remove mark name from atoms move stop an ongoing move operation objdisplay undisplay a graphics object open close a model pop equivalent to push push equivalent to pop rlabel don t display residue labels rock stop rock motion roll stop roll motion rotation remove a rotation savepos delete saved position scale stop ongoing scaling operation section stop an ongoing section operation select deselect a model set unset an option setcom use default center of mass show remove atoms from the display stereo equivalent to stereo off surface undisplay a solvent accessible surface thickness stop an ongoing thickness operation turn stop turn motion vdw remove a van der Waals surface display watch stop watch monitoring 20 UCSF MidasPlus MidasPlus Detailed Command Descriptions alphabetical order 2 4 1 Addaa Usage addaa residue_type residue_sequence conformation residue Addaa adds an amino acid of type residue_type with sequence number residue_sequence in the specified conformation after the specified residue Conformation may be one of EXT extended default ALPHA alpha helix PBETA parallel beta sheet ABETA antiparallel beta sheet Residue must be the last residue of a chain The temperature factor for the new residue is set to the highest currently fo
301. tor is 1 5 L x y Specify the window location when output format is screen or tiff 0 0 is the lower left corner If no location is specified the user gets to choose the screen location using the mouse when the win dow is created N Show normals if output is in midas format O radius Specify the radius of cylinders in angstroms used to render MIDAS graphics objects see the o flag P polygon_option Display special polygons in addition to atoms bonds and ribbons Currently two types of special polygons are supported na_base and na_sugar The na_base polygons are polygons drawn above and below the rings of the bases in nucleotides When this option is selected the atoms in the rings are automatically constrained to lie in a plane in order to avoid nonplanar ring surfaces The colors of the polygons are the same as the colors of the N1 and N9 atoms The na_sugar polygons are polygons drawn around the sugar rings in nucleotides Because the five membered sugar rings are nonplanar each ring is covered by three triangles on either side All three triangles have as one vertex the oxygen atom in the sugar The oxygen can be highlighted further by artificially increasing its radius see J above The polygon color is the same as that of atom Cl R spline type Ribbonjr constructs ribbons using splines that pass near or through control points whose coordi nates are based on the positions of guide atoms Different types of spline
302. trigonal bipyramids while 5 and 1 yields pen tagonal bipyramids This is most useful for distinguishing data points from different data files all data points from a given data file are displayed using the same ellipsoid representation The first application of discern was to display a set of points with both a calculated and an estimated poten tial The ellipsoids were colored from blue to red corresponding to the calculated potential values The sizes and axes lengths of the ellipsoids were proportional to the difference squared and ratio of the calcu lated and estimated potential values respectively This display clearly showed the potential form and highlighted the areas where the estimated and calculated values differed significantly In addition it also showed whether the estimated value was too low or too high The discern commands for setting up this display are given in the EXAMPLES section below Discern is a program designed to run in conjunction with MIDAS using the MidasPlus delegate mechanism The standard way that discern is invoked is for the user to start a MIDAS session and issue the MIDAS command delegate start disc discern which runs discern and tells MIDAS to pass commands beginning with disc through to discern for further processing The commands that discern can handle are described below COMMANDS When discern is acting as a delegate for MIDAS as above the user can give it commands by typing disc discern_command
303. uces the correct connectivity If however it consistently produces incorrect connectivity for a particular residue the user may override the algorithm with a template MIDAS uses files called templates to form the connectivity of atoms Each template consists of a map which describes how the atoms are connected and which atoms link the residue to other residues This includes the following information 1 the residue name 2 the starting atom of the residue important for connecting this residue to the previous one 3 the ending atom of the residue important for connecting this residue to the next residue and 4 connections between atoms in the residue Template file names must be the same as the corresponding residue name and have a ins extension It is the template file that is used to determine the connectivity and atom naming information when reading in PDB files The following example is a template instruction file for glycine RESIDUE GLY START N DRAW CA DRAW C DRAW O MOVE C DRAW OXT END C Notice that 1 The residue has a name GLY a starting atom N and an ending atom C Thus if GLY were found in a chain of amino acids this residue would be connected to the previous residue in the chain via atom N and to the next residue in the chain via atom C UCSF MidasPlus 77 UCSF MidasPlus 2 If you follow the DRAW and MOVE instructions on paper with a pencil starting at N draw a bond to CA draw
304. ue_type residue Both the old and new residue must be stan dard nucleotides A T G C or U New_residue_type is a one letter nucleotide code residue is a single resi due indicated by unique name e g G or number e g 24 The temperature factor for the new residue is set to the highest currently found in the model The keyword preserve is recognized although it currently does not affect swapna behavior in any way 2 4 88 System Usage system command System executes the UNIX command under the user s preferred shell Command may not be an interactive program The output from command will appear in the MIDAS reply area In the IRIS GL version of MIDAS the reply area isn t scrollable so it may be desirable to show long replies in the shell window instead of the reply area To do so the user should give the command command oy note mark instead of system command As an alternative to the system command the midaspush command may be used to access other screen windows or icons i e go off and do something else for awhile and then return to MIDAS If MIDAS was started in its own window the standard window manipulation menu may also be use for this purpose Lastly one could also use the save command to retain orientations rotation and slider assignments etc and then quit MIDAS entirely and return later for another modeling session See also run pdbrun midaspush save 2 4 89 Thickness Usage thic
305. ues with Midas 0 cc cecsscssseceeeceeceeeseeseceeceeeseaecaseeesaeeaeeereeeeaens 85 Issues Common to All Platforms 0 eee ee ceeeseecseenseceeceneceeeeeerensees 85 Competing with Background Jobs o0 eee eee cee eeeeeseeeeeeeees 85 SGI Specific Performance Issues cesseescescseeseeeeceeceseeceaecsseeceeesaeeees 85 Appendix 1 Pdbrun Format USER Records 0 ceceseceeeeseeeeeeeeeeeseseeeseesaecaecsaeeaes 87 Appendix 2 PDB Atom Naming Conventions for Amino Acids oc eseeeeseereeeeeeeeeeeers 92 Appendix 3 Special Characters and Symbols Used in MIDAS o oo eeeeeeseeceeneeeees 93 Appendix 4 Default Options Aliases and Device Assignments 0 ce eee esses cre eeeeeeee 95 Appendix 5 The MidasPlus Delegate Mechanism 000 0 c ee eeeecceeseeseeeeeeeeeseeeneeseeeaeenaeeaes 97 Appendix 6 MidasPlus Program Suite occ ceeeseceseeseceeceseceeeeseeeeeeseseaseseeeaeesaecaeenaeeaes 102 User Contributed Software ee cee eeeeceeceseceseeeeecseeeeecaeesaecaaesaecsecsaeceeseeeeeesees 103 Mamnial Pages i 5 sscsiseeuacbscdisgescesag eE a EE EEEo EE ES EEEE AE Ees 104 iv BS 1 BS 1 NAME bs generate ball and stick style diagram in PostScript SYNOPSIS bs b ball_fraction e m margin s stick_fraction fill_type PDBRUN file DESCRIPTION Bs takes a PDB file as output by the midas pdbrun command with the conect keyword argument and generates a ball and stick image of the atoms a
306. uide atoms are translated by a short distance away from the helical axis When using other types of splines the helices are not as compressed as using B splines The default extension depends on the type of spline used to produce the ribbon see R flag below The default extension is 1 5 angstrom for B splines and 0 5 angstroms for all other types F Use full screen mode Set the image size to use the entire screen G guide fraction When ribbonjr constructs the ribbon representation it uses the guide atom coordinates as the basis of its control points one per residue For each residue the control point is between its guide atom APPENDIX 6 173 UCSF MidasPlus RIBBONJR 1 RIBBONJR 1 and the guide atom of the following residue Normally the control point is exactly halfway between the two guide atoms guide fraction 0 5 This option is most useful when the ribbon must go through the guide atoms In this case the guide fraction should be set to zero the helix extension see E flag above should be set to zero and an interpolating spline type see R flag below should be selected H red green blue Set the helix color in color scheme structure The default helix color is 1 0 0 Use of this flag implicitly sets color scheme to structure see the c flag J scale_factor When using the na_sugar option see P below the oxygen atom in the sugar ring is artificially enlarged by scale_factor The default scale fac
307. umber Open causes the contents of the file filename to be read and shown as model model_number if model_number is omitted the lowest available model number is used The model number is used to uniquely reference the model in subsequent commands and therefore should be remembered The optional original keyword is used to prevent MIDAS from transforming the coordinates of the model or object that is being opened original has no effect on surfaces Normally if the display option refmodel s value is set to a model number newly opened objects and models are transformed by the same rotations and translations in effect for that model number see set unset The use of the original keyword prevents the application of these transformations to the newly opened model This keyword is normally only of interest to implementors of MidasPlus delegates How MIDAS interprets filename is controlled by the optional keyword specifier If no keyword is given or the keyword model is specified MIDAS will try to open the filename as a PDB file Note that MIDAS only recognizes PDB version records If your file contains PDB version 2 records MIDAS will note them as unknown records in the reply area and otherwise ignore them The following keywords can be shortened to as few letters as necessary to disambiguate them from other keywords Note that the original keyword above cannot be shortened The ms or surface keywords indicate that filename is the output of the
308. un2ses reads a PDBRUN file a Protein Data Bank file with additional USER records normally generated by the pdbrun command in MIDAS and converts it into a MIDAS session The i argument specifies the input PDBRUN file If no input file is given run2ses will read from standard input The o argument specifies the output session name SEE ALSO Midas User s Manual Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description FILES session Component files of the MIDAS session BUGS Silently ignores PDBRUN graphics types that MIDAS doesn t understand AUTHOR Conrad Huang Computer Graphics Laboratory University of California San Francisco APPENDIX 6 177 UCSF MidasPlus STEREOIMG 1 STEREOIMG 1 NAME stereoimg produce stereo pair of rendered molecule MIDAS COMMAND SYNTAX Command stereoimg p renderer c t s v o outfile C renderer_options DESCRIPTION Stereoimg takes the molecule s being displayed in MIDAS and creates a walleye stereo image pair using the specified renderer which must be either ribbonjr conic or neon By default the image is stored in a file called stereoimg tiff and can be displayed with the program imgview The options flags have the following meanings c Generate a crosseye stereo pair instead of walleye t Normally stereoimg fits each half of the stereo pair into a half screen by expanding one dimension of the original MIDA
309. und in the model Example addaa tyr 30 0 29 Add tyr as residue 30 after residue 0 29 2 4 2 Addgrp Usage addgrp group bond_length bond_angle dihedral_angle new_residue_name atom1 atom2 atom3 Addgrp adds a new chemical group whose position is determined by the three specified atoms The parameters required are the group name which corresponds to a file in a directory see below the bond_length from atom to the first atom of the added group and the bond_angle formed by the group being added atom and atom2 Dihedral_angle formed by the added group atom1 atom2 and atom3 must be a positive value between 0 and 360 inclusive It defaults to 0 New_residue_name defaults to the old residue name Group files are searched for in HOME groups user s groups gt and usr local midas resource midas groups system groups in that order The user should check the system groups directory to deter mine if a description of the group he she wishes to add exists and if so what the file name is If there is no system file for the group the user may create one and place it in his her personal groups directory The easi est way to create a group file is to use the pdb2group utility see Appendix 6 provided that the user has some PDB file containing the chemical group Otherwise the group description will have to be created by hand The procedure for doing so is described in Chemical Group Description Files in Par
310. until all model movement has ceased In the latter case if a command such as roll has been activated for a given number of frames that motion is completed before the next command is executed The wait may be interrupted by pressing the ESC key This breaks out of wait but does not freeze the screen i e any active motion continues until completion See also sleep 2 4 96 Watch Watchopt Usage watch atom_specification Usage watch Usage watchopt distance distance Watch monitors interatomic distances By default it checks for distances less than the sum of the van der Waals radii of two atoms Atoms in the atom_specification are checked against all other atoms to whom their distance can potentially vary i e to atoms on other models or atoms on the same model across from active bond rotations Close contacts are displayed as yellow dotted lines in the same manner as distance monitors One can specify a fixed distance by using the distance option to the watchopt command where distance is in angstroms A distance of zero means to use the default vdw radii for comparison Only dis tances that potentially vary are checked i e atoms that are fixed relative to each other are not checked watch will terminate watch monitoring See also distance 2 4 97 Window Usage window atom_specification With no arguments window puts all displayed models on the screen by changing the scale and position of the view The orienta
311. up are implicitly numbered in ascending order starting from zero So the atom men tioned in line 2 would be numbered 0 the atom in line 3 would be 1 etc The three atoms given on the addgrp command line are referred to as n3 n2 and n1 from left to right on the addgrp command line The information provided on the addgrp command line completely determines the position of the first atom of the group atom 0 line 2 so there is no corresponding position information line for it in the group file The first position information line line 70 provides information to position atom 1 line 3 The fields of a position information line reading from left to right are a or character four atom designators a bond length a bond angle and a dihedral angle The or character is required to be present for historical reasons but is otherwise ignored The four atom designators that follow indicate from left to right the atom being positioned an atom to which the first is connected an atom that forms a bond angle with the first two and an atom that forms a dihedral with the first three The trailing three fields provide the actual values of the bond length bond angle and dihedral Each positioning line causes MIDAS to draw a corresponding bond If there are more bonds in the group than there are atoms if a ring is present for example then additional positioning lines need to be provided for the additional b
312. urfaces were already com puted when the interrupt occurred will have their surfaces displayed Since computing the vdw surface is much faster than displaying it pressing the ESC key might not help Note that the default vdw radii used by MIDAS assume that no explicit hydrogens are present in the model s This behavior can be changed with the vdwopt command Details of the vdw algorithm can be found in the Bash et al reference given in full on page 3 of this manual See also makems surface vdwopt UCSF MidasPlus 58 UCSF MidasPlus 2 4 93 Vdwopt Usage vdwopt density value radii file hydrogen default extend len define atom_type radius Vdwopt sets user options for displaying van der Waals surfaces The options are as follows density value The user may change the dot density of the displayed surface relative to the initial value of 1 which corresponds to 5 dots per square angstrom The density of dots varies linearly with the value provided Thus a density value of 2 gives 10 dots per square angstrom radii file Indicates a file containing alternate van der Waals radii The alternate file must contain a complete set of radii for all atoms in the model The file contains a series of records consisting of an atom name character string followed by a space and the atom radius in angstroms floating point number This is the same format as used by the ms program see Appen dix 6 Optionally a third field can specify the
313. us 82 UCSF MidasPlus b when using ASA 100 film Fstop 2 8 c when using ASA 100 film Fstop 4 0 d when using ASA 100 film Fstop 5 6 3 9 Non Molecular Graphics Objects In addition to displaying molecular structures from PDB file information MIDAS can display graphics objects of arbitrary connectivity from instructions in a simple command file Graphics objects can be colored on a line by line basis and given textual labels in a variety of fonts and colors Graphics objects are frequently useful for writers of delegate programs that need to represent graphical information not directly supported by MIDAS User manipulation of graphics objects can be made to occur in synchrony with a particular molecular model or independently A graphics object command file consists of one or more lines of the following Explanatory comments not displayed comment text comments text comments Drawing related commands color color_designation set color see below mxy z move to location move x y z move to location dxy z draw line from last location draw x y z draw line from last location dot xy z show dot at position marker x y z show marker at position Labeling related commands color color_designation set color see below font name size set font and size cmov x y z set character position label_text label note no initial The color_designation parameter to the color directive can be simply a singl
314. ut PDB file If no output file is given unmtrix will write to stan dard output Normally unmtrix will generate coordinates for all MTRIX records which do not have atoms associated with them When given the m argument unmtrix will generate coordinates only for the MTRIX records that match the given MTRIX_serial_id EXAMPLES Since MTRIX records contain a 3x3 rotation matrix as well as a 3x1 translation vector the records are always given in groups of three like this MTRIX1 1 0 725530 0 071920 0 684420 68 86822 al 1RSL 138 MTRIX2 1 0 000100 0 994540 0 104400 81 59939 1 1RSL 139 MTRIX3 1 0 688190 0 075680 0 721570 32 52771 1 1RSL 140 The second column is a serial number for the three record group If additional MTRIX records were neces sary for additional subunits each triplet would have a unique serial number The third through fifth columns contain the rotation matrix The sixth column is the translation vector The seventh column indi cates whether the coordinates generatable with these records are already present in the PDB file If there is a 1 in the seventh column the coordinates are present in the entry If the column is blank the coordi nates are absent The trailing columns are record serial number information found on all PDB records The above MTRIX records would be for a subunit whose coordinates are already present in the PDB entry indicated by the 1 in the seventh column Unmtrix will a
315. vailable on your machine as well as each option s current setting The NeXT version does not have any device options The SGI Iris GL graphics library version older SGI hardware has a few options see the last section below All of the X Motif OpenGL versions SGI DEC UNIX IBM AIX PC Linux others support the rest X windows related xlocations Report locations of graphics window and auxiliary windows in a form suitable for a Xdefaults file move_windows on off Turn on and off the moving of auxiliary windows command panel and control panel when the graphics window is moved win_placement shell frame The move_windows code needs to know how the window manager places windows One of these will be better than the other You need to move the graphics windows after changing this option to see what effect it has spaceball_axes world mouse 6D input devices 3D rotation and 3D translation such as the Logitech Magellan or the Spacetec IMC SpaceBall can have their axes interpreted like the mouse motion perpendicular to screen or like the real world up is up assuming that the computer monitor screen is perpendicular to the desktop and that the input device is parallel to the desktop UCSF MidasPlus 30 UCSF MidasPlus Stereo related See the MidasPlus Installation Guide for a more involved discussion of these choices MIDAS only supports hardware stereo on DEC s and SGI s switch_stereo on off Control whether
316. vel at which contouring takes place If the level is outside the range of values found in the GRID file no contouring takes place The user can prompt for these maximum and minimum values with the max and min commands see below The default value for contour_level is 5 max label model_number The max command returns the maximum energy value found in the GRID file When a label parameter is provided this label will be displayed as model model_number at the position of max imum energy When no model_number is provided the lowest available model number will be used No default value is provided for label so plotting will not occur by default min label model_number The min command returns the minimum energy value found in the GRID file When a label parameter is provided this label will be displayed as model model_number at the position of minimum energy When no model_number is provided the lowest available model number will be used No default value is provided for label so plotting will not occur by default show_box model_number This command displays the boundaries of the GRID box as defined in the GRID file If no APPENDIX 6 126 UCSF MidasPlus GD 1 GD 1 model_number is defined the lowest available model number will be used gridkont file_name File_name is the name of the unformatted three dimensional energy file produced by GRID The default value for file_name is gridkont dat status The statu
317. ves corresponding to the edges of a fixed width flat ribbon and regularly spaced line segments con necting the curves The default representation is 3D n Do not draw a border around the image 0o Do not display any MIDAS graphics objects present in the input By default MIDAS objects are displayed The lines composing the object are rendered in ribbonjr as cylinders with half spheres capping the ends By default these cylinders have an extremely small radius so that they look like lines The cylinder radius can be controlled with the O flag p When output is in screen or tiff format do not wait for the user to click the mouse button By default the user must click the left mouse button before the ribbonjr window is closed r level Sets the refinement level to level The refinement level affects the output quality from ribbonjr The level ranges from 0 to 10 with the default being 0 The higher the level number the better the quality Levels greater than zero increase the sphere subdivision and levels greater than 5 cause the image to be antialiased using the accumulation buffer as well In the process of using the accumulation buffer the image will be drawn to the screen several times before the final image is displayed s count Select the number of segments used to represent one residue By default the ribbon for a residue APPENDIX 6 172 UCSF MidasPlus RIBBONJR 1 RIBBONJR 1 is divided into 10 segments Fo
318. w and selection buttons By clicking on the Sliders button the control panel will switch to showing sliders equivalent to the Assignments area of the OpenGL interface Selecting Sideview will switch back The selection buttons show only the model number not the associated file name If desired it is possible to over ride the use of the OpenGL version of MIDAS in favor of the IRIS GL version and vice versa Consult the SGI Specific Performance Issues section in Part III of this manual for details UCSF MidasPlus 5 UCSF MidasPlus Once the Command prompt appears characters typed on the keyboard are interpreted directly as commands to MIDAS You can type commands even if your mouse is in the main window rather than the command reply window The first step in displaying a model is to open the model If the name of the PDB file is gcn the command used to open the model is open 0 1gcn The model name may also be a pathname to a model in another directory The 0 zero in the above example is the optional model number If the model number is left out then the smallest unused non negative model number is used 1 2 Manipulating the Model After execution of the open command completes the model should appear in the main window On a three button mouse the left and middle mouse buttons allow direct manipulation of the selected model s and the right button calls up a sys
319. w behind all other screen windows and icons These win dows and icons can then be used normally Midaspop brings MIDAS back to the top Make sure that the mouse cursor is over the MIDAS window when midaspop is typed because MIDAS will not receive keys trokes typed with the mouse cursor positioned over other screen windows If you accidentally type with the mouse incorrectly positioned erase your input in the other window then move the mouse over the MIDAS window and type midaspop Note that if MIDAS is not using the full screen and therefore has a window frame around it it is possi ble to use the standard mouse techniques for pushing and popping windows Also on non NeXT systems clicking the right mouse button while holding down the ALT key will bring up a window manipulation menu when done over the MIDAS window 2 4 48 Move Usage move axis units frames wait_frames Usage move axis The move command translates the selected molecule s along the specified axis Axis may be x y or z Units is a floating point number in angstroms A positive value for units indicates translation to the right up or toward the user for the x y and z axes respectively Frames moves the models in the specified manner for the specified number of image update frames Wait_frames if specified indicates the number of frames to wait before beginning the move move will halt an ongoing move Frames and wait_frames default to 1 and 0 respectively T
320. way to determine the correct value is to enter stereo mode without putting on the stereo glasses There should be two overlapped images on the screen displaced slightly horizontally If the value of vpsep is correct the images should be aligned vertically If they are not aligned adjust the value of vpsep un til they are you can type set vpsep to determine the current vpsep value walleye_scale Scales the size of walleye type stereo image pairs see stereo command The default size is correct when using opticomechanical stereo viewers while a larger scale is useful for taking pictures for publications UCSF MidasPlus 53 UCSF MidasPlus 2 4 77 Setcom Usage setcom model x_coord y_coord z_coord radius natoms Usage setcom model When MIDAS is asked to rotate one or more models it needs to know the center of mass of the model s Setcom is used to change the center of mass parameters in the rare case where the ones automati cally computed by MIDAS are unacceptable X_coord y_coord and z_coord specify the new center of mass for model If radius is given it should be the shortest radius in angstroms from the new center of mass that encloses the model This helps MIDAS do a better job of framing the models in the graphics window Specifying natoms essentially tells MIDAS how much weight this model has when computing a combined center of mass for multiple models setcom will cause MID
321. y Structure Display Proteins For some PDB files ribbonjr will display the entire structure as random coil with no sheets or helices even though such structure motifs clearly exist There are two common causes for this phenomenon The first is that there are no HELIX or SHEET records in the PDB file MIDAS and ribbonjr both depend on these records to demarcate regions of secondary structure If they are missing these records need to be generated and inserted into the PDB file The MidasPlus utility ksdssp can be used to generate HELIX and SHEET records Ksdssp is fully described in Appendix 6 of this document Also the MIDAS ksdssp command will invoke the ksdssp utility from within MIDAS and apply the generated secondary structure records to the displayed structures T The second common cause of missing secondary structure is incorrectly aligned atom names in PDB records As described in section 3 4 1 of this document atom names are composed of an atomic symbol such as C right justified in columns 13 14 of ATOM and HETATM records and trailing identifying char acters such as A left justified in columns 15 16 Many programs simply left justify the entire atom name starting in column 13 The difference can be seen clearly in a short segment of hemoglobin UCSF MidasPlus 74 UCSF MidasPlus correct HETATM 976 FE HEM 1 12 763 34 157 9 102 1 00 0 00 HETATM 977
322. ype in commands at the graphics system keyboard 2 Set up a command file named midasrc which is automatically read each time MIDAS is executed 3 Set up a command file which can be executed via the source or read commands 4 Control movements via the mouse or auxiliary devices such as a joystick or Spaceball Commands which are typed in at the graphics system keyboard are echoed in the reply area Replies gen erated by MIDAS appear after the echoed command and are prepended with a gt There may be several lines of reply messages For example assign 0 clipping gt Clipping plane is missing gt Usage assign slider_num function direction appears in the reply area when the user inadvertently forgets to supply the required clipping plane argument to the assign command 2 3 MIDAS Start Up The directory usr local midas bin must be on your execution path for the midas command to be found You can put the following line in your cshrc file in your home directory to add the directory to your path set path usr local midas bin path The above would take effect upon your next login To have an immediate effect just type the above line at your shell prompt The MIDAS commands in the start up file midasrc are executed each time MIDAS is executed There is also a general system start up file and host specific start up file executed each time MIDAS runs These are located in usr local midas res

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