Home

VMD User's Guide

1. align lt matrix gt In case the molecule was aligned you can supply the alignment matrix which is then used to correct for the rotation and shift of the pbc cell 116 boundingbox PBC lt mincoord gt lt maxcoord gt With this option the atoms are wrapped into a rectangular bounding box If you provide PBC as an argument then the bound ing box encloses the PBC box but then the cutoff is added to the bounding box Negative values for the cutoff dimensions are allowed and lead to a smaller box Instead you can also provide a custom bounding box in form of the minmax coordinates list contain ing two coordinate vectors such as returned by the measure minmax command Here again the cutoff is added to the bounding box e inertia selection moments eigenvals Returns the center of mass and the principles axes of inertia for the selected atoms If moments is set then the moments of inertia tensor are also returned With option eigenvals the corresponding eigenvalues will be returned too If both flags are set then the eigenvalues will be listed after the moments e symmetry selection plane I Cn Sn vector tol value nobonds verbose level This function evaluates the molecular symmetry of an atom selection The underlying algorithm finds the symmetry elements such as inversion center mirror planes rotary axes and rotary reflections Based on the found symmetry elements it guesses the underlying point group The gue
2. Atom hot key 5 In this mode the position of an atom can be changed by clicking on the desired atom and dragging with the mouse while the button is still pressed This will change the atom coordinates Move Residue hot key 6 This mode may be used to move all the atoms in a selected residue at the same time Select an atom in a residue and move it to a new position while keeping the mouse button pressed All the atoms in the same residue as the selected one will be moved the same amount Holding down the shift key and the left mouse button while moving the mouse will rotate the atoms in the residue about the selected atom If the middle mouse button is held down instead the atoms in the residue will rotate about a line drawn through the picked atom and parallel to a line coming directly out of the screen This behavior is similar to the usual Rotate mode except that coordinates of atoms are changed Move gt Fragment hot key 7 A fragment is a set of atoms all connected by a series of covalent bonds This mode acts just like MoveResidue except that the atoms which are moved are all in the selected fragment rather than in the selected residue This will change the atom coordinates Holding down the jshift key and the left mouse button while moving the mouse will rotate the atoms in the fragment about the selected atom If the middle mouse button is held down instead the atoms in the fragment will rotate about a line
3. Ribbons 6 1 12 option which draw the ribbon with an oscillation along the sheet The other conformations are drawn as a tube Since the endpoints of the helix cylinder and cartoon sheet are not at the Ca coordinate the tube method was slightly changed to make the tube go to the new locations This does not always work resulting in a tube which does not quite connect to a cylinder 65 6 1 15 NewCartoon The NewCartoon representation is a variation of the original Cartoon combined with the NewRib bons representation look and features The main difference between the original Cartoon repre sentation and NewCartoon is that helices are left in a ribbon representation which follows curved structures much more accurately than the straight cylinders used in the original Cartoon did The Aspect Ratio parameter controls the width of the ribbon relative to the thickness value as a multiplicative factor An aspect ratio of 1 0 yields a Tube like representation The Resolution parameter controls the degree to which the ribbon surface is tesselated with triangles Higher settings yield nicer looking images at the expense of interactive rendering performance Points can be interpolated with either a Catmull Rom or B Spline by changing the value of Spline Style Note that the B Spline does not always pass through the Ca positions as it is a smoother spline 6 1 16 PaperChain The PaperChain representati
4. Some of the rendering commands have been set to call a display program on the rendered image when it is completed VMD will wait for the display program to finish which causes VMD to freeze until the display program closes so you may want to run the job in the background This can be ol done on Unix by enclosing the existing text with O s and putting an amp at the end For example the way to make the Raster3D render command run in the background is render lt s sgi 4s rgb ipaste s rgb 4 5 4 12 Tool Window Tool Controls X r Tools r Tool devices Create tool grab Position SpaceballTracker y Set tool type grab v Buttons SpaceballButtons y Delete tool Force Feedback None y Position Force Assigned Rep Selected molecule Apply force to picked atom 1 1e79 v O Apply force to molecule rep Selected rep fo all y Figure 5 12 The Tool window The Tool window is used to set up external 3D pointers buttons force feedback devices and the VMD tools that they control VMD communicates with input devices through CAVElib Free VR or via Virtual Reality Peripheral Network VRPN or with direct operating system interfaces Since VRPN provides networked device abstraction VMD doesn t have to be running on the same computer that VRPN devices are attached to With VRPN you may use buttons trackers and also force feedback haptic devices such as the PHA
5. vecscale c v e C vecscale v c Returns the vector of the scalar value c applied to each term of v Examples vmd gt vecscale 2 1 2 3 0 2 0 4 0 6 vmd gt vecscale 5 4 3 2 2 10 8 6 4 vmd gt vecscale 2 3 6 e vecdot v1 v2 Returns the scalar dot product of the two vectors 162 Examples vmd gt vecdot 1 2 3 4 5 6 12 vmd gt vecdot 3 4 3 4 25 vmd gt vecdot 1 2 3 4 5 5 4 3 2 1 35 vmd gt vecdot 3 2 6 veccross vi v2 Returns the vector cross product of the two vectors Examples vmd gt veccross 1 0 0 0 1 0 001 vmd gt veccross 2 2 2 1 0 0 0 2 2 veclength v Returns the scalar length of v jvl Examples vmd gt veclength 5 5 0 vmd gt veclength 5 12 13 0 vmd gt veclength 3 4 12 13 0 vmd gt veclength 1 2 3 4 5 47723 veclength2 v Returns the square of the scalar length of v u 1 Examples vmd gt veclength2 5 25 vmd gt veclength2 5 12 169 vmd gt veclength2 3 4 12 169 vmd gt veclength2 1 2 3 4 30 vecnorm v Returns the vector of length 1 directed along v Examples vmd gt vecnorm 10 1 0 163 vmd gt vecnorm 1 1 0 707109 0 707109 vmd gt vecnorm 2 3 1 0 534522 0 801783 0 267261 vmd gt vecnorm 2 2 2 2 2 2 0 408248 0 408248 0 408248 0 408248 0 408248 0 408248 e vecdist vi v2 Returns the distance between the two vectors v2 v1 Exampl
6. 37 described in Chapter 4 If VMD is unable to guess the appropriate file type or guesses incorrectly you must select it from the list manually You can control into which VMD molecule you want to load your data by selecting it from the Load files for popup menu at the top of the window If the file being loaded is intended for a new molecule select New Molecule instead If the file being loaded contains additional coordinate frames electron density map or other ancillary data for an existing molecule choose the appropriate molecule from the selection list at the top of the window If the file being loaded contains trajectory frames you have the option of loading a subset of the trajectory skipping ranges or strides of frames rather than the whole thing You can also select for VMD to load all frames before continuing on or to load them in the background so that you may continue to interact with the menus and windows while it loads additional frames If the file being loaded contains multiple volumetric data you may select which data sets you would like to load Once you have selected the file to be loaded the appropriate file type and the way it will be loaded press the Load button and VMD will being loading the selected file Any informational messages errors or warnings which occur while loading the file will appear in the text window Reading Trajectory Frames VMD can read in new coordinate sets from one of several file formats
7. Molecular Drawing Methods Each molecule in VMD is drawn as a collection of several representations of the molecule A repre sentation is just one particular way of drawing the molecule and consists of several characteristics e An atom selection which determines which of the atoms in the molecule will be included in the view This selection is entered in the text input field at the bottom of the Graphics window Atom selections don t apply when drawing volumetric data such as an electron density map electrostatic potential map etc Section 6 3 describes the syntax used to select atoms e A drawing method representation style which determines what shape to draw the atoms bonds and other components of the molecule Section 6 1 describes the rendering methods available in VMD e A coloring method which determines how to color each of the atoms and bonds included in the view The Graphics window contains controls to set the coloring method at the right of the window Section 6 2 describes VMD s coloring methods e A material which determines the shininess opacity and other lighting and shading charac teristics used when rendering the molecule A molecule can contain any number of different representations and complex pictures of the molecule can be generated by creating views with different selections coloring schemes and ren dering methods For example the protein backbone can be drawn as a smooth tube in one view and i
8. VMD User s Guide Version 1 9 1 January 29 2012 NIH Resource for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois at Urbana Champaign 405 N Mathews Urbana IL 61801 http www ks uiuc edu Research vmd Description The VMD User s Guide describes how to run and use the molecular visualization and analysis program VMD This guide documents the user interfaces displaying and grapically manipulating molecules and describes how to use the scripting interfaces for analysis and to customize the behavior of VMD VMD development is supported by the National Institutes of Health grant P41 RR005969 http www ks uiuc edu Contents Introduction 1 1 Contacting the authors e 1 2 Registering VMD 222 00 ok eRe A a A e a 1 3 Citation Referenc jvc al a A A RE 14 Acknowledgments 02 03 40 9 wee oe RA a a a ae OS 1 5 Copyright and Disclaimer Notices 2 0 0 0 0 00000 eee ee eee 1 6 For information on our other software 2 0 ee Hardware and Software Requirements 2 1 Basic Hardware and Software Requirements 2 2 00004 2 2 Multi core CPUs and GPU Acceleration 2 a a Tutorials 3 1 Rapid Introduction to VMD e 3 2 Viewing a molecule Myoglobin 000002 eee eee 3 3 Rendering an Image 2 ee 3 4 A Quick Animation 2
9. You can also use this in combination with the molecule file browser as a way to make PDB files from a DCD CRD trajectory You can either save the entire stored trajectory or a slice of the data by using the Amount chooser 5 4 4 Then select the appropriate output file type in the File Type chooser and press the Save button in the bottom right corner This brings up the file browser which you can use to enter the new filename Once you press the Save button in the browser the file will be written without further confirmation See the section on the atomselect writexxx 9 3 2 command for information on how to write atom coordinates for an atom selection in a PDB file Deleting Trajectory Frames You can delete frames from memory through a dialog box To bring it up start by selecting a molecule and choosing the Delete Frames from the Molecule menu or by double clicking on the 35 Frames column for that molecule in the Molecule Browser On this is done choose the range of frames you wish to delete with the First and Last controls and then press the Delete button There is no confirmation of deletions The Stride control allows you to keep some frames in the range using the specified interval For example if your range contains 10 frames labeled 0 through 9 and you use a stride of 4 the frames numbered 0 4 and 8 will be kept A stride of 0 zero implies that all frames will be deleted Deleting a Molecule The Delete Mole
10. text string size s thickness 1 Displays the text string with the bottom left of the string starting at the given coordinates with the font size scaled by the optional size parameter and drawn with line thickness deter mined by the optional thickness parameter color colorld color name color trans_name Each of the above geometrical objects are drawn using the current color Initially that color is blue which has the colorid of 0 The color command changes the current color and stays info effect until the next color command Thus to draw a red cylinder then a red sphere first use the command color red command to change the color then use the cylinder and sphere commands materials lt on off gt Material properties are used to make the graphical objects lines cylinders etc be affected by the light sources These make the objects look more realistic but are slower on machines which don t implement materials in hardware see chapter 6 2 and sections on color 9 3 4 and colorinfo 9 3 5 commands for the information on how to turn off material characteristics for all objects in VMD One surprising effect of material characteristics is that lines are affected In some lighting situations the lines can even appear to disappear Thus you may want to turn off materials before drawing lines material lt name gt Sets the material to use for the corresponding graphics molecule name must be a valid material name as dis
11. viewpoint 169 vmd state 22 RMS Fit 178 RMS Alignment 178 RMSD 141 144 177 180 181 rock 37 command 97 127 rotate command 97 127 side chain 174 rotation continuous 28 hot keys 32 stop 28 using mouse 28 save configuration 22 logfile 22 viewpoint 169 vmd state 22 160 scale command 97 127 scaling using mouse 28 screen parameters 42 scripts play 95 source 95 secondary structure codes 57 selection 18 20 42 60 98 121 170 comparison 79 keywords 45 75 82 boolean 77 logic 77 math functions 84 modes 75 text 170 volumetric data 84 sensor configuration file 52 sensors 52 sequence 56 caveats 58 dna 56 window 56 zooming 57 short circuit logic 77 80 sleep command 97 135 source command 95 spaceball driver 12 31 MacOS X 31 Unix 31 Windows 31 modes 31 using 31 stage 41 command 97 127 startup files 30 187 190 stereo mode 87 checkerboard 88 column interleaved 88 cross eyed 87 CrystalEyes 87 DTI side by side 88 Quad buffered 87 row interleaved 88 scanline interleaved 88 side by side 87 off 86 parameters 41 89 103 104 stop rotation 40 stride 13 surf 13 surface molecular 70 solvent accessible 70 Tachyon 14 Tcl 96 199 tcl commands 96 text displayed 107 Tk 96 tool CAVE 52 command 97 128 FreeVR 52 Spaceball 52 VRPN 52 window 52 tools 53 topology files 24 trajectory draw multiple fr
12. 42 drawn 35 electrostatics volumetric data 130 environment variables 187 DISPLAY 187 MSMSSERVER 68 SURF_BIN 67 TCL_LIBRARY 190 VMD_EXCL_GL_EXTENSIONS 189 VMDBABELBIN 25 187 VMDCAVEMEM 188 VMDCUSTOMIZESTARTUP 187 VMDDIR 187 VMDDISABLESTEREO 189 VMDFILECHOOSER 187 VMDFORCECONSOLETTY 188 VMDFORCECPUCOUNT 188 VMDFREEVRMEM 188 VMDGDISPLAY 188 VMDGLSLVERBOSE 188 VMDHTMLVIEWER 188 VMDIMAGEVIEWER 188 VMDIMMERSADESKFLIP 189 VMDMSECDELAYHACK 189 VMDMSMSUSEFILE 189 VMDNOCUDA 189 VMDPREFERSTEREO 189 VMDSCRDIST 189 VMDSCRHEIGHT 189 VMDSCRPOS 189 VMDSCRSIZE 189 VMDSHEARSTEREO 189 VMDSIMPLEGRAPHICS 190 VMDSPACEBALLPORT 31 VMDTMPDIR 187 VMDVMDMACENABLEEEXTENSIONS 189 VMDWIREGL 190 evaltcl Python module 149 example scripts Python callbacks 146 Tel customized startup file example 190 exit command 97 eye separation 89 103 file load 17 file types input 24 38 output 35 files output 19 read 98 reading 17 19 24 37 38 121 startup 30 187 190 writing 35 98 fit RMSD 180 195 focal length 89 103 frame delete 35 98 duplicate 96 write 98 frames 34 frames per second indicator 41 geometric center 172 gettimestep command 97 107 gopython command 138 graphics command 106 delete 107 loading 106 primitives 106 Python module 149 replace 107 user defined 105 window 42 Gromacs files 24 38 gyration radius
13. 92 93 DIOS SOX lt b docs a tie A at ahs IS A AR eA o Bie ale da 106 MIO lt praphicss e aa e fe ieee ts a ees ae ee a ote ee amp ela 106 9 3 10 CettIMeStep an ee foe eo ee AD A pee ee et oe SA 108 9 311 helpi yee oa ae eee oe a a ee a ee le 108 9 312 A A a a A a a GE BOROA T E eaS 108 SS A uA eee E a te AR 109 SLAM seori St ect cal BOS i ad dl AA A aaa 110 3 Lo logfiles aru atui A A O a Bee S es A ee 110 3216 material siasi ti A A A E oat e hee BA AA 111 IL AMOASUTE A A A A A AS ee a ER 111 gS MEL A Ree a ter AE E A AA bt 119 O A A E AO a Soe ee ead a ae oi 119 9 3 20 molecule 2 v3 a dee bee ek A he Bae a g 123 9 73 21 lt mOlniO lt 2 Mw ares a ge a ele eos BO he hai eee See Yee as 123 93 22 MOUSE id te Paes 8 dole edna Soke winks Mee hE gee Bees Ye raise 125 93235 Play a rr SAP a Ee E Stee eee ice ese 126 IDA QUIE she Sete a ia Gok a Le ee oe ee At ee 126 OS 257 render Scie sees ho Gad Whe Ae hk Geo BAAR Ode le yA gregh eed dpe ee Be 126 93 20 TOCK fac ode A al oe eee ee ce eS ok a ia 127 IDE TOLLE y Bese ye Ba Sa ee ee hile Se A ae A ee hae Se 127 93 28 SEAS eyi a e Behe BAe she ao Ee ee ow Re alas ale bay 127 D529 Bla a Bos Syke ates a A Be ROMP a Meee ee aE ey Soh Ss BM 128 9 3 30 O L at a eS BE eee a ee Shale ee 128 9 3 31 translates lt 0 a a a AP Dee eS 128 93392 US fen of ee a A ee teats elec deh eo ae tee een A ae 129 953 33 VMO s 4 4 As whey Aas fis Ana a A Mone nada oa a ie ae es et
14. Delete frames from the specified molecule Optional arguments beg end and skip may be specified with keywords the default is to delete all coordinate frames dupframe molid frame Copy the coordinates from the given frame and append them as a new frame numframes molid Return the number of coordinate frames in the specified molecule get_frame molid Return the current coordinate frame for the specified molecule 153 set_frame molid frame Set the current coordinate frames in the specified molecule numatoms molid Returns the number of atoms in the specified molecule ssrecalc molid Recalculate the secondary structure for the given molecule using the current set of coordinates name molid Returns the name of the given molecule rename molid newname Rename the given molecule get_top molid set_top molid Get set the molid of the top molecule get_periodic molid frame 1 set_periodic molid frame 1 a b c alpha beta gamma Get set periodic im age settings for the given molecule and timestep frame get periodic returns a dictionary whose keys are a b c alpha beta gamma set_periodic sets the corresponding val ues negative values will be ignored 10 5 11 molrep Python operations available from the molrep module used to add and modify representation of molecules num molid Returns the number of representations in the given molecule addrep molid style None color None selection None
15. For example to change the color used to draw Arginine residues when molecules are colored by residue you would use the Color window select the Resname category select the Arg name there and then pick the color to use for Arginine s from the list of colors next to the names 6 2 2 Coloring Methods As described in chapter 6 each representation for a molecule has a specific coloring method The coloring method determines how the color for each atom in the representation view is determined These different methods use the colors assigned to the names in the categories listed above and use those names to color the atoms Molecular drawing methods which also draw the bonds between atoms will always color each half of the bond separately using the color of the nearest atom for each half Table 6 3 lists the different coloring methods available The description for each method explains the source of the information used to determine the color 6 2 3 Coloring by color categories The default method is to color by the atom name The way it works is that there is a color category called Name which contains a list of all the atom names e g CA N 05 and H that have been 71 Category Display The background color Axes The components of the axes Stage The colors for the checkboard stage Name The available atom names color by Name Type The available atom types color by Type Resname The residue names color by
16. Note that there is currently no way to undo Move operations so the atom coordinates should first be saved to a file e Force applies a force to selected atoms in a running simualtion These forces will be visible only if an IMD connection has been established Clicking and dragging with the left mouse button will apply a force to the selected Atom Residue or Fragment as in Move Mode Clicking with the middle or right button will cancel the force on the selected atoms e Move Light allows the lights to be positioned around the scene Individual lights are turned on or off in the Display window Selecting one of the lights in the Move Light menu rotates 39 the selected light about the origin The Move Light Mode can also be cancelled by changing into any other pick mode or mouse mode e Add Remove Bonds adds a bond between two clicked atoms if there is not one present and removes the bond otherwise Both atoms must belong to the same molecule 5 4 6 Display Menu Reset View Stop Rotation Perspective Orthographic M Antialiasing L Depth Cueing M Culling L FPS Indicator M Light 1 TO Light 2 M Light 3 Axes Background Stage Stereo Stereo Eye Swap Cachemode Rendermode Display Settings E gt Le Figure 5 4 The Display menu The Display menu controls many of the characteristics of the graphics display window The characteristics which may be modified include e Re
17. The Render window provides a simple mechanism for generating image files from snapshots of the VMD graphics window and through the use of external rendering and ray tracing programs 8 1 Screen Capture Using Snapshot The simplest way to produce raster image files in VMD is to use the Snapshot feature The snapshot feature captures the contents of the VMD graphics window and saves them to a raster image file On Unix systems the captured image is written to a 24 bit color Truevision Targa file On Windows systems the captured image is written to a 24 bit color Windows Bitmap or BMP file To use the snapshot feature simply open the Render 5 4 11 window and choose the snapshot option VMD will capture the contents of the graphics window and attempt to save the resulting image to the filename given in the Render window You may find that it is important not to have other windows or cursors in front of the VMD graphics display when using snapshot since the resulting images may include obscuring windows or cursors This is a platform dependent behavior so you will need to determine if your system does this or not 8 2 Higher Quality Rendering Sometimes images produced by screen capture aren t good enough you may want a very large high quality picture or a picture with shadows reflections or high quality rendering of transpar ent surfaces While VMD generally produces nice looking images in its graphics window it was d
18. The returned value is a score between 0 and 1 where 1 denotes a perfect match plane lt vector gt Instead of guessing the symmetry pointgroup of the selection deter mine if the plane with the defined by its normal vector is a mirror plane of the selection The returned value is a score between 0 and 1 where 1 denotes a perfect match Cn Sn lt vector gt Instead of guessing the symmetry pointgroup of the selection deter mine if the rotation or rotary reflection axis Cn Sn with order n defined by vector exists for the selection E g if you want to query wether the Y axis has a C3 rotational sym metry you specify C3 0 1 0 The returned value is a score between 0 and 1 where 1 denotes a perfect match 117 imposeinversion Impose an inversion center on the structure imposeplanes lt vector gt lt vector gt Impose the planes given by a list of nor mal vectors on the structure imposeaxes imposerotref lt vector gt order lt vector gt order Impose rotary axes or rotary reflections on the structure specified by a list of pairs of a vector and an integer Each pair defines an axis and its order The scores for the individual symmetry elements depend on the specified tolerance Imposing symmetry elements on a structure will wrap the atoms around these elements and average the coordinates of the atoms and its images Atoms for which no image is found with respect to that transformation will not
19. bond This makes for a nice smooth transition and is one of the most often used representations It can be rather slow for large molecules 6 1 9 Polyhedra Polyhedra draws a collection of triangles that connect all triplets of groups of atoms within a user defined radius This is commonly used in conjunction with specific atom selections for visualization of amorphous silicon nanodevice structures and the like At present a single atom selection is used for all candidate atoms and only the radius parameter can be modified 63 6 1 10 Trace This representation applies much of the procedure used to construct the Tube 8 6 1 11 In the end it connects the alpha carbon atoms of successive residues by cylindrical segments with adjustable width In the case of nucleic acids it is the P backbone atoms which are connected As always the segment pieces are colored according to the atom they are associated with If the cylinder radius is made 0 00 then the cylinder segments are replaced with lines Note the Trace option is useful for people doing threading or protein folding work who only look at the Cg coordinates and residue names for then they don t have to build the sidechains necessary to see their structure Also people working on polymers can fake their structure by naming everything CA in the PDB file and then using Trace 6 1 11 Tube There are two ways to draw a Tube representation one for proteins and
20. commands to add these items in your vmdrc file which is a file containing VMD text commands that is executed every time VMD starts up The basic method for setting up this file is described in section 13 3 3 Once you have such a file put the user add commands in it 30 Hot Key enter rotate mode stop rotation enter translate mode enter scaling mode query item assign rotation center pick atom pick bond 2 atoms pick angle 3 atoms pick dihedral 4 atoms move atom move residue move fragment move molecule move highlighted rep apply force on atom apply force on residue apply force on fragment n ct n HH OAOANODOOTFWNFODWO O 0 c a 2 3 4 5 6 T 8 9 KAR SS SS SS RB RRB BR DBO Table 5 1 Mouse control hot keys 5 2 Using the Spaceball in the Graphics Window VMD provides optional support for Spaceball six degree of freedom input devices The Spaceball may be used to rotate translate and scale molecules using up to 6 control axes simultaneously 3 axes in translation 3 in rotation The Spaceball can be used independently and simultaneously with the mouse With the spaceball in one hand and the mouse in the other a user can perform complex picking and identification operations more efficiently since the mouse can be left in pick mode for example while the Spaceball is used to perform rotations translations and scaling operations with the other hand The Spaceball can be run in one of several mo
21. filename All callback functions must take two arguments The first argument will be an object given at the time the function is registered VMD makes no use of this object it simply saves it and passes it to the callback when the callback function is called The second argument to the callback function will be a tuple containing 0 or more elements depending on the type of callback The type of information for each callback is listed in the third column of Table 10 4 Callbacks are registered deregistered using the add callback del_callback methods of the VMD vmdcallbacks module The syntax for these methods is def add_callback name func userdata None def del_callback name func userdata None name should be one of the callback names in Table 10 4 func is the function object userdata is any object if no object is supplied None will be passed as the first argument to the callback function To unregister a callback use the same name func and userdata as were used when the callback was registered The same function may be registered multiple times with different userdata objects 146 10 4 1 Using Tkinter menus in VMD The object oriented interface to Tk known as Tkinter is included with the embedded Python interpreter You can create Tkinter GUI s in the usual way with one caveat the Tkinter mainloop method should never be called as it will interfere with VMD s own event loop VMD will take care of updating yo
22. material None Adda representation to the specified molecule If any of the optional keywords are specified as well the new rep will have the specified properties Note that these properties become the default for future calls to addrep so that addrep 0 style VDW addrep 0 color Name will create two reps each with a style of VDW delrep molid rep Delete the specified rep from the given molecule modrep molid rep style sel color material Modify the style atom selection color and or material for the specified molecule and representation Any combination of the last four arguments may be specified using positional or keyword arguments Returns SUCCESS gt gt gt modrep 0 0 color name Color the first rep of molecule 0 by name gt gt gt modrep 0 2 selection name CA material Transparent For the third represen tation of molecule 0 change the atom selection to name CA and the material to Trans parent get_style molid rep get_selection molid rep get_color molid rep 154 e get_material molid rep Returns the representation style selection color or material respectively for the given representation of the given molecule e get_repname molid rep e repindex molid name These two commands let you assign names to reps and access them by that name The name returned by get_repname is guaranteed to be unique for all reps in the molecule and wil
23. of the colors yellow orange etc become useless 12 5 3 Revert all RGB values to defaults After some of the color definitions have been changed and you want to restore the default definitions the following procedure might be useful proc revert_colors 4 display update off foreach color colorinfo colors color change rgb color 183 display update on 12 5 4 Coloring Trick Override a Coloring Category There is currently no user defined coloring method This makes it hard to color residues by property X if X is not already defined in VMD It is possible to get around this limitation somewhat by overriding one of the values in the PDB or PSF For instance suppose you wanted to color the atoms by the distance of the atom from a given point One way is to compute the distance and put it in either the occupancy or beta field of the PDB file Then when the molecule is colored by occupancy it is actually coloring by distance You could also override say the segment name field or even the residue name Don t override the atom name unless you are really desperate as VMD uses it to determine which residues are proteins and nucleic acids and hence which residues can be drawn as a tube or ribbon 184 Chapter 13 Customizing VMD Sessions There are a number of ways to change the behavior of VMD from the default settings both in how the program starts up and in how the program behaves during a session This Chapt
24. pop out of the screen a bit more and can be used for greater dramatic effect Screen Height Hgt and Distance Dist These controls are found in the Display Settings window The screen height along with the screen distance defines the geometry and position of the display screen relative to the viewer The screen height is the vertical size of the display screen in world coordinates Each molecule is initially scaled and translated to fit within a 2 x 2 x 2 box centered at the origin so the screen height helps determine how large the molecule appears initially to the viewer The screen distance parameter determines the distance in world coordinates from the origin to the display screen If this is zero the origin of the coordinate system in which molecules and all other graphical objects are drawn coincides with the center of the display If distance is negative the origin is located between the viewer and the screen if it is positive the screen is closer to the viewer than the origin A negative value puts any stereo image in front of the screen aiding the three dimensional effect a positive value results in a stereo image that is behind the screen a less dramatic effect but easier to see for some people stereo effect Figure 5 5 describes the relationship between the screen height the screen distance and the world coordinate space 5 4 7 Graphics Window The Graphical Representations or Graphics windo
25. transvec 16 5 7 transvecinv 6 5 7 0 999999 2 29254e 07 6 262e 09 0 0 2 29254e 07 0 999999 4 52228e 07 0 0 6 262e 09 4 52228e 07 1 0 0 0 0 0 0 0 0 0 1 0 C transoffset v Returns the transformation matrix needed to translate by the given offset Examples vmd gt transoffset 1 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 O 0 0 0 0 1 0 O 0 0 0 0 0 0 1 0 vmd gt transoffset 6 5 4 3 1 0 0 0 0 0 6 0 0 1 0 0 0 5 0 0 0 0 1 0 4 3 0 0 0 0 0 0 1 0 transabout v amount deg rad pi Generates the transformation matrix needed to rotate by the given amount counter clockwise around axis which goes through the origin and along the given vector As with transvec the units of the amount of rotation can be degrees radians or multiples of pi Examples this is a rotation about x by 180 degrees vmd gt transabout 1 0 0 180 1 0 0 0 0 0 0 0 0 0 1 0 2 65359e 06 0 0 0 0 2 65359e 06 1 0 0 0 0 0 0 0 0 0 1 0 a rotation about z by 90 degrees compare this to transaxis z 90 vmd gt transabout 0 0 1 1 5709 rad 0 999624 0 027414 0 0 0 0 0 027414 0 999624 0 0 0 0 10 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 vmd gt transabout 1 1 1 1 pi 1 0 333335 0 666665 0 666669 0 0 0 666668 0 333334 0 666666 0 0 0 666666 0 66667 0 333332 0 0 0 0 0 0 0 0 1 0 trans center x y z origin z y z offset x y z axis x amount rad deg pil axis y amount rad deg lpil axis z amount rad d
26. 2 ee 64 48 A a a a 3 5 An Introduction to Atom Selection 00000002 eee eae 3 6 Comparing Two Structures ee 3 7 Some Nice Represenations oao 3 8 SAVIN VOUT WORK Aeon eA bo ee a ek ahd ae es Ba o eed 3 9 Tracking Script Command Versions of the GUI Actions Loading A Molecule 4 1 Notes on common molecular file formats o e e 4 2 What happens when a file is loaded 2 0 o e e e 4 3 Babel intertace 24 0420 fs A AA Re A A A th Bee ed 4 4 Raster3 fle formats pudo Pee Rak et ote as ee ow eb eas User Interface Components 5 1 Using the Mouse in the Graphics Window 0 00 00040 eee 5 1 1 Mouse Modes 2 ee ee 51 2 Pick Modest a AE h Ska SHOU KEYS ts a og Mk og Ad A AE hee al Sd 5 2 Using the Spaceball in the Graphics Window 0 00004 5 21 Spaceball Driver Fo econ ace ek ee Bee a Gee a ae Be es 5 3 Using the Joystick in the Graphics Window 0 0 00000 ee ee 10 11 11 11 12 12 14 16 16 16 17 17 17 19 19 20 20 21 22 22 24 24 25 25 26 5 4 Description of each VMD window oaoa a 34 DAL gt Maiti Wd 2 a a a ae a a do aa 34 5 4 2 Main Window Molecule List browser 34 5 4 3 Main Window Animation Controls 0 0 0 0 ee ee 36 5 4 4 Molecule File Browser Window 37 B20 Mouse Menu cco i Ave gna etl ee ee EA a a 38 5 4 6 Display Menu iros ote de o
27. Eargle Peter Freddolino Todd Furlong Luis Gracia Paul Grayson Justin Gullingsrud James Gumbart David Hardy Konrad Hinsen Barry Isralewitz Sergei Izrailev Robert Johnson Axel Kohlmeyer Michell Kuttel John Mongan Jim Phillips Jan Saam Alexander Spaar Charles Schwieters Marcos Sotomayor John E Stone Leonardo Trabuco Dan Wright and Kirby Vandivort The entire VMD user community now benefits from your contributions The authors would like to thank individuals who have indirectly helped with development by making suggestions pushing for new features and trying out buggy code Thanks go to Aleksei Aksimentiev Daniel Barsky Axel Berg Tom Bishop Robert Brunner Ivo Hofacker Mu Gao James Gumbart Xiche Hu Tim Isgro Dorina Kosztin Ioan Kosztin Joe Landman Ilya Logunov Clare Macrae Amy Shih Lukasz Salwinski Stephen Searle Charles Schwieters Ari Shinozaki Svilen Tzonev Emad Tajkhorshid Michael Tiemann Elizabeth Villa Raymond de Vries Simon Warfield Willy Wriggers Dong Xu and Feng Zhou Many external libraries and packages are used in VMD and the program would not be as capable without them The authors of VMDwish to thank the authors of FLTK the authors of Tcl and Tk the authors of Python the authors of VRPN Jon Leech for uniform point distributions Amitabh Varshney for SURF Dmitrij Frishman for developing STRIDE Jack Lund for the url_get perl script Brad Grantham for the ACTC triangle consolidation library J
28. Following these will be a more in depth description of how selections work name CA resid 35 name CA and resname ALA backbone not protein protein backbone or name H name A 1 name A name C x mass lt 5 numbonds 2 abs charge gt 1 x lt 6 and x gt 3 sqr x 5 sqr y 4 sqr z gt sqr 5 within 5 of name FE exwithin 3 of protein protein within 5 of nucleic same resname as protein within 5 of nucleic protein sequence C C name eq atomname There are two types of selection modes The first is a keyword followed by a list of either values or a range of values For example name CA selects all atoms with the name CA which could be a Ca or a calcium resname ALA PHE ASP selects all atoms in either alanine phenylalanine or asparagine 75 index 5 selects the 6th atom in the internal VMD numbering scheme VMD can also do range selections similar to X PLOR s notation mass 5 to 11 5 selects atoms with mass between 5 and 11 5 inclusive resname ALA to CYS TYR selects atoms in alanine arginine asparagine aspartic acid cystine and also tyrosine The keyword selection works by checking each term on the list following the keyword The term is either a single word eg name CA or a range eg resid 35 to 90 The method for determining the range checking is determined from the keyword data type numeric comparisons are different than string comparisons The comparis
29. Tcl code block due to the way VMD processes its commands e time wait time seconds 9 3 36 sleep Specify a number of seconds to sleep before reading another command Animation stops during this time e time sleep time seconds 9 4 Tcl callbacks When certain events occur VMD notifies the Tcl interpreter by setting certain Tcl variables to new values You can use this feature to customize VMD for instance by causing new graphics to appear when the user picks an atom or recalculating secondary structure on the fly To make these new feature happen at the right time you need to write a script that takes a certain set of arguments and register this script with the variable you are interested Registering scripts is done with the built in Tcl command trace see http www tcl tk man tcl8 4 TclCmd trace htm for documentation on how to use this command The idea is that after you register your callback when VMD changes the value of the variable your script will immediately be called with the new value of the variable as arguments Table 9 4 summarizes the callback variables available in VMD In the VMD script library at http www ks uiuc edu Research vmd script_library you can find a number of scripts that take advantage of Tcl variable tracing Below we give a simple example The following procedure takes the picked atom and finds the molecular weight of residue it is on proc mol_weight args use the picked atom s index
30. To move the molecule towards or away from you hold the middle button down and move the mouse right or left respectively Scale Mode hot key s Pressing either the left or middle button down and moving to the right enlarges the molecules and moving the mouse left shrinks them The difference is that the middle button scales faster than the left button Scaling can also be accomplished with the mouse wheel irrespective of the current mode setting on computers equipped with an appropriate mouse Move Light VMD provides four directional lights to illuminate the molecular scene The lights provide diffuse lighting and specular highlights and help the user perceive surface shape in rendered objects You can use the mouse to rotate each of the light source directions to a new position If the light isn t on moving it will not affect the displayed image To turn a light on or off use the Lights item within the Mouse menu Add Remove Bonds When the mouse is in add remove bonds mode clicking on atoms in a molecule will add a bond between those atoms if one is not already present or remove the bond between those atoms if there is already a bond The two atoms must belong to the same molecule 5 1 2 Pick Modes Mouse picking can be used to turn on or off various types of labels to query for information about an object or to move items around on the screen You can label an atom and display the atom name or you can label geometric v
31. Tutorials 3 1 Rapid Introduction to VMD For those of you who don t like reading manuals here is a quick introduction to VMD The molecules and data files used in this tutorial can be downloaded from the VMD home page from the doc umentation area associated with this version and is clearly labeled as User s Guide tutorial data The rest of this tutorial assumes that you have downloaded and unpacked this data set To start VMD type vmd on the command line of your shell Unix or start it by clicking the VMD icon in your desktop or Start menu Apple MacOS X and Microsoft Windows VMD should start up with a window titled vmd console a display window entitled VMD OpenGL Display and a main menu entitled VMD Text commands are typed in the console window molecules are displayed and manipulated in the graphics window and other interfaces and extensions are available from the menu interface All of the windows can be closed or minimized using your computer s standard windowing controls or the menu command 9 3 18 in text console Most functions can be performed with both the menu interface and the text console though some of the more sophisticated scripting features are only available as text commands 3 2 Viewing a molecule Myoglobin In our quick tour of VMD we ll start out by demonstrating a few of its visualization features To load a new molecule select New Molecule from the File menu in the Main window this will open the Files w
32. VMD animates frames value should lie between 0 and 1 If a value less than 0 is given then the speed will not be changed The new value of the speed is always returned e skip value Get set the number of frames to skip when animating A value of 1 means every frame is shown 2 means every other frame is shown etc If value is 0 or less no change is made The new value of the speed is always returned 147 e is_active molid Returns whether the molecule with the given id is active that is whether it responds to animation or not e activate molid trueorfalse Make the molecule with the given id active or not Active molecules update their coordinate frames during animation inactive molecules do not 10 5 2 axes Python operations available from the axes module used to change where the axes are displayed in the graphics window OFF ORIGIN LOWERLEFT LOWERRIGHT UPPERLEFT UPPERRIGHT String constants de fined in the ares module for setting the location of the axes get_location Returns a string object corresonding the current location of the axes set_location location Set the location of the axes using one of constants defined in the module 10 5 3 color Python operations available from the color module used to change the color definitions color maps or edit the color scale All rgb and color scale values should be in the range 0 to 1 categories Returns a list of available color categories get_col
33. a dash and is not part of another option it is assumed to be a filename and its extension is matched to the extension registered by the proper plugin Thus the Unix command vmd molecule pdb will start VMD and load a molecule from the file molecule pdb while the command vmd molecule psf molecule dcd 185 will load the corresponding structure and coordinate files into the same molecule On the Windows platform one must preface the VMD invocation with the Windows start command start vmd molecule pdb e h help Print a summary a command line options to the console e e filename After initialization execute the text commands in filename and then resume normal operation e python After initialization switch to the Python interpreter before executing commands in the file specified by e if any and leave the text interpreter in Python mode e filename Load the specified file at startup The file type will be determined from the filename extension if there is no filename extension and the filename contains 4 letters it is assumed to be a PDB accession code and will be loaded accordingly otherwise the format is assumed to be PDB e lt filetype gt filename Load the specified file using the given filetype e f Load all subsequent files into the same molecule This is the default A new molecule is created for each invocation of f thus vmd f 1 pdb 2 pdb f 3 pdb loads 1 pdb and 2 pdb into the same mole
34. a little more difficult The Molecule class defines a function for each draw style to make it easier to generate the required strings to pass to the changeStyle methods Each function accepts keyword arguments for specifying the draw style parameters and returns a string suitable for changeStyle 10 6 4 Saving and Restoring Molecule State Molecule and MoleculeRep instances can be saved used the pickle module from the Python stan dard library Molecules will be saved with information about their name files and reps The files themselves are not saved with the molecule they will be reloaded when the molecule instance is recreated using pickle load MoleculeRep instances can also be pickled when restored they will be unassigned to any Molecules 160 Chapter 11 Vectors and Matrices Tcl does not handle mathematical expressions very well It is slow at evaluating expressions and provides no facility for handling vectors or matrices Since the latter two are needed for structure analysis we have added routines to manipulate them A vector in VMD is a list of numbers All of the vector routines but one will work with vectors of any length veccross will only use vectors of three numbers A matrix is a 4x4 collection of numbers stored as a list of 4 vectors of 4 numbers in row major order Following are descriptions and examples of all the commands For more examples of vectors though without much documentation the script used to test t
35. amount deg rad pi Returns the transformation matrix needed to rotate around the specified axis by a given amount By default the amount is specified in degrees though it can also be given in radians or factors of pi Examples vmd gt transaxis x 90 1 0 0 0 0 0 0 0 0 0 3 67321e 06 1 0 0 0 0 0 1 0 3 67321e 06 0 0 0 0 0 0 0 0 1 0 vmd gt transaxis y 0 25 pi 0 707107 0 0 0 707107 0 0 0 0 1 0 0 0 0 0 0 707107 0 0 0 707107 0 0 0 0 0 0 0 0 1 0 vmd gt transaxis z 3 1415927 rad 1 0 2 65359e 06 0 0 0 0 2 65359e 06 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 transvec v Returns the transformation matrix needed to bring the x axis along the v vector This matrix is not unique since a final rotation is allowed around the vector The matrix is made from a rotation around y then one about z Examples vmd gt transvec 0 1 0 3 67321e 06 1 0 0 0 0 0 1 0 3 67321e 06 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 vmd gt vectrans transvec 0 0 2 1 O 0 0 0 0 0 1 0 transvecinv v Returns the transformation needed to bring the vector v to the x axis This produces the inverse matrix to transvec and is composed of a rotation about z then one about y Examples vmd gt transvecinv 0 1 0 3 67321e 06 1 0 0 0 0 0 1 0 3 67321e 06 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 vmd gt vectrans transvecinv 3 4 12 3 4 12 13 0 1 8e 05 5 8e 05 165 vmd gt transmult
36. angles and improper dihedrals in Angstrom or degree kub lt value gt Urey Bradley force constant for angles in kcal mol A s0 lt value gt Urey Bradley equilibrium distance for angles in Angstrom n lt value gt dihedral periodicity delta lt value gt dihedral phase shift in degree usually 0 0 or 180 0 rmin1i lt value gt VDW equilibrium distance for atom 1 in Angstrom rmin2 lt value gt VDW equilibrium distance for atom 2 in Angstrom eps1 lt value gt VDW energy well depth epsilon for atom 1 in kcal mol eps2 lt value gt VDW energy well depth epsilon for atom 2 in kcal mol q1 lt value gt charge for atom 1 q2 lt value gt charge for atom 2 cutoff lt value gt nonbonded cutoff distance switchdist lt value gt nonbonded switching distance For all omitted parameters a default value of 0 0 is assumed For the electrostatic energy the default charges are taken from the according atom based field of the molecule If the cutoff is not set or zero then no cutoff function will be used e surface selection gridsize radius depth Returns a list of atom indices comprising the surface of the selected atoms The method for determining the surface is to construct a grid with a spacing approximately equal to gridsize where each grid point is either marked full or empty depending on whether any atoms from the selection are within radius distance of the grid point
37. appropriate for Unix environments The file chooser can be overridden at any time by changing the environment variable e g in Tcl set env VMDFILECHOOSER FLTK VMDFORCECPUCOUNT Specifies the maximum number of CPUs or CPU cores that VMD should use when running on a multiprocessor or multicore computer system By default VMD will use all of the processors on the host machine This option can be used to prevent VMD from hogging CPUs or to make it abide by job submission policies required on large supercomputer systems when running batch mode VMDCAVEMEM Unix only This overrides the default size of the shared memory arena which is allocated by VMD when the CAVE starts up The variable must be an integer number of megabytes Since this is the only shared memory pool allocated and it is done only once you must choose a value sufficient to account for the largest scene you intend to render in VMD in that CAVE session The default value unless otherwise specified is 80 Megabytes Values of 200MB to 512MB are commonly needed for large molecular systems containing several hundred thousand atoms VMDFREEVRMEM Unix only This overrides the default size of the shared memory arena which is allocated by VMD when the FreeVR starts up The variable must be an integer number of megabytes Since this is the only shared memory pool allocated and it is done only once you must choose a value sufficient to account for the largest scene you intend t
38. atoms in selection using the given weight 111 e cluster selection num numclusters distfunc flag cutoff cutoff first first last last step step selupdate bool weight weight Performs a cluster analysis find clusters of timesteps that are similar with respect to a given distance function for the atoms in selection using the given weight The implementation is based on the quality threshold QT algorithm See http dx doi org 10 1101 gr 9 11 1106 and Cluster Analysis on Wikipedia for more details on the algorithm Typically only a small number of the largest clusters are of interest This implementation takes this into account and trades low memory consumption on data sets with many frames for fast determination of multiple clusters Use the num keyword to adjust how many clusters to determine default is 5 The distfunc flag selects the distance function available options are rmsd root mean squared atom to atom distance fitrmsd root mean squared atom to atom distance after alignment and rgyrd difference in radius of gyration The cutoff flag defines the maximal distance value between two frames that are considered similar default value is 1 0 The weight flag allows to use an atom property e g mass or radius to be used as weighting factor default is no weighting The command returns a list of numcluster 1 lists each containing the list of trajectory frame indices belonging to a cluster of
39. backbone sidechain water waters fragment pfrag nfrag sequence numbonds resname resid segname X y Z radius mass charge beta occupancy user at acidic acyclic aliphatic alpha amino aromatic basic bonded buried cg charged cyclic everything nothing atom name atom type the atom number starting at 0 the atom number starting at 1 atomic number 0 if undefined atomic element symbol string X if undefined alternate location conformation identifier the one character chain identifier a set of connected atoms with the same residue number a residue with atoms named C N CA and O a residue with atoms named P 01P 02P and either 03 C3 C4 C5 05 or 03x C3x C4 C5 Obx This definition assumes that the base is phosphorylated an assumption which will be corrected in the future the C N CA and O atoms of a protein and the equivalent atoms in a nucleic acid non backbone atoms and bonds all atoms with the resname H20 HHO OHH HOH 0H2 SOL WAT TIP TIP2 TIP3 or TIP4 a set of connected residues a set of connected protein residues a set of connected nucleic residues a sequence given by one letter names number of bonds residue name residue id segment name x y or z coordinates atomic radius atomic mass atomic charge temperature factor occupancy time varying user specified value residues named ADA A THY T residues named ASP GLU protein and
40. can be used as is or they can be customized to perform complex animation tasks beyond the scope of this user guide In general movies are created by driving render commands with a script producing a sequence of individual image files When the script has completed rendering all of the individual frames the images are ready for import into an animation package or can be converted to one of several popular compressed movie formats by further processing The vmdmovie extension provided with VMD completely automates the movie creation process though it requires a number of software packages be installed in order to do the job Please see the separate documentation on the movie scripts and vmdmovie in the VMD script library 93 Default Reader Command ART Gelato PostScript POV3 Radiance Raster3D Rayshade RenderMan STL Tachyon TachyonInternal VRML 1 VRML 2 Wavefront Simple VORT ray tracer NVIDIA Gelato PYG Format Simple Vector PostScript Output POV Ray 3 x ray tracer Radiosity ray tracer Fast raster file generator Rayshade ray tracer PIXAR RenderMan RIB Format ren der with Aqsis Gelato Pixie PRMan RenderDotC Stereolithography format only Fast high quality parallel ray tracer triangles Fast built in high quality parallel ray tracer generates images with no inter mediate step Virtual Reality Markup Language V1 0 Virtual Reality Markup Language V2 0 Wavefront
41. cancel molecule_number Cancel loading trajectories reanalyze molecule_number Re analyze structure after bonding and atom name changes bondsrecalc molecule_number Recalculate bonds from distances for current timestep ssrecalc molecule_number Recalculate secondary structure rename molecule_number newname Rename the specified molecule repname molecule_number rep_number Returns the name of the given rep This name is guaranteed to be unique for all reps in the molecule and will stay with the rep even if the rep_number changes repindex molecule_number name Return the rep_number for the rep with the given name or 1 if no rep with that name exists in that molecule selupdate rep_number molecule number onoff Update the selection for the specified rep each time the molecule s timestep changes If onoffis not specified returns the current update state colupdate rep_number molecule_number onoff Update the calculated color for the specified rep each time the molecule s timestep changes If onoff is not specified returns the current update state drawframes molecule_number rep_number frame _specification Draw multiple trajectory frames or coordinate sets simultaneously This setting allows the user to select one or more ranges of frames to display simultaneously The frame specification takes one of the follow ing forms now frame_number start end or start step end If the frame_specification is not specified the command ret
42. case since they are applied to the same AtomSel instance Either use the frame argument as illustrated here or create a new AtomSel instance for the reference 145 Perform a mass weighted RMSD alignment and compute the mass weighted RMS distance from the first frame w sel get mass rms ref AtomSel backbone frame 0 for i in range n rms append sel frame i align ref ref weight w rmsd ref weight w 10 4 Python callbacks Some of your Python scripts may wish to be informed when various events in VMD occur The mechanism for expressing this interest is to register a callback function with a special module supplied by VMD When the event of interest occurs all registered will functions will be called VMD will pass the functions information specific to the event The set of callbacks events is listed in Table 10 4 Table 10 1 Description of callbacks available to scripts running in the embedded Python interpreter display_update Screen redraw none frame Molecule changes coordinate frame molid frame help User pushes help button on Main window name of topic initialize_structure Molecule created or deleted molid 1 or 0 pick_atom Atom picked in graphics window molid atomid key_shift_state 1 if shift pressed 0 otherwise pick_value Bond angle or dihedral label created value timestep New IMD coordinate frame received molid frame trajectory Completion of coordinate file read write molid
43. color r g b puts i color r g b incr i 9 3 6 display Change various aspects of the graphical display window For information about the options see the section describing the Display window 85 4 6 get lt backgroundgradient eyesep focallength height distance antialias depthcue culling rendermode size stereo projection nearclip farclip cuestart cueend cuedensity cuemode shadows ambientocclusion aoam bient aodirect backgroundgradient gt Return the current value of the requested option get lt rendermodes stereomodes projections details gt Return a list of the available values for the given options See section 5 4 6 and chapter 7 for more information antialias lt on off gt Turn antialiasing on or off ambientocclusion lt on off gt Turn ambient occlusion lighting on or off This only affects renderers that support ambient occlusion lighting It will have no visible effect on the interactive VMD display or on renderers that don t support it At present only the Tachyon and TachyonInternal renderers are capable of ambient occlusion lighting aoambient value Set ambient occlusion lighting factor to value Useful values tend to range from 0 7 to 1 0 At present only the Tachyon and TachyonInternal renderers are capable of ambient occlusion lighting aodirect value Set ambient occlusion direct lighting rescaling factor to value Useful values tend to
44. costly in terms of computation time Also since the fluctuation of the protein backbone is on the order of 1 2 Angstrom a higher grid resolution doesn t make much sense e subres num Number of points in each dimension of the subsampling grid e g 2 for a 2x2x2 subgrid or 3 for a 3x3x3 subgrid A value of 1 means is no subsampling the default is subres 3 Without subsampling the probe is placed at each grid cell center for diatomic probes in numconf different random orientations see argument orient This position is 132 assumed to be representative for the interaction of the probe in this voxel with the system However for a typical voxel size of 1x1x1 the energy value can differ significantly within the voxel and the value at the center might not be close to the average Subsampling averages over the interaction on a regular subgrid in each voxel thus producing a more accurate free energy value for placing the probe into each voxel Even though this severely increases the computational cost it is highly recommended that you use subsampling A 3x3x3 subgrid for a 1 A resolution map is a good choice T temperature The temperature in Kelvin at which the MD simulation was performed default 300 probesel selection Atom selection that defines the probe molecule The radius and occu pancy fields should be populated with the VDW radii and VDW epsilon parameters from the force field see option probevdw Alternatively you ca
45. data 124 deleting 36 drawn 35 fixed 21 35 graphics 106 id 119 index 119 info 169 list 34 loading 17 19 106 178 Python module 152 status 35 121 changing 35 123 169 top 35 37 123 translation 21 molinfo command 123 169 keywords 124 molrep Python module 154 mouse add or remove bonds 28 callback 125 command 97 125 modes 17 21 27 31 125 mouse mode 39 move 39 atom 39 fragment 39 highlighted rep 39 molecule 39 residue 39 object menus 39 pick information 48 rocking 125 stop rotation 125 using 27 movies 93 NAMD 15 files 24 38 occupancy volumetric data 130 orthographic view 40 86 output format 19 PCRE 13 periodic boundary conditions 46 periodic image display 46 perspective view 40 86 picking angles 28 29 atoms 20 28 29 bonds 20 28 29 center 29 dihedrals 28 29 distances 20 hot keys 31 modes 21 28 move atom 29 move fragment 29 move highlighted rep 30 move molecule 30 move residue 29 query 29 text command 125 play command 95 97 125 186 plot geometry monitors 49 postscript 92 potential of mean force volumetric data 130 Python 13 197 interface 138 RMSD 141 Tkinter 147 version 138 python atomsel 139 environment variables 138 libraries 138 Numeric 139 156 startup 186 Tkinter 139 quit 34 command 105 126 quoting 77 radius of gyration 176 Ramachandran plot 58 R
46. drawn through the picked atom and parallel to a line coming directly out of the screen This behavior is similar to the usual Rotate mode except that coordinates of atoms are changed 29 e Move Molecule hot key 8 This mode may be used to move all the atoms in a selected molecule at the same time Select an atom in a molecule and move it to a new position while keeping the mouse button pressed All the atoms in the same molecule as the selected one will be moved the same amount Holding down the shift key and the left mouse button while moving the mouse will rotate the atoms in the molecule about the selected atom If the middle mouse button is held down instead the atoms in the molecule will rotate about a line drawn through the picked atom and parallel to a line coming directly out of the screen This behavior is similar to the usual Rotate mode except that coordinates of atoms are changed e Move Rep hot key 9 This mode may be used to move all the atoms in a selected representation at the same time You select a representation by clicking on one of the reps in the browser window of the Graphics window In order to move the atoms in this rep the atom you pick with the mouse must be selected by that rep When you have clicked on an atom in the rep move the mouse to a new position while keeping the mouse button pressed All the atoms selected by the highlighted rep will be moved the same amount Holding down the j
47. gt gt 10 3 4 Changing the selection and the frame When molecule in VMD contains multiple coordinate sets frames atom selections must know which frame they are referring to especially when you make distance based atom selections or 142 request time varying properties like the x y or z coordinates By default atom selections in Python use frame 0 i e the first coordinate set You can specify the frame either when you create the atom selection or by using the frame method Passing no arguments to frame returns the current value of the frame gt gt gt load psf alanin psf dcd alanin dcd gt gt gt residb AtomSel resid 5 frame 50 gt gt gt resid5 frame 50 gt gt gt resid5 frame 22 gt gt gt resid5 frame 22 In a similar way you can change the selected atoms of an atom selection object using the select operation Continuing with the previous example gt gt gt resid5 resid 5 gt gt gt residb select resid 7 gt gt gt resid5 resid 7 gt gt gt 10 3 5 Combining atom selections Once you ve created one or more atom selections you can combine them to create new ones gt gt gt CA AtomSel name CA gt gt gt resid5 AtomSel resid 5 gt gt gt CA name CA gt gt gt resid5 resid 5 gt gt gt ANDsel CA amp resid5 gt gt gt ORsel CA resid5 gt gt gt NOTsel CA gt gt gt ANDsel name CA
48. image atoms that are within cutoff A of the PBC unitcell in form of two lists The first list holds the atom coordinates while the second one is an indexlist mapping the image atoms to the atoms in the unitcell Since the PBC cell center is not stored in DCDs and cannot be set in VMD it must be provided by the user as the first argument The second argument cutoff is the maximum distance in A from the PBC unit cell for atoms to be considered In other words the cutoff vector defines the region surrounding the pbc cell for which image atoms shall be constructed i e 6 8 0 means 6 A for the direction of A 8 A for B and no images in the C direction The following options can be specified molid lt molecule_number gt The default molecule to which an atom belongs unless a molecule number was explicitely specified for this atom in the atom list Further all frame specifications refer to this molecule Default is the current top molecule frame lt frame gt By default the value for the current frame will be returned but a specific frame can be chosen through this option One can also specify all or last instead of a frame number in order to get a list of values for all frames or just the last frame respectively sel lt selection gt If an atomselection is provided then only those image atoms are returned that are within cutoff of the selected atoms of the main cell In case cutoff is a vector the largest value will be used
49. image file named plot dat tga on MacOS X or Unix or plot dat bmp on Windows in your current working directory This image is in either Windows BMP or Targa graphics format and can be read by many programs such as display ipaste xv Gimp or Photoshop 3 4 A Quick Animation Another strength of VMD lies in its ability to playback trajectories resulting from molecular dynam ics simulations A sample trajectory alanin dcd is provided in the proteins directory included with VMD To load it open the molecule file browser as described previously Next click on the Browse button and select the alanin psf file in the file browser Once selected press the Load button to load the structure file Next select the alanin dcd file and load it as well This will read the DCD trajectory frames into the same molecule with the previously loaded alanin psf file In the display window you should see a simulation of an alanin residue in vacuo It isn t particularly informative but you can easily see that the structure is quite unstable in an isolated environment After the DCD file has loaded animation will stop To see it again or to fine tune playback use the animation controls 5 4 3 found at the bottom of the main VMD window Press the button that looks like gt to play the animation Use the Speed slider at the bottom of the window to change the speed of playback By rotating the molecule around etc you should get an idea about how the system d
50. in lt gt s and the items are separated by Words in italics indicate a string or value to be specified by the user 9 3 1 animate These commands control the animation of a molecular trajectory and are used to read and write animation frames to from a file or Play Pause Rewind a molecular trajectory e dup frame frame_number 1 molld Duplicate the given frame default now of molecule mold and add the new frame to this molecule e forward Play animation forward e for Same as forward e reverse Play animation backward e rev Same as reverse e pause Pause animation e prev Go to previous frame e next Go to next frame e skip n Set stride to n 1 frames e delete all Delete all frames from memory 96 Fist Word animate atomselect axes color colorinfo display exit quit gettimestep help imd label light logfile material measure menu molecule or mol molinfo mouse play render rock rotate scale stage tool translate user vmdinfo volmap wait sleep Play Pause Rewind a molecular trajectory Create atom selection objects for analysis Position a set of XYZ axes on the screen Change the color assigned to molecules or edit the colormap Tcl Obtain color properties for various objects Change various aspects of the graphical display window Quit VMD Retrieve a timestep as a binary Tcl array use for plugins Display an on line help file with an HTML viewer Control the
51. is defined as gt mj 7 Fo Y mi This uses the center of mass function defined earlier in this chapter a faster version would replace that with measure center Note that the measure rgyr command does the same thing as this script only much much faster proc gyr_radius sel make sure this is a proper selection and has atoms if sel num lt 0 error gyr_radius must have at least one atom in selection gyration is sqrt sum r i r center_of_mass 2 N set com center_of_mass sel set sum 0 foreach coord sel get x y z 4 set sum vecadd sum veclength2 vecsub coord com return expr sqrt sum sel num 0 0 176 Applying this to the alanin pdb coordinate file vmd gt mol new alanin pdb vmd gt set sel atomselect top all vmd gt gyr_radius sel Info 5 45443 Root mean square deviation Compute the rms difference of a selection between two frames of a trajectory This takes a selection and the values of the two frames to compare proc frame_rmsd selection framel frame2 Y set mol selection molindex check the range set num molinfo mol get numframes if framel lt 0 frame1 gt num frame2 lt 0 frame2 gt num error frame_rmsd frame number out of range get the first coordinate set set sel1 atomselect mol selection text frame frame1 set coords1 sel1 get x y z get the second coordinate set set sel2 atomselect m
52. make various modeling and simulation tasks easier More information is available at the MDTools home page For more information on our software efforts see the Theoretical and Computational Biophysics Group home page http www ks uiuc edu Research biocore http www ks uiuc edu Researach namd http www ks uiuc edu Development MDTools http www ks uiuc edu 15 Chapter 2 Hardware and Software Requirements 2 1 Basic Hardware and Software Requirements The basic hardware requirements for running VMD vary depending on how it was compiled and how it will be used VMD has two primary modes of operation the typical full featured graphics enabled mode and a purely text based mode of operation suited for remote analysis on supercomputers embedded use in other packages and similar batch oriented analytical uses The full featured graphics enabled mode of VMD is the most demanding and requires an OpenGL capable graphics accelerator with up to date drivers Some graphics chipsets or GPUs come with drivers that are below spec and will not be able to run VMD with full graphics ca pability These will either automatically or as the result of user defined environment variables e g VMDSIMPLEGRAPHICS use a reduced functionality graphics mode within VMD Since the choice of the GPU chipset or card has the biggest impact on the visualization capabilities and performance of VMD this is the hardware component that is worth spen
53. matrix get set the overall viewing matrix the number of representations the string for the 1 th selection the string for the i th representation the string for the i th coloring method number of animation frames number of volumetric data sets current frame number number of elapsed timesteps in an interactive simulation topology angle types and definitions type al a2 a3 topology dihedral types and definitions type al a2 a3 a4 topology improper types and definitions type al a2 a3 a4 the bond energy for the current frame the angle energy the dihedral energy the improper energy the van der Waal energy the electrostatic energy the hydrogen bond energy the total kinetic energy the total potential energy the total energy the overall temperature the simulation pressure the simulation volume efield unit cell angle alpha in degrees for the current frame unit cell angle beta in degrees for the current frame unit cell angle gamma in degrees for the current frame unit cell length a in Angstroms for the current frame unit cell length b in Angstroms for the current frame unit cell length c in Angstroms for the current frame Table 9 3 molinfo set get keywords Examples vmd gt molinfo top get numatoms 568 molinfo 0 get filetype filename pdb home dalke pdb bpti pdb vmd gt molinfo O get rep 0 color 0 rep 1 color 1 VDW 1 000000 8 000000 ColorID 5 Lines 1 0000 SegName 9 3 22
54. menu_name status Return on if on off if off e menu_name loc Return the x y location e menu_name move z y Move a menu to the given zx y location The parameter menu_name is one of the following menu names color display files graphics labels main material ramaplot render save sequence simulation or tool 9 3 19 mol Load modify or delete a molecule in VMD In the following molecule_number is a string describing which molecules are to be affected by the command It is one of the following all top active inactive displayed on off fixed free or one of the unique integer ID codes assigned to the molecules when they are loaded starting with 0 The codes molIDs are not reused after a molecule is deleted so if you for example have three molecules loaded numbered 0 1 2 delete molecule with molID equal to 0 and then load another molecule the new molecule will have molID 3 Thus the list of available molecule IDs becomes 1 2 3 The index of the molecule on this list is among many other things accessible through the molinfo command 9 3 21 In the above 119 case for example molecule that was loaded the last has molID equal to 3 however it is the third on the list of molecules so it has the index equal to 2 since we start countin from 0 The molecule representations views are assigned integer number starting with 0 for each molecule which appear in the list on the Graphics window 5 4 7 Th
55. molid set_scale molid scale Get set the scale factor used to display the given molecule get_rotation molid set_rotation molid matrix Get set the rotation matrix for the given molecule as a 16 element Python list in row major order get_trans molid set_trans molid vector Get set the global translation applied to the given molecule as a Python list is_fixed molid Returns whether the molecule with the given id is fixed that is whether it is affected by translation rotation or scaling Fixed molecules may still be animated see is_active in the animate section fix molid trueorfalse Make the molecule with the given id fixed or not is_shown molid Returns whether the molecule with the given id is shown or not show molid trueorfalse Make the molecule with the given id shown or not 10 5 14 vmdnumpy This optional module is made available from within the toplevel VMD module if VMD detects a Numeric Python installation in the Python search path When present the following methods are provided 156 e timestep molid frame Returns a single precision Numeric array containing a direct reference to the given set of atom coordinates Atom coordinates are arranged xyzryzvyz for each atom in the molecule No copy of VMD s internal coordinates is made therefore modifications to this array will directly affect atom coordinates in VMD Using the array after the timestep has been deleted will likely cause V
56. mouse Change the current state mode of the mouse optionally active TCL callbacks e mode 0 Set mouse mode to rotation e mode 1 Set mouse mode to translation e mode 2 Set mouse mode to scaling e mode 3 N Set mouse mode to rotate light N e mode 4 N Set mouse mode to picking mode N where N is one of the following 0 query item pick center pick atom pick bond pick angle pick dihedral move atom move residue move fragment CON AoA FwWNY rH OO move molecule 10 force on atom 11 force on residue 12 force on fragment e callback on off Turn the callbacks on or off To use the callbacks trace the variable vmd_pick_atom_silent See below for information on tracing e rocking on off Enable disable persistent rotation of the scene with the mouse e stoprotation Stop any mouse initiated scene rotation as well as any rocking initiated with the rock command 125 9 3 23 play Start executing text commands from a specified file instead of from the console When the end of the file is reached VMD will resume reading commands from the previous source This command may be nested so commands being read from one file can include commands to read other files e filename Execute commands from filename 9 3 24 quit Same as exit 9 3 25 render Output the currently displayed image scene to a file using the global VMD display settings and any renderer specific
57. not be misrepresented either by explicit claim or by omission 3 Altered versions must be plainly marked as such and must not be misrepresented as being the original software 4 If PCRE is embedded in any software that is released under the GNU General Purpose License GPL then the terms of that license shall supersede any condition above with which it is incompatible STRIDE STRIDE the program used for secondary structure calculation is free to both academic and commercial sites provided that STRIDE will not be a part of a package sold for money The use of STRIDE in commercial packages is not allowed without a prior written commercial license agreement See http www embl heidelberg de argos stride stride info html SURF The source code for SURF is copyrighted by the original author Amitabh Varshney and the University of North Carolina at Chapel Hill Permission to use copy modify and distribute this software and its documentation for educational research and non profit purposes is 13 hereby granted provided this notice all the source files and the name s of the original author s appear in all such copies BECAUSE THE CODE IS PROVIDED FREE OF CHARGE IT IS PROVIDED AS IS AND WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED This software was developed and is made available for public use with the support of the National Institutes of Health National Center for Research Resources under grant RR02170 e
58. of the colors used for the molecules and the other graphical objects in the display window The database consists of several color categories each color category contains a list of names and each name is assigned a color The assignment of colors to names can be changed with this window There are 16 colors as well as black the VMD color map and this window can also be used to modify the definitions of these 17 colors For more about colors see the chapter on Coloring 86 2 To see the names associated with a color category click on the category in the Category browser located on the left side of the window Click on the name to see the color to which it is mapped To change the mapping click on a new color in the browser to the right of the Category browser For instance to change the background to white pick Display in the left browser and Background in the center one The right browser will indicate the current color which is initially black for the background Scroll through the right browser and select white to change the background Changing the RGB Value of a Color The Color Definitions tab at the bottom of the Color menu lets you change the RGB definition of the 17 palette colors Select a color to edit using the browser at the bottom left corner of the 49 menu then slide the three sliders to set the amount of each red green and blue component Default restores the original color definition and Grayscale toggles
59. one hydrogen bond The first list contains the indices of the donors the second contains the indices of the acceptors and the third contains the index of the hydrogen atom in the hydrogen bond Known Issue The output of hbonds cannot be considered 100 accurate if the donor and acceptor selection share a common set of atoms inverse matrix Returns the inverse of the given 4x4 matrix minmax selection Returns two vectors the first containing the minimum x y and z coor dinates of all atoms in selection and the second containing the corresponding maxima rgyr selection weight weights Returns the radius of gyration of atoms in selection using the given weight The radius of gyration is computed as n n rip Lune 0 Luo 9 1 i 1 i 1 where r i is the position of the ith atom and 7 is the weighted center as computer by measure center rmsd selection selection weight weights Returns the root mean square distance between corresponding atoms in the two selections weighted by the given weight selection1 and selection2 must contain the same number of atoms the selections may be from different molecules that have different numbers of atoms rmsf selection first first last last step step Returns the root mean square position fluctuation for each selected atom in the selected frames If no first last or step values are provided the calculation will be done for all frames 113 e sasa srad selection point
60. only ones supported presently The periodic images to be drawn are selected by enabling images in one or more of the six faces of the unit cell The Self image selects the untranslated unit cell itself so that one my render a representation consisting of only replica images This feature allows the unit cell and its periodic images to be displayed using different materials for cases where it is desirable to draw more attention to the original unit cell or to one 46 ore more of the replicas The Number of Images counter controls how many replicas are made in each of the six directions Some file formats read by VMD may not include unit cell information in such cases you can use the scripting interface to set the unit cell information manually PDB files containing CRYST1 records are an example of a file format that provides unit cell information 5 4 8 Labels Window v Labels BE Atoms y Show Hide Delete Picked Atom Graph Properties Global Properties Molecule E XYZ 32 947 105 505 81 758 ResName ASN Chain H ResiD faz SegName Name cA Index 24044 Type cA Value 0 000 Figure 5 8 The Labels window The Labels window is used to manipulate the labels which may be placed on atoms and the geometry monitors which may be placed between atoms Labels are selected with a mouse as discussed in section 5 1 2 Once selected the Labels window can be used to turn different labels on or off or to delet
61. option enables or disables on the fly display of the achieved VMD rendering frame rate The frame rate is displayed in the upper right hand corner of the graphics window when it is enabled Lights The graphics display window can use up to four separate light sources to add a realistic effect to displayed graphical objects The Lights On browser turns these light sources on or off If the number is highlighted the light is on and clicking on it turns the light off See section 5 1 1 for more discussion regarding lights Axes A set of XYZ axes may be displayed at any one of five places on the screen each of the corners or the center or turned off This is controlled by the Axes chooser Stage The Stage browser controls the stage which is a checkerboard plane that can be located in any one of six places or turned off Stereo Eye Sep and Focal Length These controls are found in the Display Settings window These controls set the stereo mode and parameters stereo is discussed fully in chapter 7 The Stereo chooser changes the stereo mode while the Eye Sep and Focal Length controls change the eye separation distance and the focal length respectively Cachemode The Cachemode toggle controls whether or not VMD uses a display list caching mechanism to accelerate rendering of static geometry This feature can be extremely beneficial for achieving good interactive display performance on tiled display walls and for remote displa
62. or molecule file It is also possible to install the previous script in the global mailcap file to make it accessible to everyone You will have to consult the documentation for your web browser s to find out how 13 4 3 Example sites Some web sites that send chemical pdb types are the Protein Data Bank at http www rcsb org and Molecules R US at http www nih gov htbin pdb 192 Index mailcap 192 vmdrc 30 95 190 vmdsensors 52 vmd rc 95 190 ACTC 12 AMBER files 24 38 ambient occlusion lighting 103 126 analysis scripting 171 speed 171 angles 47 animate command 96 97 Python module 147 window controls 36 animation 19 frames 38 appending 38 delete 35 96 98 duplicate frame 96 goto end 98 goto start 98 hot keys 33 jump 37 98 movie 93 play 96 read 38 98 smoothing 46 123 155 speed 36 98 step 36 style 98 loop 37 once 37 rock 37 write 35 98 antialiasing 41 103 126 atom 193 changing properties 173 color auto update 122 coordinates 127 128 changing 21 173 min and max 176 info 98 170 name lists 44 picking 20 selection 18 20 60 75 98 170 auto update 122 changing properties 141 comparison 79 default 121 examples 20 75 keywords 45 75 82 83 logic 77 macros 45 99 139 math functions 84 modes 75 Python 139 quoting 77 regular expression 78 same 80 sequence 80 text 170 update 175 volumetric data 84 wit
63. origin and the three cell vectors a b and c are the number of grid points in the respective cell vector directions and finally the data has to be provided as one list with the data following the grid points along the c axis fastest then the b axis and finally the a axis 9 3 20 molecule Same as mol 9 3 21 molinfo The molinfo command is used to get information about a molecule or loaded file including the number of loaded atoms the filename the graphics selections and the viewing matrices It can also be used to return information about the list of loaded molecules Each molecule has a unique id which is assigned to it when it is first loaded These start at zero and increase by 1 for each new molecule When a molecule is deleted the number is not used again There is one unique molecule called the top molecule 5 4 2 which is used to determine some parameters such as the center of view the data in the animation controls etc list Returns a list of all current molecule id s num Returns the number of loaded molecules top Returns the id of the top molecule index n Returns the id of the n th molecule molecule_id get list of keywords molecule_id set list of keywords list of values Access and in some cases modify informa tion about a given molecule The list of recognized keywords is given in Table 9 3 123 Keyword Ais Arg Se DoS Keyword id index numatoms name filename filetype d
64. program bugs or inaccuracies If you have any suggestions bug reports or general comments about VMD please send them to us at vmd ks uiuc edu 1 2 Registering VMD VMD is made available free of charge for all interested end users of the software but please see the Copyright and Disclaimer notices Please check the current VMD license agreement for details Registration is part of our software download procedure Once you ve filled out the forms on the VMD download area and have read and agreed to the license you are finished with the registration process 1 3 Citation Reference The authors request that any published work or images created using VMD include the following reference Humphrey W Dalke A and Schulten K VMD Visual Molecular Dynamics J Molec Graphics 1996 14 1 33 38 11 VMD has been developed by the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology of the University of Illinois at Urbana Champaign This work is supported by the National Institutes of Health under grant number P41 RR005969 1 4 Acknowledgments The authors would particularly like to thank those individuals who have contributed suggestions and improvements particularly those contributing new features Special thanks go to Anton Arkhipov Andrew Dalke Michael Bach Alexander Balaeff Ilya Balabin Robert Brunner Eamon Caddi gan Jordi Cohen Simon Cross Markus Dittrich John
65. range from 0 0 to 0 4 At present only the Tachyon and TachyonInternal renderers are capable of ambient occlusion lighting backgroundgradient lt on off gt Enable or disable the gradient background culling lt on off gt Turn backface culling on or off depthcue lt on off gt Turn depth cueing on or off eyesep value Set the eye separation to value fps lt on off gt Turn frames per second indicator on or off 103 focallength value Set the focal length to value height value Set the screen height to value distance value Set the screen distance to value nearclip lt set add gt value Add or set near clipping plane position to it value farclip lt set add gt value Add or set far clipping plane position to value projection lt perspective orthographic gt Set the projection mode to mode rendermode lt Normal GLSL Acrobat3D gt Set the rendering mode to mode This parameter allows the use of various OpenGL extensions to implement alpha blended transparency or programmable shading for higher quality molecular graphics The default rendering mode does not enable these features since they significantly alter the rendering and performance characteristics of VMD when they are enabled The Acrobat3D mode is used to allow successful capture of molecular geometry into Acrobat3D resetview Reset the view resize valueX value Y Set the size of the display window to valueX x value Y repos
66. representation windowed averaging smoothing function This simple smoothing feature can be used to eliminate much of the thermal noise inherent in a molecular dynamics trajectory so that one can more easily see structural changes occuring over a wider time scale The window size parameter controls how many frames are averaged together to produce the coordinates which are actually displayed One important consideration when using the trajectory smoothing feature is that VMD does not take periodic boundary conditions into consideration when smoothing trajectory coordinates so any atoms which wrap around within the span of the window will cause erratic motions in the displayed representation This can be avoided by unwrapping trajectory coordinates prior to loading into VMD or by using atom selections to eliminate atoms which wrap around Periodic Tab The Periodic tab controls the display of periodic images of a molecule In order to display periodic images a molecule must have unit cell information set for a b c alpha beta and gamma which are discussed in section 9 3 21 When the proper unit cell information is present the periodic display feature can show periodic images of the unit cell by transforming and rendering additional copies of the structure The current implementation of this feature doesn t provide for complex crystallographic symmetry operations Unit cells that can be replicated by translation along the three unit cell axes are the
67. routines use a simple trilinear interpolation of the volume gradients are along with a fast but simple application of Euler s method to advect the particles at each integration step The user adjustable gradient magnitude control affects which points within the volumetric dataset are considered candidates for field line seeds The resulting set of seed points are the initial points from which particles begin advection integration The min and max length controls affect the minimum and maximum length of the resulting field lines that will be selected for display Field lines shorter than the minimum or longer than the maximum are not displayed Similarly field lines that collide with a critical point in the dataset early in their integration are discarded 69 6 1 24 Orbital The Orbital representation draws a molecular orbital isosurface corresponding to a user defined wavefunction amplitude computed on a regularly spaced grid resulting from the selected wave function type spin excitation and orbital index The size parameter controls the thickness of points and line isosurface representations and the grid spacing parameter controls the density of the regular grid upon which the wavefunction amplitude is computed 6 1 25 Beads A bounding sphere is drawn in place of each residue in the atom selection This representation can be used as a crude means of drawing very large structures in a space filling representation and can be partic
68. selection If no selection is given the macro for the given name is returned If no name is given a list of all macro names is returned If a macro already exists for the given name the old selection will be replaced with the new selection Singlewords that are not defined as macros like protein and water cannot be redefined with the macro command e delmacro name Delete the macro corresponding to name Singlewords that are not defined as macros cannot be deleted e molecule_id selection_text frame frame number Creates a new atom selection and returns its name The returned name can be used as a Tcl proc in order to access the atom selection The selection text is the same language used in the Graphics window 5 4 7 and described in Chapter 6 3 It is used to pick a given subset of the atom The text cannot be changed once a selection is made Some of the terms in the selection depend on data that change during a trajectory so far only the keywords x y and z can change over time For these the optional frame value is used to determine which specific frame to use The frame number can be a non negative integer the word now the current frame the word first for frame 0 and last for the last frame Some examples are vmd gt atomselect top name CA atomselect0O vmd gt atomselect 3 resid 25 frame last atomselect1 vmd gt atomselect top within 5 of resname LYR frame 23 atomselect2 The ne
69. start VMD with the options vmd e filename where filename was the name of the file you saved before e After starting VMD from the text console type play filename The most common source of problems is when VMD can t find the files you used to load the molecule If this happens try changing to the directory you were in when you first loaded the molecule or edit the state file and use the full path names where you see mol new mol addfile or mol load commands 3 9 Tracking Script Command Versions of the GUI Actions For most actions performed from the VMDGUI there is an equivalent script command VMDcan print these commands to a log file or the console This is a convenient way to automate file 22 processing by first doing all steps interactively while logging to a file and then editing the logfile to turn it into a Tcl script operating on multiple files There are two ways to do this in VMD e In the main menu press the Log TCL Commands to File button found in the File menu this will bring up a browser window where you can enter a file name in which you can save the resulting script code e In the text console type logfile filename where filename is the name of the log file The resulting file will contain Tcl script code that can be executed from the VMDcommand prompt The Log TCL Commands to Console button or the command logfile console will print the Tcl commands to the console window instead This is most useful if you just
70. supports a number of more advanced input devices such as the Spaceball Magellan and Phantom which provide the ability to manipulate molecules with six degrees of freedom Some devices such as the Phantom can also provide haptic sense of touch force feedback VMD also provides a text console interface for executing built in commands or running scripts This chapter describes how to use the mouse based user interfaces and some of the advanced input devices supported in VMD The the text and scripting interface is described fully in chapter 9 5 1 Using the Mouse in the Graphics Window The graphics window is labeled VMD OpenGL Display and contains a view of the molecules and other objects which make up the scene When the mouse is in the graphics display window it may be used to perform the following actions such as e Rotate translate or scale the displayed molecules e Select or pick atoms or other objects in order to move them or label them e Translate and rotate a set of atoms e Apply a force acceleration to a set of atoms e Move the lights User defined keyboard accelerators or hot keys are also available when the mouse is in the graphics display window These keys are bound to VMD text commands which are executed when the key is pressed VMD has many built in default hot key commands see Tables 5 1 5 2 5 3 and 5 4 Users can add new hot keys overriding default settings if desired 5 1 1 Mouse Modes The mouse is
71. the MIME type to determine how to view the body of the message Some of the documents are viewed by the browser itself like text html which describes HTML documents In other cases the browser has to start up another application From here on we ll describe how Mosaic and Netscape do this First it saves the incoming message body to a temporary file It then scans the global and local mailcap files to determine which application is used to view the given MIME type The application which must take a file name on the command line is then executed When the application exits the temporary file is deleted 191 13 4 2 Setting up your mailcap The Unix versions of VMD have an extra webhelper command line flag which causes VMD not to be spawned in the background so that it has time to read temporary files downloaded by the web browser This command line flag is just slightly simpler to use than the chemical2vmd script as it does not depend on having Perl installed so may be more appropriate for some cases In the VMD installation directory VMDDIR scripts vmd there is a perl script called chemical2vmd which will create a VMD command file and execute VMD Since VMD does not block the calling process Netscape and other web browsers cannot directly call VMD as they do not know when to delete the temporary file containing the molecule or other data The chemical2vmd script starts VMD with the e command line option which runs the saved VMD script
72. the current coloring method for the given representation in the specified molecule modmaterial rep_number molecule_number material_name Change the current material for the given representation in the specified molecule modstyle rep_number molecule_number rep_style Change the current rendering method style for the given representation in the specified molecule modselect rep_number molecule_number select_method Change the current selection for the given representation in the specified molecule addrep molecule_number Using the current default settings for the atom selection coloring and rendering methods add a new representation to the specified molecule default category value Set the default settings for color style selection or material to the supplied value 121 delrep rep_number molecule_number Deletes the given representation from the specified molecule modrep rep_number molecule_number Using the current default settings for the atom se lection coloring and rendering methods changes the given representation to the current defaults delete molecule_number Delete molecule s active molecule_number Make molecule s active inactive molecule_number Make molecule s inactive on molecule_number Turn molecule s on make drawn off molecule_number Turn molecule s off hide fix molecule_number Fix molecule s free molecule_number Unfix molecule s top molecule_number Set the top molecule
73. the first timestep for the given molecule id default top proc print_rmsd_through_time mol top use frame O for the reference set reference atomselect mol protein frame 0 the frame being compared set compare atomselect mol protein set num_steps molinfo mol get numframes for set frame 0 frame lt num_steps incr frame 181 get the correct frame compare frame frame compute the transformation set trans_mat measure fit compare reference do the alignment compare move trans_mat compute the RMSD set rmsd measure rmsd compare reference print the RMSD puts RMSD of frame is rmsd To use this load a molecule with an animation for example VMDDIR proteins alanin DCD from the VMD distribution Then run print_rmsd_through_time Example output is shown here vmd gt print_rmsd_through_time RMSD RMSD RMSD RMSD RMSD RMSD RMSD RMSD RMSD RMSD RMSD RMSD Es 12 5 of of of of of of of of of of of of O is 0 000000 1 is 1 060704 2 is 0 977208 3 is 0 881330 4 is 0 795466 5 is 0 676938 6 is 0 563725 7 is 0 423108 8 is 0 335384 9 is 0 488800 10 is 0 675662 11 is 0 749352 VMD Script Commands for Colors In order to fine tune color parameters one typically needs more sophisticated controls than those offered in the GUI For this reason VMD provides a number of scripting level commands for color access These commands will be di
74. to a maximum of eight and for density map volumes approaching 1 GB in size or larger the algorithm may reduce the number of CPU cores used to four or less to prevent out of memory conditions from occuring at runtime On machines equipped with appropriate GPU hardware the QuickSurf representation will use a GPU accelerated implementation that runs one to two orders of magnitude faster than the CPU version The speed of the GPU algorithm is somewhat dependent on the memory capacity of the target GPUs since density maps larger than the capacity of the GPU must be computed in multiple passes 6 1 19 Surf This option uses the molecular surface solver written by Amitabh Varshney when he was at the University of North Carolina When this option is used the radii and coordinates are written to a temporary file and the surf executable is run with the Probe Radius as a parameter When finished the output is written to another temporary file which is then read by VMD and colored and displayed The value of the probe radius is controlled by the sphere radius and this is identical to the probe size in e Probe Radius Probe radius used to construct the molecular surface e Representation Method The surface can optionally be drawn using lines rather than solid triangles This surface is rather slow in both generation and display for systems over several hundred atoms The SURF calculation is quite exact and will show complete detail even
75. want to find out which VMDcommand is used to perform a specific action Finally the logfile off command or clicking on the Turn Off Logging button will stop the log and close the log file if needed 23 Chapter 4 Loading A Molecule The File menu is the primary means for loading molecules and other data into VMD The built in file readers will load molecular structures from combinations of topology files coordinate files and trajectory files Readers are also included for data such as potential maps electron density maps Grasp surface data and arbitrary 3 D geometric data from Raster3D scene files VMD can load structures directly from Protein Data Bank over the internet provided that a network connection is present Entering the four character PDB accession code in the molecule file broswer form will retrieve and load the structure over the network 4 1 Notes on common molecular file formats VMD natively understands several popular molecular data file formats PDB coordinate files CHARMM NAMD and X PLOR style PSF topology files CHARMM NAMD and X PLOR style DCD trajectory files NAMD binary restart coordinate files AMBER structure PARM and trajectory CRD files including both the old format and the new formats used by AMBER 7 0 and Gromacs e g GRO G96 XTC TRR structure and trajectory files These files may contain some redundant information and can be loaded in different combinations PDB files contains data about
76. when it isn t needed The use of disk space as an interprocess communications medium takes up about half of the run time There is an environment variable 13 2 which can affect the Surf display option e SURF_BIN location of the SURF binary defaults to SURF_ ARCH as defined in the vmd startup script 67 A helpful trick when constructing surfaces is to use the Apply Changes Automatically toggle button on the graphics window wisely That is since surfaces often take a long time to build changing viewing parameters such as the probe radius can cause long delays By default each time you hit the probe radius button VMD rebuilds the surface If you want to reduce or enlarge the probe radius by several increments then you would end up rebuilding the surface multiple times By toggling the afore mentioned button you can force VMD to update on your command only This trick is sometimes helpful with other representations as well For a much faster surface rendering method see the descriptions of MSMS 6 1 20 Quick Surf 6 1 18 6 1 20 MSMS Another molecular surface renderer is MSMS a program written by Michael Sanner of Olsen s lab at Scripps This program is much faster than Surf and can be a better choice depending on how it is used See the web page http www scripps edu pub olson web people sanner html msms home html for more details Available options include e Which Atoms should the surfa
77. with those of molecule 1 You could also use a weighting factor in these calculations The best way to understand how to do this is to see another example set weighted_rmsd measure rmsd sel1 sel2 weight mass Info 10 403022 In this case the weight is determined by the mass of each atom Actually the term is really one of the standard keywords available to an atom selection Other ones include index and resid which would both be rather strange to use as well as charge beta and occupancy These last terms useful if you want to specify your own values for the weighting factors Computing the Alignment The best fit alignment is done in two steps The first is to compute the 4 x 4 matrix transformation that takes one set of coordinates onto the other This is done with the measure fit command Assuming the same selections as before 180 set transformation_matrix measure fit seli sel2 Info 0 971188 0 00716391 0 238206 13 2877 0 0188176 0 994122 0 106619 3 25415 0 23757 0 108029 0 965345 2 97617 0 0 0 0 0 0 1 0 As with the RMSD calculation you could also add an optional weight lt keyword gt term on the end The next step is to apply the matrix to a set of atoms using the move command So far you have two coordinate sets You might think you could do something like sel1 move transformation matrix to apply the matrix to all the atoms of that selection You could but that s not the right selection The thing to
78. 0 1 signifying if there is an inversion center axes Normalized vectors defining rotary axes rotreflect Normalized vectors defining rotary reflections planes Normalized vectors defining mirror planes ideal Idealized symmetric coordinates for all atoms of the selection The coordinates are listed in the order of increasing atom indices same order asa returned by the atomselect command get x y z Thus you can use the list to set the atoms of your selection to the ideal coordinates see example below unique Index list defining a set of atoms with unique coordinates orient Matrix that aligns molecule with GAMESS standard orientation 118 If a certain item is not present e g no planes or no axes then the corresponding value is an empty list The pair format allows to use the result as a TCL array for convenient access of the different return items Example set sel atomselect top all Determine the symmetry set result measure symmetry sel Create array symm containing the results array set symm result Print selected elements of the array puts symm pointgroup puts symm order puts symm elements puts symm axes Set atoms of selection to ideally symmetric coordinates sel set x y z symm ideal 9 3 18 menu The menu command controls or queries the on screen GUI windows e list Return a list of the available menus e menu_name on Turn a menu on e menu_name off Turn a menu off e
79. 08 4 183 12 5 4 Coloring Trick Override a Coloring Category 184 13 Customizing VMD Sessions 185 13 1 VMD Command Line Options 185 13 2 Environment Variables 0 a a 187 133 Startup Files Le ar ts A ae a Si ba A we oe 190 13 3 1 Gore Script Files se so stw daa e a 190 13 3 2 User Script Files a pe s macna he we ee Pe ee ee oe ee eh ee 190 13 3 3 vmdrc and vmd rc Files 0000000 eee ee 190 13 4 Using VMD as a WWW Client for chemical documents 191 TS Ase MIME YDES A begs ed Sik ep Adi Bod eee As 191 13 4 2 Setting up your Mallcap 2 2 0 0000 eee ee ee 192 13 4 3 Example sites gi Dto ace we eee Bena GOS aha Se eat 192 Index 193 List of Figures 3 1 5 1 5 2 5 3 5 4 5 9 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 6 1 6 2 Sample VMD session displaying myoglobin 0 0 0004 18 The Maii WOW ees a aee Woes ek oe Re A ee Pa doe S 34 The Main window animation controls 00000 o 36 The Molecule File Browser window oaao ee 37 The Display menue meia 8 sea a A EAA A eae ae 40 Relationship between screen height SCRHEIGHT screen distance to origin SCRDIST and the Viewer teta a o ds is E a AA Eek eS 43 The Graphics window in Draw Style mode o o 44 The Graphics window in Selections mode 0 o e 45 The Labels window sess te toein E a rt Se a ma de cd 47 The Color window e
80. 1 and the atom coordinates with vmd gt sel get x y z 0 710000 4 211000 1 093000 0 026000 3 700000 0 697000 0 541000 4 841000 2 388000 0 809000 4 462000 2 976000 1 591000 4 371000 3 381000 2 212000 5 167000 4 085000 Note that the format of the data you get back from the get command depends on how many attributes you requested If you request only one attribute as in the get name example above you will get back a simple list of elements On the other hand if you request two or more attributes you will get back a list of sublists Specifically it is a list of size n where each element is itself a list of size i where n is the number of atoms in the selection and 7 is the number of attributes requested Your scripts will run faster if you retrieve only one attribute at a time because then VMD does not have to construct the sublists for each attribute Remember that in Tcl you can loop over several lists at once using the foreach command 171 foreach resid sel get resid resname sel get resname process each resid and resname here One quick function you can build with the coordinates is a method to calculate the geometrical center not quite the center of mass that s a bit harder This also uses some of the vector commands discussed in the section about vectors and matrices 11 but you should be able to figure them out from context proc geom_center selection set the geometrical center to 0
81. 1 letter codes Click on 1 letter code to switch from 3 letter to 1 letter amino acid codes The same button then reads 3 letter code click it to switch back from 1 letter to 3 letter codes e Print contents of sequence window Select File Print to File to create a postscript file containing the current sequence listing and highlighting Turn off highlighting Change highlight style To clear all highlights reselect the current molecule from the Molecule pop up menu To turn the highlight representation off completely for a given molecule find the representation in the Graphics window which the Sequence window has created appears with Bonds ColorlD 4 and set the style to none To change highlighting style set this same representation to your preferred style and coloring The selection for this representation will still change whenever the sequence window selection changes Example application specify Multiple Frames in the Trajectory tab of the highlight representation This will display the trajectory motions of the residues clicked on in the main VMD window or in the Sequence window Caveats e Pause on first use Since the sequence window displays secondary structure of loaded molecules there may be a pause for structure calculation the first time the sequence for a protein is dis played e Selections by chain When there are multiple segments in a chain it is possible for several residues to have the same residue
82. 11 Render Window The Render window is used to export the currently displayed graphics scene to an image file or to a geometric scene description file suitable for use by one of several external renderers which can produce a final image The supported rendering packages are listed in table 8 1 See Chapter 8 for detailed information on how rendering is performed using external programs as well as information on 3 D printing and other uses of the exported scene description files P v File Render Controls Render the current scene to a file Render using Tachyoninterna y Filename plottga Browse Render Command display s Restore default Start Rendering Figure 5 11 The Render window The rendering process works in two stages The first stage exports the displayed VMD scene to a text or image file in the selected format The second optional stage renders the exported file potentially displaying the results when complete The exported file is named in the Filename field a default name is given when a new format is selected so it is best to hold off entering the filename until after the file format is selected Another way to select the filename is available by pressing the Browse button which opens up a file browser Pressing the Start Rendering button writes the data file After that the Render Command is executed The default command should start the appropriate rendering program if it is available
83. 129 93 34 volmap ts Bb EAP a a A Bee ee eee ake ae a 129 OSSD Walls ra al cee A Y A dae ae a ed 135 93 36 Sleepe sn ts hte ell te eo a a eR A Pe a ei 135 9 4 Tel callbackS 20200 do Sak be a eed Ghee ae Yes a 135 10 Python Text Interface 138 10 1 Using the Python interpreter within VMD 138 10 2 Python modules within VMD a 138 10 3 Atom selections in PythoN e 139 10 3 1 The built in atomsel type 02 0002 eee ee ee 139 10 3 2 The AtomSel class DEPRECATED lt lt 139 10 3 3 An atom selection example 000002 pee eee ee 141 10 3 4 Changing the selection and the frame 142 10 3 5 Combining atom selections o 143 10 3 6 RMS example i 2 2 no asa hacen Goes ane bow a den 144 10 4 Python callbacks ss aon ee A a Heo Goal nn cate eed 146 10 4 1 Using Tkinter menus in VMD 0200220004 147 10 5 Controlling VMD from Python 0 0 00 0002 ee ee 147 10 5 1 animate eme SA eee ae Ae a elie Bee we a a le e 147 TUSZ ARES 6 whoo yk ie te Sk a ee Be ee a Rea Se ee de E 148 10 59 38 COlOP E BP EAE ER ee Sek PSY SAS 148 10 04 displays e A A yD ee a 149 105S evalo ts eS E A A AA Ad he ees 149 10 0507 PTAPLIES Lora ETA A ae A ee Read a de a 149 HET A ok es gaits 2 Soe ee a ae ee Bae Set Dee gl Bess 150 OD label x 4 ce dap Gite a a GA Ba ar Aiea ee ie ee ow Sy bes amp Le 151 105 9 ma
84. 180 to 180 degrees The most allowed region of Ramachandran space is colored blue partially allowed regions are colored green After loading a molecule using the pulldown menu in the upper right part of the window to choose a molecule Protein residues in the current molecule are mapped to the Ramachandran diagram with yellow squares Clicking on a square causes the square to turn red displays residue information in the fields on the right side of the window and if trajectory data is present draws the location of the selected residue in Ramachandran space for all frames in the trajectory as empty black squares Clicking one of the empty squares causes VMD to redraw the graphics display window with coordinates from the timestep corresponding to that square Clicking a second time on a red highlighted residue switches off the trajectory information in the RamaPlot window When a protein contains many residues it may be inconvenient to display all residues at once Enter an atom selection in the Selection input to choose which residues to display Note that the selection must contain the alpha carbons name CA of the residues you want to show Note also that just like the Graphics window the selection will not be recomputed if you change the animation frame To print the contents of the white Ramachandran plot select Print to file from the RamaP lot File pulldown menu Enter a filename to save the contents of the window 59 Chapter 6
85. 2 1 Add a label involving the atom s atomID of the molecule molID to the given category show category lt all label_number gt Turn on labels in the given category hide category lt all label_number gt Turn off labels in the given category delete category lt all label number gt Delete labels in the given category graph category label_number filename Retrieve the values of the labels for all timesteps If the optional filename is given the data will be written to that file otherwise it will be returned as a list You can use the Tcl exec command to launch an external graphing program to plot the data if you wish 109 e addspring molID1 atomID1 atomID2 k Add a spring connecting the atom s atomID and atomID2 of the molecule molID The spring will have spring constant k e textsize newsize Get set the text size for all labels which is 1 0 by default newsize should be a decimal value greater than zero e textthickness newthickness Get set the text line thickness for all labels which is 1 0 by default newthickness should be a decimal value greater than zero 9 3 14 light There are four light sources numbered 0 to 3 which are used to illuminate graphical objects They are point sources located at infinity so setting their positions places them along a ray from the origin through the given point e num Return the number of lights available o lightnumber on Turn a light on o light number off T
86. 202 6 1 i 1 where the density p is evaluated at a position 7 by summing over all N atoms Each atom i is located at position 7 and has an associated weighting factor which is determined by multiplying its radius with user defined weighting and scaling factors that customize the visualization to produce a surface with an appropriate user defined level of detail The QuickSurf representation includes several controls which modify the parameters of Eq 6 1 to produce a surface that meets the required spatial fidelity and interactive rendering performance 66 e Resolution An overall spatial resolution approximation slider which automatically sets the values of the detailed parameters below e Radius Scale A radius scaling factor applied to all atoms prior to computing their density map contributions e Density Isovalue The density isovalue to use when extracting the generated isosurface e Grid Spacing The density map uniform lattice spacing parameter e Surface Quality The maximum cutoff distance to use when gathering Gaussian density contributions from atoms or particles in the neighborhood of each lattice point Several factors influence the interactive calculation and display performance of the QuickSurf representation The CPU version of the QuickSurf algorithm is multithreaded but due to the potential for significant memory usage associated with CPU core the number of CPU cores used by the algorithm may be clamped
87. 23 eeo e S448 als be kee ORS ae Oe ed i eaaa 49 The Material Window 23060 58 24 3458 a ee ee es 50 The Render window in 36 netna Ta ea oe EEO ea eh ee eae ee RG 51 The Tool window s ess c e 24239 R RR ANE RE Ree a ee A 52 The Sequence window oaoa 56 The RamaPlot Window ee 59 RGB color scale the three plots shows the contributions of each color and the resulting colors are on the bottom oaoa a a 74 The shift to the red component of the RGB scale caused by the value of min 75 RMS calculation and alignment extension 000002 eee 179 List of Tables 5 1 5 2 5 3 5 4 5 9 6 1 6 2 6 3 6 4 6 5 6 6 6 7 6 8 6 9 6 10 8 1 9 1 9 2 9 3 9 4 Mouse control hot keys e 31 Rotation amp scaling hot keys o ooa o 32 Menu control hot keys olaa a aa ia A es 32 Animation hot Keys use e A a Oak Ee ec 33 Description of secondary structure codes in the Sequence window 57 Molecular view representation styles o e e e 61 Color categories used in VMD 1 2 72 Molecular coloring Methods e 73 Available Color Scale Gradations ooe o ee 74 Atom selection keywords ooa a 82 Atom selection keywords continued o oo o 83 Atom selection functions 84 Read only atom selection keywords which may be used to query the values of an underlying volumetric map in the same molecule The value of N which c
88. 3957 70873 Erase from list Allin memory Only active l Assembly E EA PEE EA Figure 12 1 RMS calculation and alignment extension The RMSD calculator button is used to calculate RMS distances between molecules The upper left corner of the menu is where you specify which atoms are to be used in the calculation In the input field type the atom selection text just as you would in the Graphics window The checkbox below the input field entitled Backbone only restricts whatever atom selection you typed to just the backbone atoms of the selection in effect it adds and backbone to the atom selection text The upper right corner of the menu has a button labeled RMSD Its effect depends on which of the Top Average or Selected radio buttons are selected If Top is selected VMD calculates the RMS distance between the top molecule which is usually the last molecule loaded and every other molecule If Average is selected VMD first computes the average x y z coordinates of the selected atoms in each molecule then computes the RMS distance of each molecule from that average structure Results of the RMS calculations for each molecule are shown in the browser in the bottom half of the menu Note that this list is not updated until you presse the RMSD button so the effects 179 of loading deleting molecules will not be immediately reflected The Total RMSD label at the bottom of the menu shows the average RMSD for all molecules listed R
89. ALIGN the frames of the structure yourself prior to the calculation It will totally mess up the definition of your PBC cells Instead you should use the alignsel option and let volmap handle the alignment However you CAN align the sturcture globally i e align all frames using the SAME transformation matrix to a reference frame In this case you have to provide the transformation matrix you used via transform e pbccenter vector Since the PBC cell origin is stored neither in DCD files nor in VMD you have to specify it in case it is different than the default 0 0 O e maskonly This flag requests to compute only a mask map telling for which gridpoints we expect valid energies i e the points for which the maps overlap for all frames will contain 1 all other points will be 0 This is useful if you don t use periodic boundary conditions where it can happen that due to the choice of the grid and or the rotation of the protein the box including your grid plus the interaction cutoff will lie partially outside your system which means you would miss some of the interactions The map produced by the maskonly mode will tell where are these ill defined regions 134 9 3 35 wait Specify a number of seconds to wait before reading another command Animation continues during this time The wait command will not behave as expected if called within a complex Tel proc or loop structures The wait command doesn t actually run until the next complete
90. AtomSel class has been deprecated in favor of a new built in type called atomsel The atomsel type functions much the same way as the old AtomSel class but also provides methods similar to the Tcl interface for returning RMS fit matrices and applying those transformations to coordinates The new atomsel type is found in a new built in module also called atomsel Use help atomsel to get the complete documentation 10 3 2 The AtomSel class DEPRECATED VMD provides an atom selection class for use in the Python interpreter Instances of this class correspond to a set of atom indices in a particular molecule for a particular coordinate set Once an atom selection is made you can query the properties of the selected atoms such as their names residue ids or coordinates In a similar fashion you can set the values of these properties You can also perform logical operations on atom selections including finding the intersection or union of two atom selections or finding the inverse of the set Finally you can perform tuple operations on the atom selection object to query the indices of the atoms in the selection Atom selection macros can be defined using the macro method of the AtomSel module The syn tax is just as in the corresponding atomselect macro and atomselect delmacro Tcl commands see section 9 3 2 for details Below we summarize the methods available from the AtomSel class e AtomSel selection all molid 0 frame 0 Crea
91. If the periodic cell parameters are defined in VMD the molecule is considered periodic and the grid reflects the coordinates of periodic images of the selection The grid size may be modified from that passed to the routine so that an integer grid dimension fits the dimensions of the box containing the molecule Finally each atom that falls within depth distance of an empty grid point is considered a surface atom and the command returns a list of atom indices for all such atoms 115 e pbc2onc center frame framellast Computes the transformation matrix that transforms coordinates from an arbitrary PBC cell into an orthonormal unitcell Since the cell center is not stored by VMD you have to specify it Here is a 2D example of a nonorthogonal PBC cell A and B are the are the displacement vectors which are needed to create the neighboring images The parallelogram denotes the PBC cell with the origin O at its center The square to the right indicates the orthonormal unit cell i e the area into which the atoms will be wrapped by transformation T B B EAEE ER T ee ee Des ES al y TAR TOE ee Oe ey ee F A displacement vector along X axis with length a B displacement vector in XY plane with length b A displacement vector along X axis with length 1 B displacement vector along Y axis with length 1 O origin of the PBC cell e pbcneighbors center cutoff options Returns all
92. Intensiny gt a N K pa midpoint 0 1 midpoint Color scale range gt Resulting calor scale Figure 6 1 RGB color scale the three plots shows the contributions of each color and the resulting colors are on the bottom direction of the light source with respect to the surface of the displayed object e Specular a number describing the intensity of specular reflections Produces highlights the higher the value the smaller and the brighter the highlight e Shininess a number describing how large is the angle of the specular reflections The smaller the number the wider the angle and the more shiny objects appear Default corresponds to a Phong exponent of 40 For details regarding these material properties consult an elementary graphics book such as Foley amp Van Dam Computer Graphics k Mic o 1 v pant Figure 6 2 The shift to the red component of the RGB scale caused by the value of min 6 3 Selection Methods VMD has a rather powerful atom selection language available It is based around the assumption that every atom has a set of associated with it values which can be accessed through keywords These values could be boolean is this a protein atom numeric as in the atom index or atomic mass or string the atom name The values can even be referenced via a Tcl array To start off here are some examples of valid selection commands in VMD
93. LS below e mask Creates a map which is set to 0 or 1 depending on whether they are within a specified cutoff distance use the cutoff argument of any atoms in the selection The mask map is typically used in combination with other maps in order to hide mask data that is far from a region of interest e occupancy Each grid point is set to either 0 or 1 depending on whether it contains onbe or more atoms or not When averaged over many frames this will provide the fractional occupancy of that grid point By default atoms are treated as spheres using the atomic radii and a gridpoint is considered to be occupied if it lies inside that sphere Use the points argument to treat atoms as points a grid point is occupied if its grid cube contains an atom s center The following optional arguments are universally understood by every volmap map types e allframes Use every frame in the molecule instead of just the current one to compute the volumetric map The method used to combine the various trajectory frame maps can be specified using the combine argument By default volmap only uses the current frame e combine lt avg max min stdev pmf gt Specifies the rule to use to combine frames when using the allframes argument These correspond to keeping the average maximum or minimum values from the range of calculated frames stdev will return the standard deviation for each point over the range of frames and pmf uses
94. MD The combination vmd dispdev text eofexit lt input tcl gt output log is useful for batch mode scripting e startup filename Use filename as the VMD startup command script instead of the default vmdrc or vmd rc file e args Pass subsequent command line arguments to the text interpreter The Tcl interpreter will store these arguments in the list variable argv By default no arguments are stored in this variable e debug level Turn on output of debugging messages and optionally set the current debug level l few messages 5 many verbose messages Note this is only useful if VMD has been compiled with debugging option included 13 2 Environment Variables Several environment variables are used by VMD to determine the location of certain files and directories These variables are accessible to text interface through array env These variables include e DISPLAY Unix only The X Windows display that VMD should use for displaying the VMD windows and menus as well as the graphics window If this environment variable is not overridden by VMDGDISPLAY all VMD windows will be directed to this display e VMDDIR The directory which contains the VMD data files such as this help file and architecture specific executables By default this is usr local lib vmd on Unix systems and C Program Files University of Illinois VMD on Windows sytems e VMDTMPDIR The directory which VMD should use for temporary data files By defa
95. MD to crash The advantage is maximum efficiency and the ability to easily modify atom coordinates without going through the atom selection interface e atomselect molid frame selection Returns an array of int s representing flags for on off atoms in the given atom selection The syntax for the selection is the same as for the AtomSel class An array of this form can be used in conjunction with the Numeric take function to get selected coordinates from a timestep Creating the array in this way can be 50 100 times faster than converting from an AtomSel object 10 6 High level Python Interface VMD provides three modules for accessing and manipulating VMD state with objects that represent important entities These objects can be thought of as references for the actual object within VMD you can create as many references as you want and delete them but modifying the reference changes the actual state of VMD This is different from the AtomSel class where each AtomSel instance is independent of the molecules and reps in VMD These proxy classes are written in pure Python and use the lower level built in interfaces to communicate with VMD 10 6 1 Molecule The Molecule class is a proxy for molecules loaded into VMD Most operations raise ValueError if the proxy no longer refers to a valid molecule i e if the molecule has been deleted Molecule instances provide the following methods e _init__ id None Creating a new Molecule instance with n
96. MS Alignment The RMS Alignment button fits molecules based on selected groups of atoms Whereas the RMSD calculator button finds the RMS distance between molecules without disturbing their coordinates the RMS Alignment button actually moves molecules to new positions This button is quite simple Enter an atom selection in the input field and press Align to align the molecules based on the atoms in that selection If you recompute the RMSD between molecules with the RMSD calculator button you will probably find that the values are different this is because the calculation is made based on the current positions of the atoms 12 4 2 RMS and scripting The same actions can be taken on the scripting level The Text interface also gives you more flexibility through the atom selection mechanism allowing to choose the atoms to fit compare RMSD Computation There are two atom selections needed to do an RMSD computation the list of atoms to compare in both molecules The first atom of the first selection is compared to the first atom of the second selection fifth to fifth and so on The actual order is identical to the order from the input PDB file Once the two selections are made the RMSD calculation is a matter of calling the measure rmsd function Here s an example set sel1 atomselect 0 backbone set sel2 atomselect 1 backbone measure rmsd sel1 sel2 Info 10 403014 This prints the RMSD between the backbone atoms of molecule 0
97. NTOM In the CAVE or Free VR VMD recognizes two types of devices buttons and trackers The built in Spaceball driver can also be used to control tools Configuring input devices To use input devices with VMD tools you need a sensor configuration file in your home directory called vmdsensors see the VMD Installer Guide In this file any number of devices can be specified using a universal sensor locator USL The format for a USL is as follows USL type place name nums e type the type of sensor vrpntracker vrpnbuttons vrpnfeedback cavetracker cavebuttons or sballtracker e place the machine that controls it Devices that cannot yet be used on arbitrary computers over the network must have the keyword local here to be compatible with future versions 52 e name the name of the device within that machine If multiple devices can t currently exist such as with the CAVE then a standard name should be used such as cave so that the same USL will make sense in the future when multiple devices are allowed e nums a comma separated list of numbers of devices belonging to that names optional defaults to zero Some devices demand only one number or a specific number but button devices should work correctly now The lines of a sensor configuration file come in four flavors e Comments begin with and are ignored e Empty lines are also ignored e Device lines have the form device name USL whe
98. OBJ MTL scene format loads into 3DS Max Blender Maya and others art s 500 650 gelato s ghostview s amp povray H500 W400 I s O s tga D X A FT oconv 4S gt s oct rview pe 100 vp 3 5 00 vd 100 48 oct render lt 4s sgi s rgb ipaste 48 rgb rayshade lt s gt s rle prman s true tachyon aasamples 2 mediumshade s format TARGA o 4s tga true l Available from http bund com au dgh eric along with the rest of VORT package 2See http www povray org for more info 3See http radsite 1b1 gov radiance HOME html for Radiance 4See http www bmsc washington edu raster3d for more info 5See http www graphics stanford edu cek rayshade rayshade html for more info See http www photonlimited com johns tachyon for more info Table 8 1 Miscellaneous Rendering Options 94 Chapter 9 Tcl Text Interface The Tcl text interface provides complete access to all the VMD commands Anything that can be done from the menus can be done with VMD text commands 9 1 Using text commands Text commands can be entered into VMD in several ways e Commands can be entered by typing them at the VMD prompt in the text console window This window normally contains the prompt vmd gt When other text e g from a mouse pick is displayed to the screen it will scroll the screen up so the prompt is not at the last line of the screen To make it reappear press enter When entering multi li
99. OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CON TRACT STRICT LIABILITY OR TORT INCLUDING NEGLIGENCE OR OTHER WISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE 1 6 For information on our other software VMD is part of a suite of tools developed by the Theoretical and Computational Biophysics group at the University of Illinois e BioCoRE BioCoRE is a web based collaborative environment for structural biology which provides tools to allow collaboration between researchers down the hall or around the world Anyone with access to the internet and a standard web browser can join BioCoRE and create or be 14 added to research projects and information about a particular project is shared among all members of that project More information is available at the BioCoRE home page e NAMD A parallel object oriented molecular dynamics code designed for high performance simula tion of large biomolecular systems NAMD uses the CHARMM force field and file formats compatible with both CHARMM and X PLOR NAMD supports both periodic and non periodic boundaries with efficient full electrostatics multiple timestepping constant pressure and temperature ensemble simulation methods More information is available at the NAMD home page e MDTools MD Tools is a collection of programs scripts and utilities provided for researchers to
100. R Pine 66 6 1 18 QuickSurf o 408 ve ea a ee Pb ea ee BE SAG 66 AA SU A a ae ees wee Braids Mle ved Sea ie oe Spt Bo he Se Oe E T 67 Ol QO A iste ok Boke cen cos ode Sr 8 As Bn Be ce ab ieee He Ge Mes Wiehe ce Sn tt 68 6 121 Volumesli ce sao ates ote ES A Sos Bod Bee Bee eat Se ea ie ed 68 651 22 ISOSULLACe eta da a ra Qari e ee Se ee eae s E E 69 6 11 23 Ped Dimes 0 a rta he Gere E ok A AA IA tee a 69 6 18 24 Orbital e ma 2s rl ok a da 70 61 20 Beads 3 Senin eke Some hie Bel Roi A ce hel a a a a 70 6 1 267 Dotted oo fh we E te Be Blac tke Cl oe ee we re 70 Ehon SOlvelit raaraa e a o ra Ae le ee hee EAA 70 6 2 Coloring Methods 2 22 24 58 48 HE S49 ed wee eee eae Des 71 6 2 1 Color categories cial A a ARA ig da 6 2 2 Coloring Methods 0 0 00 2 ee ee 6 2 3 Coloring by color categories 2 e 6 2 4 Colorseale mais ke fe ee ge a et Zo Soe ad ele EA 6 2 0 Materials s ai ae m Ae ve Oe a a ae eg eh Gy bod a a Shas 6 3 Selection Methods saaa aa 6 3 1 Definition of Keywords and Functions a 6 3 2 Boolean Keywords 2 i e doaa D y ieee ek eRe Be ee oe a A 6 3 3 Short Cireuiting 2 4 teed Aggy ee De Pe a ete a ae See a 6 3 4 Quoting with Single Quotes 2 0 0000000 2 eee ee ee 6 3 5 Double Quotes and Regular Expressions 00 005 ee 6 3 6 Comparison selections osoo ee 6 3 7 Comparison Operators 6 3 8 Other selections ee 7 Viewing Modes TL Perspe
101. ResName Chain The one character chain identifier Segname The segment names color by SegName Molecule The names assigned to each molecule color by Molecule Highlight The protein nucleic and non backbone colors Restype The residue types color by ResType Structure The secondary structure type helix sheet coil color by Structure Surface The surface types Labels The different labels atoms bonds etc Table 6 2 Color categories used in VMD loaded into VMD Each name is assigned one of the 16 main colors e g cyan blue red and white When the drawing representation needs a color for a specific atom it looks in the appropriate color category and finds that CA is colored cyan N is blue and so on Most of the coloring methods are based on color categories so coloring by ResName colors each residue name differently SegName colors each segment differently and so on The mapping between a given item in a color category and a color can be changed using the Color window 5 4 9 This allows users to make atoms with the name CA be black and the residue CYS be yellow Some attention was given to making the colors reasonable so that oxygens are red nitrogens blue sulphur and cysteines yellow etc 6 2 4 Color scale Several of the coloring methods including Beta Charge and Occupancy describe a range of floating point values rather than a set of names These are colored via
102. Tachyon The Tachyon multiprocessor ray tracing system and derivative code built into VMD is Copy right c 1994 2011 by John E Stone See the Tachyon distribution for redistribution and licensing information e Desmond and Maestro plugins by D E Shaw Research Copyright 2009 D E Shaw Research LLC All rights reserved Redistribution and use in source and binary forms with or without modification are permit ted provided that the following conditions are met Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer Redistributions in binary form must reproduce the above copyright notice this list of con ditions and the following disclaimer in the documentation and or other materials provided with the distribution Neither the name of D E Shaw Research LLC nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBU TORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FIT NESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT IN DIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSEQUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOSS
103. The botton left browser contains a list of the keywords and functions understood by the selection command 86 3 If a keyword is selected which can take on a value for instance name and index then the possible names will be displayed in the bottom rightmost browser The functions can be identified by the to the right of the name After selecting a keyword the right browser will display all the names associated with the keyword For example selecting resname in the left browser will show all the three letter residue names known for the selected molecule Clicking on a field in the value browser will add it to the selection text field Double clicking a keyword field adds the keyword to the text field Press Apply to actually change the atom selection for the current rep Press Reset to restore the atom selection to its original value The Selections tab also shows the atom selection macros that have been defined These macros let you define a commonly used atom selection as a single word so that it can be inserted into a rep more conveniently Atom selection macros can currently be defined only through the Tcl 9 3 2 or Python 810 3 text interfaces see these sections for details 45 Trajectory Tab Selection and Color auto update When an atom selection such as water within 3 of protein is made the atoms in the selection are computed for the current animation frame When the animation frame changes the selection is not normally recalcu
104. Tk Toolkit a simple user interface toolkit that interfaces with Tcl e Easy to extend VMD is written in C and C and employs object oriented design VMD implements a plugin interface for extending its file format support and for general purpose extensions in functionality e Support for multimodal input and various display systems A number of different visual display and control systems are supported in addition to the usual monitor keyboard and mouse The VRPN library is used to get position and orientation information from a wide variety of spatial input devices including magnetic trackers haptic force feedback devices Spaceballs etc VMD works with WireGL and Chromium on tiled display walls and immersive VR environments via compiled in CAVE and Free VR support 1 1 Contacting the authors The current developer of VMD is John E Stone The list of individuals that made signficant contributions to this version of VMD in the form of patches bug fixes and completely new plugins includes Anton Arkhipov Michael Bach Robert Brunner Jordi Cohen Simon Cross Markus Dittrich John Eargle Peter Freddolino Luis Gracia Justin Gullingsrud David Hardy Konrad Hinsen James Gumbart Robert Johnson Axel Kohlmeyer Michell Kuttel John Mongan Jim Phillips Elijah Roberts Jan Saam Alexander Spaar Marcos Sotomayor Leonardo Trabuco Dan Wright and Kirby Vandivort We are very interested in and grateful for any user comments and reports of
105. Tool except that force is applied only along the axis defined by the orientation of the tracker e The Print Tool is meant to be used as a debugging aid when one first sets up VMD for use with VRPN the CAVE or other 3 D input devices When enabled this tool prints text messages to the VMD console indicating the current position of the tool in question This tool is useful when calibrating the various transformation matrices that operate on tracker position and orientation data whether in VMD or in VRPN CAVElib etc To add a new tool to a VMD session open the Tool window and click the Create Tool button The tool s number and type are displayed in the list to the left Devices can be added to the tool by selecting them from the Add Device menu or removed with the Delete Device button Some of the options that can be specified in the sensor configuration file can be edited in using the controls below and the tool s type can be changed with the Type menu 54 5 4 13 IMD Connect Simulation Window VMD has the ability to work with a molecular dynamics program running on another computer to interact with and display the results of a simulation as they are calculated A major feature in VMD is the ability to add perturbative steering forces to a running simulation which are incor porated directly into the dynamics calculation we refer to this capability as Interactive Molecular Dynamics IMD In order to run and IMD simulation it is nece
106. a thermal average In ae e values N for each point The default is avg except for ligand maps where the default is pmf 130 e res resolution Sets the resolution of the map This means that the volume will be subdivided into many small cubes whose side have a length of resolution e minmax min Ymin 2min max Ymar Zmax Allows the user to specify the min max boundaries of the grid in which the volumetric map will be computed The argument to minmax is a list of two 3 vectors specifying the minimum and maximum coordinates of the desired volumetric data grid e checkpoint frequency For the analysis of long trajectories it can be desirable to have intermediate outputs of the volmap computation The checkpoint option forces the volmap computation to output a map of what has been computed so far at every frequency frames The default frequency is 500 setting the frequency to zero disables the checkpointing feature e mol lt molid top gt Exports the final volumetric data into the VMD molecule specified by molid By default all maps are exported to a file or name maptype_out dx using the mol option overrides this e o filename Exports the final volumetric data into a DX file dx extension is added if missing By default all maps are exported to a file or name maptype_out dx The following optional arguments are special arguments understood only by some volmap map types Some arguments may only apply to certain map t
107. advertising materials mentioning features or use of this software must display the fol lowing acknowledgment This product includes software developed by Brad Grantham and Applied Conjecture 4 Neither the name Brad Grantham nor Applied Conjecture may be used to endorse or promote products derived from this software without specific prior written permission 5 Notification must be made to Brad Grantham about inclusion of this software in a product including the author of the product and the name and purpose of the product Notification can be made using email to Brad Grantham s current address grantham plunk org as of September 20th 2000 or current U S mail address Python Python is made available subject to the terms and conditions in CNRI s License Agreement This Agreement together with Python may be obtained from a proxy server on the Internet using the following URL http hd1 handle net 1895 22 1012 PCRE The Perl Compatible Regular Expressions PCRE library used in VMD was written by Philip Hazel and is Copyright c 1997 1999 University of Cambridge Permission is granted to anyone to use this software for any purpose on any computer system and to redistribute it freely subject to the following restrictions 1 This software is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE 2 The origin of this software must
108. ain residue 22 get the CA coordinates could do next two on one line set CA atomselect top name CA and residue 22 set CAcoord lindex CA get x y z 0 and get the CB coordinates set CB atomselect top name CB and residue 22 set CBcoord lindex CB get x y z 0 apply a transform of 10 degrees about the given bond axis sidechain move trans bond CAcoord CBcoord 10 deg 12 3 Analysis scripts Following are some more examples of routines that could be used for analysing molecules These are not the best routines to use since many of these can be implemented with the measure command which calls a much faster built in function Finding waters near a protein This example finds the waters near the protein for each frame of a trajectory and writes out a PDB file containing those waters set sel atomselect top water and same residue as within 2 of protein set n molinfo top get numframes for set io i lt n incr i 4 sel frame i sel update sel writepdb water_ i pdb The frame option sets the frame of the selection update tells the atom selection to recompute which waters are near the protein and writepdb writes the selected waters to a file Total mass of a selection proc total_mass selection set sum 0 foreach mass selection get mass set sum expr sum mass return sum Note the curly braces after the expr command in the above example Omitting those bra
109. aining three floats specifying the RGB value 2 an integer corresponding to a color index or 3 a string corresponding to a color name e cone id vi v2 radius 1 0 resolution 6 Draw a cone with base at v1 and point at v2 radius and resolution may optionally be specified with keyword arguments e sphere id center 0 0 0 0 0 0 radius 1 0 resolution 6 Draw a sphere The sphere center radius and resolution may optionally be specied with keyword argu ments e text id pos text size 1 0 Draw text at the given position specified by a tuple of three floats using the string text Size may optionally be specified using keyword argu ments e delete id index Deletes the graphics primitive with the given index Alternatively if the string all is passed as the index all graphics primitives will be deleted e replace id index Deletes the graphics primitive with the given index The next graph ics primitive added will go in the newly vacated position Subsequent graphics primitives will resume at the end of the list e info ind index Returns a string describing the graphics primitive with the given index If the index is invalid an IndexError exception is raised e listall ind Returns the indices of the valid graphics primitives in a list 10 5 7 imd Python operations available from the imd module used to display and interact with a molecule in a molecular dynamics simulation e connect host port Co
110. al with the given name e rename oldname newname Rename the material with the given name The new name must not yet be used e change name ambient specular diffuse shininess opacity Change one or more of the material settings for the material with the given name Keyword arguments may be used to specify each property 10 5 10 molecule Python operations available from the molecule module used to load molecules and change their representations e num Returns the number of loaded molecules e listall Returns the molid s of the all the loaded molecules e exists molid Returns true if the molid corresponds to an existing molecule e new name Creates a new empty molecule with the given name and returns its id 152 load structure sfname coor cfname Load a molecule with structure type structure and filename sfname Additionally a separate coordinate file may be provided of type coor and name cfname New in VMD 1 8 All frames from cfname will be processed before the function returns If successful the function will return the id of the new molecule gt gt gt load pdb alanin pdb gt gt gt load psf alanin psf dcd alanin dcd cancel molid Cancel loading of coordinates file for the given molecule delete molid Delete the specified molecule read molid type filename beg 0 end 1 skip 1 waitfor 1 volsets 1 write molid type filename be
111. align ref sel frame 20 does not work That s because sel frame 10 overrides frame 20 in this case since they 144 are applied to the same AtomSel instance Either use the frame argument as illustrated here or create a new AtomSel instance for the reference Perform a mass weighted RMSD alignment and compute the mass weighted RMS distance from the first frame w sel get mass rms ref AtomSel backbone frame 0 for i in range n rms append sel frame i align ref ref weight w rmsd ref weight w Initialize result list rms Go for i in range m numFrames rms append sel rmsd sel frame i weight mass Here s another RMSD example that uses the align method from AtomSel import AtomSel from Molecule import Molecule mol1 Molecule mol1 load proteins alanin psf mol1 load proteins alanin dcd n mol1 numFrames sel AtomSel backbone align all frames with the first frame using the backbone atoms for i in range 1 n sel align frame i align all frames with frame 10 for i in range 1 n sel align ref sel frame 10 frame i Align residues 1 3 from frame 10 with frame 20 but use all backbone atoms to perform the fit resid123 AtomSel resid 1 to 3 sel align ref sel frame 20 frame 10 move resid123 GOTCHA ALERT sel frame 10 align ref sel frame 20 does not work That s because sel frame 10 overrides frame 20 in this
112. alues such as the distance between two atoms a bond label an angle between three atoms an angle label or the dihedral angle formed by four atoms a dihedral label This is done by setting the mouse into the proper picking mode and then selecting the relevant atoms with the mouse Picking modes are selected from the Mouse menu The available pick mode actions are 28 Center hot key c This mode is used to change the point about which a molecule rotates when the molecule is rotated To cause a molecule to rotate about a specific atom select this mode and then click on that atom The rotation point may be restored to its default position the center of volume of the molecule by executing the Reset View option from the Mouse menu Query hot key 0 Clicking on an item will print out the name of the item e g the atom name to the text console window Label Atom hot key 1 Clicking on an atom will toggle on off a label for the atom Label Bond hot key 2 Clicking on two atoms in a row will toggle on off a bond distance label between the two atoms a dotted line with the distance printed at the midpoint Label Angle hot key 3 Clicking on three atoms in a row will toggle on off a label showing the angle formed by the three atoms Label Dihedral hot key 4 Clicking on four atoms in a row toggles on off a label showing the dihedral angle formed by the four atoms Move
113. ame counters shown in the animation control reflects the state of the top molecule Commands entered via this control however affect all active molecules 5 4 2 not just the top molecule allowing concurrent animation of multiple molecules Animation Speed The rate of playback can be controlled in two ways The Step control changes the animation step size By default the frame step is 1 so each step of the playback increases or decreases the 36 animation frame number by one If the frame step is 5 then the animation proceeds five times faster because only a fifth of the frames are shown The Speed slider at the bottom of the window also affects the playback speed Internally this controls how many screen updates are needed between each step By default the slider is at the far right indicating that one step is performed for each screen redraw Moving the slider to the left increases the minimum time required between updates Jumping to Specific Frames The start and end buttons are used to simplify the comparison between the initial and final struc tures The start button resets the current animation to the first frame and end jumps to the last frame If you need to jump to a specific frame enter the frame number in the frame counter text area next to the start button and press enter One thing to bear in mind is that the frame number starts at 0 so to jump to the 5th frame you must actually enter 4 here The animation controls a
114. ames 46 122 files 24 read 38 smoothing 46 123 155 write 35 trans Python module 156 translate command 97 128 translation change atom coordinates 174 using mouse 28 transparency 43 unit cell information 46 universal sensor locator 52 user command 97 128 user interfaces python 138 text 95 USL 52 variables env 187 190 M_PI 167 trace 135 vector command coordtrans 167 vecadd 161 veccross 163 vecdist 164 vecdot 162 vecinvert 164 windows 119 veclength 163 veclength2 163 XPLOR vecmean 162 files 24 38 vecnorm 163 vecscale 162 vecstddev 162 vecsub 162 vecsum 162 vectrans 167 veczero 161 vector routines 161 view 120 viewing modes changing 86 VMD as MIME helper application 191 command line options 185 compile options 129 copyright 12 customizing 30 185 vmdinfo command 97 129 volmap command 97 129 volumetric data 68 69 generating 129 wait command 97 134 window animate 19 color 21 49 71 72 display 40 files 17 graphics 18 20 42 hot keys 32 IMD simulation 55 label 47 main 34 36 material 50 molecule file browser 37 mouse menu 38 RamaPlot 58 render 19 51 sequence 56 tool 52 200
115. an be 0 to 7 inclusively refers to the volID of the underlying volumetric data e g you could type interpvol2 A A IA Bs ee aie ad 84 Regular expression methods o oo aa a ee 84 Regular expression conversions soosoo o a e a 85 Miscellaneous Rendering Options e 94 Summary of core text commands in VMD oaaae 97 On line Help Sources a t ee 108 molinfo set get keywords 2 0 124 Description of Tcl callback variables in VMD 0 0 2 00 136 Description of callbacks available to scripts running in the embedded Python inter Chapter 1 Introduction VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins nucleic acids lipids and membranes VMD runs on all major Unix workstations Apple MacOS X and Microsoft Windows Online information about VMD is available from http www ks uiuc edu Research vmd List of key VMD features General molecular visualization At its heart VMD is a general application for displaying molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities VMD reads data files using an extensible plugin system and supports Babel for conversion of other formats User defined atom selections can be displayed in any of the standard molecular representations Displayed graphics can be exported to an image file to a scene file usa
116. and resid 5 gt gt gt ORsel name CA or resid 5 gt gt gt NOTsel not name CA gt gt gt When the combined atom selections are from different molecules or have different frame num bers the molecule and frame from the first atom selection are used 143 10 3 6 RMS example Example find the mass weighted RMS distance from the initial frame This assumes a molecule and its timesteps have already been loaded see the description of the Molecule class from AtomSel import AtomSel from Molecule import Get a reference to the first molecule m moleculeList 0 Select all atoms sel AtomSel We are comparing to the first frame sel frame 0 Get the mass weights mass sel get mass Here s another RMSD example that uses the tt align method begin verbatim from AtomSel import AtomSel from Molecule import Molecule mol1 Molecule mol1 load proteins alanin psf mol1 load proteins alanin dcd n mol1 numFrames sel AtomSel backbone align all frames with the first frame using the backbone atoms for i in range 1 n sel align frame i align all frames with frame 10 for i in range 1 n sel align ref sel frame 10 frame i Align residues 1 3 from frame 10 with frame 20 but use all backbone atoms to perform the fit resid123 AtomSel resid 1 to 3 sel align ref sel frame 20 frame 10 move resid123 GOTCHA ALERT sel frame 10
117. and molecule id global vmd_pick_atom vmd_pick_mol set sel atomselect vmd_pick_mol same residue as index vmd_pick_atom set mass 0 foreach m sel get mass set mass expr mass m get residue name and id set atom atomselect vmd_pick_mol index vmd_pick_atom lassign atom get resname resid resname resid print the result puts Mass of resname resid mass 135 Table 9 4 Description of Tcl callback variables in VMD When called Molecule molid was deleted Molecule molid was created data may not have been loaded yet Molecule molid was renamed Structure file loaded Coordinate file loaded Molecule molid changed ani mation frames Any VMD command executed An atom has been picked using the Pick mouse mode Pointer moved Pointer moved Pointer moved Atom picked IMD coordinate set received Set of labels to be graphed Tcl interpreter is shutting down vmd_molecule molid vmd_molecule molid vmd_molecule molid vmd_initialize_structure molid vmd_trajectory read molid vmd_frame molid vmd_logfile vmd_pick_event vmd_pick_client vmd_pick_mol_silent vmd_pick_atom_silent vmd_pick_shift_state vmd_timestep molid vmd_graph_label vmd_quit 136 1 name of coordinate file new animation frame Tcl text equivalent of com mand When receiving this event the following global variables are also set vmd_pick_atom id of picked atom vmd_pick_
118. apability there may be alternate ways to perform full screen antialiasing by selecting an option in the display driver setup Windows machines most commonly place these controls in the display driver configuration panel Depth Cueing Turns depth cueing on or off Depth cueing causes distant objects to blend into the background color in order to aid in 3 D depth perception The depth cueing settings controlled in the Display Settings window The Cue Mode parameter controls which type of fog equation is used The Linear depth cueing mode provides a simple depth gradient with a defined starting point and endpoint The Exp and Exp2 depth cueing modes take a density parameter and generally blend into the background color much more sharply than the linear depth cueing mode Scaling up the molecule will increase the amount of depth cueing effect that is visible since it will occupy a larger depth range Scaling the molecule size down decreases the depth cueing effect Translating the molecule into and out of the screen will cause it to blend into and out of the background color Culling Turns backface culling on or off This feature is primarily used to accelerate ren dering performance on software based implementations of OpenGL such as Mesa Backface culling actually reduces performance on some hardware renderers so you ll have to use your own best judgement on whether or not it is helpful to use on your specific computer system FPS This
119. ar to a PSF in that it too contains 24 no coordinate information It must be loaded along with a CRD trajectory file If a PARM and CRD file are loaded together then only the segname and chain ID for the atoms are left blank A CRD or DCD file can be specified along with the PDB in which case the PDB file will be read as normal and then coordinate sets are read from the DCD or CRD until the end of the file is reached Gromacs GRO and G96 files can be loaded on their own since they contain the necessary atom data and coordinates They can also be loaded along with TRR and XTC files to obtain trajectory data Additional coordinates from a PDB CRD or DCD file can be appended to the current coordinate set using the Molecule File Browser form 4 2 What happens when a file is loaded When a coordinate file is loaded by itself i e just a PDB no PSF VMD uses heuristics to replace missing values that would normally be provided by a structure file If necessary VMD does a distance based bond search to determine connectivity A bond is formed whenever two atoms are within R Ra x 0 6 of each other where R and Ra are the respective radii of candidate atoms If both structure and coordinate files are loaded no approximations or guesses are made After the molecule is read in new names are added to the coloring categories 6 2 3 and assigned colors Next bond connectivity is established and the molecule is analyzed to identify its compon
120. aster3D 26 92 regular expression 78 84 X PLOR conversion 85 remote connection 108 detaching 56 killing 56 modifiable parameters 55 options 108 simulation control 108 render command 97 126 Python module 155 window 19 51 rendering 19 51 90 ambient occlusion lighting 103 126 antialiasing 126 ART 94 caveats and considerations 91 exec command 127 Gelato 94 in background process 52 list of supported renderers 94 methods 94 126 PostScript 94 POV Ray 94 Radiance 94 Raster3D 94 Rayshade 94 RenderMan 94 stereo 92 STL 94 Tachyon 12 14 19 94 126 TachyonInternal 94 126 VRML 1 94 VRML 2 94 Wavefront 94 rendering modes 104 rendermode 42 representation 60 120 add new 43 adding 43 auto update 46 Beads 70 Bonds 61 Cartoon 65 changing 20 43 121 clipping planes user defined 121 CPK 63 deleting 44 dotted van der Waals 70 draw multiple frames 122 DynamicBonds 62 examples 21 FieldLines 69 HBonds 62 hiding 44 Isosurface 69 Licorice 63 Lines 61 list of available 61 MSMS 68 NewCartoon 66 NewRibbons 65 Orbital 70 PaperChain 66 Points 62 Polyhedra 63 QuickSurf 66 Ribbons 64 show hide 123 155 solvent representation 70 style 18 42 60 121 Surf 67 198 Trace 64 Tube 64 Twister 66 van der Waals 63 VolumeSlice 68 represention auto update 122 reset view 40 resetview 104 restore
121. at you type In order to use the Python interpreter you have to tell VMD to switch to Python mode There are three ways to do this 1 Type gopython in the console window 2 pass python as a command line option or 3 put gopython on the last line of your vmdrc file If VMD prints an error message reporting that the Python interpreter is not available your version of VMD was not compiled with Python support contact the VMD developers for help If all goes well you should see Python command prompt gt gt gt in the console window To switch back to the Tcl interpreter press Ctrl D as though you were exiting Python Switching back and forth between Python and Tcl does not destroy any of your work all variables and modules will still be defined until you exit VMD Typing gopython lt filename gt where lt filename gt is the name of a file containing Python code will cause VMD to switch to Python mode process the file then switch back to Tcl In this way you can embed Python functions inside your Tcl scripts You can also type gopython command your code here to run an arbitrary line of python code 10 2 Python modules within VMD Once you enter the VMD Python environment you will find a module called VMD already loaded This module contains all the other built in modules for writing VMD Python scripts VMD is not distributed with an entire Python environment In order to use the set of libraries that no
122. atabase accession remarks active drawn fixed top center center_matrix rotate_matrix scale_matrix global_matrix view_matrix numreps selection 2 rep 2 color i numframes numvolumedata frame timesteps angles dihedrals impropers bond angle dihedral improper vdw electrostatic hbond kinetic potential energy temperature pressure volume efield alpha beta gamma displayed ant int int str str str str str str bool bool bool bool vector matrix matrix matrix matrix matriz int string string string int int int int list list list float float float float float float float float float float float float float float float float float float float float KKM KK KKK KAZ Z Z Z Z Z Z Z Z Z ZK KKK Z Z Z Z Z Z Z K KKK KKK Z Z Z Z Z Z Z molecular id index on the molecule list number of atoms the name of the molecule usually the name of the file list of filenames for all files loaded for this molecule list of file types for this molecule list of databases for this molecule list of database accession codes for this molecule list of freeform remarks for this molecule is make the molecule active is make the molecule drawn is make the molecule fixed is make the molecule top get set the coordinate used as the center get set the centering matrix get set the rotation matrix get set the scaling matrix get set the global rotation scaling
123. ate 2 about x k Cntl p rotate rotate 2 about x 1 Cntl f rotate rotate 2 about y h Cntl b rotate rotate 2 about y rotate rotate 2 about z rotate rotate 2 about z scale by 1 enlarge 10 percent scale by 0 shrink 10 percent Table 5 2 Rotation amp scaling hot keys Hot Key menu main off menu main on Show main menu menu files off menu files on Show files menu menu graphics off menu graphics on Show graphics menu menu labels off menu labels on Show labels menu menu render off menu render on Show render menu menu display off menu display on Show display menu menu color off menu color on Show color menu display resetview Reset display quit confirm Quit VMD with confirmation quit Quit VMD hyperref invert Invert hyper text mode NOT help Table 5 3 Menu control hot keys The Windows version of VMD uses the vendor provided SpaceWare driver exclusively and oper ates somewhat differently from the serial interface software used on Unix The SpaceWare software runs as a separate process from VMD and must be started and fully operational before VMD is run At startup time VMD attempts to open the SpaceWare interface displaying the success or failure of initialization as it occurs with applicable diagnostic information The SpaceWare driver provides detailed control over the sensitivity and configuration of the Spaceball In order to use the Spaceball function keys with VMD the SpaceWare driver mus
124. ating columns in the final image This mode is generally supported by low cost gaming GPUs 7 3 6 Row Interleaved Stereo Row interleaved stereo also referred to as scanline interleaved or line blanking stereo works by interleaving the left and right eye views every other scanline in the display The stereo hardware then decodes the interlaced signal and either separates them into two separate displays or blanks the even or odd scanlines to display only the left or right eye image at the same time that shutter glasses are polarized in the appropriate way The only special requirements for the graphics accelerator are that it provide a stencil buffer which is used to generate the alternating scanlines in the final image This mode is generally supported by low cost gaming GPUs 7 3 7 Anaglyph Stereo Anaglyph stereo refers to the use of colors to separate the left and right eye views from each other The user must wear glasses with colored lenses such as the red blue glasses one finds at some sci fi and horror movie showings Anaglyph stereo has one major disadvantage when compared with quad buffered stereo which is that its color rendition is severely constrained This is an unavoidable limitation of anaglyph stereo and it is up to the user to use color schemes for their molecules that still look visually pleasing in this mode This mode is supported by all GPUs 88 7 3 8 Stereo Parameters A stereo image is generated by drawing two images
125. atoms residues segment names occupancy and beta factor and one coordinate set PSF and PARM files contain atoms residues segment names residue types atomic mass and charge and the bond connectivity VMD supports four file formats used by Gromacs GRO G96 TRR and XTC GRO and G96 files contain structure information including atoms residue and segment data and one coordinate set CRD DCD TRR and XTC files contain only coordinate data frames It should be noted that while PDB GRO and G96 files were designed to contain only one coordinate set multiple files can be concatenated into one larger file to create a makeshift trajectory file which can be loaded by VMD When VMD loads a file it requires information about atom names and coordinates and tries to fill in the rest Since the PDB file contains all this information it does not need to be loaded with any other data files However the PDB file doesn t contain the atom types masses and charges so these are guessed or assigned default values In particular charges will be assigned a value of 0 0 if the file does not contain explicit charge information A PSF file does not contain coordinate information so it must be loaded along with a PDB or DCD file If a PDB and PSF are given there is no missing data and VMD makes no assumptions If a PSF and DCD are given then only the chain identifier and occupancy and beta values are missing so they are given a default value A PARM file is simil
126. bc flag which automatically takes atoms of the neighboring cells into account Before starting the computation the atomic radii of each atom in the molecule should be set to the corresponding CHARMM Lennard Jones Rmin 2 parameter in Angstrom and the beta value of each atom should be set to the CHARMM Lennard Jones e energy well depth in kcal mol parameter This can be done using VMD s VolMap plugin Simply call in succession the following commands within the VMD console environment to use default CHARMM values for the various atoms of a molecule package require ilstools ILStools readcharmmparams list of CHARMM parameter files ILStools assigncharmmparams lt molid gt The following optional arguments are understood e first frame First frame to process default frame 0 e last frame Last frame to process default last frame of molecule e o filename Exports the final volumetric data into a DX file dx extension is added if missing By default all maps are exported to a file or name maptype_out dx e res resolution Sets the resolution of the final map This means that the volume will be subdivided into many small cubes whose side have a length of resolution The computa tion should be performed on a finer grid see subres option but at the end the map is downsampled to this resolution A good choice for the grid resolution 1 A argument res Lower resolutions make it difficult to see features higher ones will be very
127. be about the same as the angular spacing of the orientation vector itself If the probe has at least one symmetry axis then the rotations around the orientation vectors are reduced accordingly If there is an infinite oder axis linear molecule the rotation will be omitted In case there is an additional perpendicular C2 axis the half of the orientations will be ignored so that there are no antiparallel pairs Probes with tetrahedral symmetry Here n denotes the number of rotamers for each of the 8 orientations defined by the vertices of the tetrahedron and its dual tetrahedron 133 e cutoff cutoff Set the CHARMM van der Waals cutoff beyond which the interaction between the probe and protein atoms is set to zero e maxenergy energy Cutoff energy above which the occupancy of a grid cell is regarded zero For GPUs energies of more than 87 always correspond to floating point values of zero for the occupancy Hence there is no point going higher than that For CPUs that number is higher however the lower the occupancy the more severely these points will be undersampled and the according error will be very high Thus in the final map it probably does not make sense to look at values higher than 10kT which not a big loss since the low energy regions are the ones we are interested in So you probably want to set this to a value between 10 and 87 we are in thye process of testing this but I suppose 20 kT would be a safe number e alignsel selec
128. be wrapped Le if you for instance impose an axis on a molecule that has no such rotary symmetry within the given tolerance then nothing will happen Result The return value is a TCL list of pairs consisting of a label string and a value or list For each label the data following it are described below pointgroup The guessed point group For point groups that have an order associated with it like C3v or D2 the order is replaced by n and we have Cnv or Dn The order is given separately see below order Point group order i e order of highest axis 0 if not applicable elements Summary of found symmetry elements i e inversion center rotary axes rotary reflections mirror planes Example i C3 3 C2 S6 3 sigma for point group D3d missing Elements missing with respect to ideal set of elements same format as above If this is not an empty list then something has gone awfully wrong with the symmetry finding algorithm additional Additional elements that would not be expected for this point group same format as above If this is not an empty list then something has gone awfully wrong with the symmetry finding algorithm com Center of mass of the selection based on the idealized coordinates see ideal below inertia List of the three axes of inertia the eigenvalues of the moments of inertia tensor and a list of three 0 1 flags specifying for each axis wether it is unique or not inversion Flag
129. bel in the central browser and pressing the Hide button To turn it back on select it again then press the Show button Press the Delete button to delete it This browser allows multiple selections which for example allows you to delete several labels at once To select everything in the current category press Select All to unselect them press Unselect All If nothing is selected the action is applied to everything Thus one way to turn everything off is to press Unselect All then press Hide It may seem counterintuitive but it was done this way so all the labels could be deleted by just pressing Delete Pick information The Picked Atom tab displays information about the last atom picked by the mouse This informa tion is also echoed to the vmd console The data in the will remain in until a new label is selected by the mouse Information about the following fields is identified e Molecule the name of the molecule referenced e XYZ the position of the atom in 3D space e Resname the type of the amino or nucleic acid to which this atom belongs e ResID the internal VMD ID number of the entire residue to which the particular atom belongs E g ResId for an atom of a protein is the same as the residue number of that atom as listed in its PDB file e Name the name of the atom as it appeared in the coordinate file e Type the type of the atom as determined by an internal VMD match up of the given name to a likely atom type ass
130. between atoms 3 and 5 of molecule 1 for all frames measure bond 3 5 1 molid O first 7 Returns the bond energy between atoms 3 of molecule 0 and atom 5 of molecule 1 The value is computed for all frames between the seventh and the last frame of molecule 0 e angle atom_list options Returns the angle spanned by three atoms Same input format as the measure bond command 114 e dihed atom_list options Returns the dihedral angle defined by four atoms Same input format as the measure bond command e imprp atom_list options Returns the improper dihedral angle defined by four atoms Same input format as the measure bond command e energy energy term atom_list parameters options Returns the specified energy term for a given set of atoms The energy term must be one of bond angle dihed imprp vdw or elect where vdw stands for van der Waals and elect for electrostatic energy The energy is computed based on the CHARMM force field functions the given parameters and the current coordinates All options for the measure bond command work for measure energy too Thus you can for instance request energies for a range of frames of a trajectory Also the format of the atom list is the same The following parameters can be specified k lt value gt force constant for bond angle dihed and imprp energies in kcal mol A or kcal mol rad respectively x0 lt value gt equilibrium value for bond length angle dihedral
131. bjects from graphics primitives The first argument to all operations is the id of a Graphics molecule Graphics molecules are created using the load command in the molecule module load graphics gt test creates a Graphics molecule named test For vertices and normals a tuple with three float items is required e triangle id vi v2 v3 Draw a triangle with the given vertices e trinorm id vi v2 v3 n1 n2 n3 Draw a triangle with the given vertices and vertex normals 149 e cylinder id v1 v2 radius 1 0 resolution 6 filled 0 Draw a cylinder with endpoints specified by the given points Radius resolution and filled whether the ends should be capped or not may be optionally specified with keyword arguments e point id v Draw a point at the given coordinates e line id vi v2 style solid width 1 Draw a line between the given vertices Optionally the line style may be specified as either solid or dashed and width may be any positive integer e materials id onoff Turns materials on off for subsequent graphics primitives Primi tives lying earlier in the stack are not affected onoff should be either 0 off or 1 on e material id name Sets the material for all graphics primitives in this molecule name should be one of the material names returned by material listall e color id color Set the color for subsequent graphics primitives color may be 1 a tuple cont
132. ble by ray tracing programs or to a geometry description file suitable for use with 3 D printers Visualization of dynamic molecular data VMD can load atomic coordinate trajectories from AMBER Charmm DLPOLY Gromacs MMTK NAMD X PLOR and many other simulation packages The data can be used to animate the molecule or to plot the change in molecular properties such as angles dihedrals interatomic distances or energies over time Visualization of volumetric data VMD can load generate and display volumetric maps Supported map formats include CryoEM maps electrostatic potential maps electron density maps and many other map file formats Interactive molecular dynamics simulations VMD can be used as a graphical front end to a live molecular dynamics program running on a remote supercomputer or high performance workstation VMD can interactively apply and visualize forces in an MD simulation as it runs Molecular analysis commands Many commands are provided for molecular analysis These include commands to extract information on sets of atoms and molecules vector and matrix routines for coordinate ma nipulation and functions for computing values such as center of mass and radius of gyration 10 e Tcl and Python scripting languages VMD uses the freely available Python and Tcl scripting languages for processing text com mands These popular languages which contain variables loops subroutines and much more VMD also uses the
133. bone conformational angles selects atoms within a specified distance of a selection i e within 5 of name FE exclusive within equivalent to within 3 of X and not X selects atoms which have the same keyword as the atoms in a given selection i e same segname as resid 35 force to apply in the x y or z coordinates Table 6 6 Atom selection keywords continued 83 interpvolN float square of x square root of x absolute value of x largest integer not greater than x smallest integer not less than x sine of x cosine of x tangent of x arctangent of x arcsin of x arccos of x hyperbolic sine of x hyperbolic cosine of x hyperbolic tangent of x e to the power x natural log of x log base 10 of x Table 6 7 Atom selection functions value of the voxel of the volumetric data of ID N nearest to the atom interpolated value of the voxels of the volumetric data of ID N around the atom Table 6 8 Read only atom selection keywords which may be used to query the values of an under lying volumetric map in the same molecule The value of N which can be 0 to 7 inclusively refers to the volID of the underlying volumetric data e g you could type interpvol2 Read only atom selection keywords for querying volumetric data A C ABCabc A Ca c Z 2 XYZ CO TALS co G Cx ab C ab c l0 CA x z match any character match any char in the li
134. c images can be rendered with a simple sequence of text commands cycling between the left and right monoscopic stereo modes and exporting one scene for each eye display stereo left render Tachyon left dat display stereo right render Tachyon right dat External renderers don t always support the ability to draw stereo images In principle it is possible to write the scene to the file twice with the appropriate transformations applied to make the view correct for each eye but then the shadows would be incorrect Instead we suggest making one image of the current scene then shift the molecules to the left or right to make the other image The text commands for this are something like 92 display stereo off render Raster3D left r3d trans by 1 0 0 render Raster3D right r3d The two files must then be rendered to produce the rgb file As it turns out this method makes it easy to produce stereo images of ordinary Raster3D files Since VMD can read the Raster3D format all you have to do is read the file and then execute the commands listed above The text commands for generating left or right views also have equivalents in the GUI under the Stereo option of the Display window 8 6 Making a Movie It is possible to make movies with VMD through the use of Tcl or Python scripts or with the vmdmovie extension included with VMD Several movie making scripts are provided in the VMD script library on the VMD home page These scripts
135. cal Journal 91 1844 1857 2006 The command syntax differs from the other volmap commands and it has its own set of options 131 volmap ils molid lt minmazr pbcbox gt options Here minmaz denotes the boundaries of the grid in which the volumetric map will be computed It is given as a list of two 3 vectors specifying the minimum and maximum coordinates of the desired volumetric data grid min Ymin Zmin Umax Ymax Zmax If you provide the keyword pbcbox instead of the minmaz coordinates then the target grid will be set to the rectangular box that encloses the PBC cell A typical choice for the minmax parameters would be the minmax box of a subset of your system for instance the just protein as returned by the measure minmax command Based on the grid dimensions a selection that includes all atoms within the interaction cutoff distance specified by cutoff is automatically chosen for the computation of the interactions In case your minmax box exceeds the periodic bounday box the non overlapping parts of your map will be ill defined and a warning is printed In this case you should consider wrapping the coordinates so that the requested grid lies in the center of the box You can use the pbc wrap command from the PBCtool plugin for this In case the nonbonded interaction margin exceeds the periodic boundaries regions of your map will be based on incomplete interactions and a warning is printed If this happens you should use the p
136. can change the view of the scene either by rotating translating or scaling It can also pick objects in the scene causing some further action to be taken These behaviors are all reflected in the state of the Mouse menu Below we describe the main parts of the Mouse menu 38 Mouse modes The top three menu items select whether the mouse will rotate translate or scale the scene when the user clicks and drags with the left mouse button Pick modes These modes located right below the mouse modes in the Mouse menu control how the mouse affects objects in the scene as opposed to how the mouse changes the view of these objects Note that any time you choose a new pick mode the current mouse mode changes to Rotate e Center changes how VMD rotates and scales the scene To get a feel for how this works select Center from the Mouse menu then click on an atom in the scene If you now rotate the scene by clicking and dragging with the left mouse button the scene should rotate about the picked atom If you change the view mode to Scale using the View Mode pulldown menu the scene will expand while keeping the picked atom in view The picked atom will remain the center atom until a new atom is selected as Center the Reset View button is pressed or a new molecule is loaded e Query prints information about the item e g the atom name on the text console window e Label adds labels to atoms in the s
137. ce be of the selection 0 or of the contribution of this selection to the surface of all the atoms 1 e Sample Density triangle density on the surface typical values are 1 0 for molecules with more than one thousand atoms and 3 0 for smaller molecules e Probe Radius Probe radius used to construct the molecular surface e Representation Method The surface can optionally be drawn using lines rather than solid triangles There is an environment variable 13 2 which can affect the MSMS display option e MSMSSERVER location of the MSMS binary defaults to msms which is assumed to be in the user s path On Windows machines sets this as a systemwide environment variable in the environment variables window found in the system properties control panel 6 1 21 VolumeSlice The VolumeSlice representation draws a texture mapped two dimensional slice from a volumetric data set already loaded into VMD using the mol volume 9 3 19 text command or by other means The colors span the scalar value range of the data set with red indicating low values and blue indicating high values in the data The slice is drawn as a plane perpendicular to the X Y or Z axis and can be positioned anywhere within the coordinate system of the volumetric data set This feature is currently only available on machines that have full support for hardware 3 D texture mapping On machines lacking 3 D texturing nothing will be displayed Future ver
138. cene Labels include atoms bonds angles and dihedrals These labels require respectively one two three and four atoms to be picked For the latter three label types the numerical value of the geometric label is displayed along with a stippled line connecting the picked atoms The units for Bonds corresponds to whatever units the coordinate file is written in Angles and Dihedrals are measure in degrees Labels can then be manipulated through the Labels window e Move changes the actual coordinates of atoms in the scene Note that this is different from simply changing the view Clicking on one of the buttons in the Mode Mode menu selects what group of atoms to move Atom moves only the selected atom Residue moves all atoms in the same residue e g amino acid or nucleotide as the selected atom Fragment moves all atoms connected by a bond to the picked atom Molecule moves every atom in the molecular structure Highlighted Rep is the most flexible it moves all atoms in the highlighted representation in the browser window of the Graphics window Atoms are moved by clicking and dragging with the left mouse button If the shift key is held while the mouse is moved the affected atoms are rotated about the selected atom Rotating atoms with the left button rotates about the x or y axis of the screen rotating with the middle or right button rotates about an axis perpendicular to the screen
139. ces causes this script to run about three times slower The moral of the story is always put curly braces around the expression that you pass to expr Here s another slightly slower way to do the same thing This works because the mass returned from the selection is a list of lists Putting it inside the quotes of the eval makes it a sequence of vectors so the vecadd command will work on it 175 proc total_mass1 selection set mass selection get mass eval vecadd mass Coordinate min and max Find the min and max coordinate values of a given molecule in the x y and z directions see also the measure command minmax The function takes the molecule id and returns two vectors the first contains the min values and the second contains the max proc minmax molid 4 set sel atomselect top all set sx sel get x set sy sel get y set sz sel get z set minx lindex sx 0 set miny lindex sy 0 set minz lindex sz 0 set maxx minx set maxy miny set maxz minz foreach x sx y sy z sz if x lt minx set minx x else if x gt maxx set maxx x if y lt miny set miny y else if y gt maxy set maxy y if z lt minz set minz z else if z gt maxz set maxz z return list list minx miny minz list maxx maxy maxz Radius of gyration Compute the radius of gyration for a selection see also measure rgyr The square of the radius of gyration
140. ck on the last line in the Names chooser which says star pdb This time choose red from the Colors chooser The display should be much easier to understand The myoglobin with the bound CO is in blue and the intermediate state is in red At this point it is easy to measure the change in position between the two different states by using the middle mouse button to pick the same atom in the two conformations Once that is done it is easy to point out one interesting aspect of the way VMD handles the graphics Go to the main window select one of the two molecules and press Toggle Fixed Enter translation mode and move the other molecule around Notice that the number which lists the distance between the two atoms never changes That s because the mouse only affects the way the coordinates are translated to the screen image It does not affect the real coordinates at all It is possible to change the coordinates in a molecule using the text command interface or by using the atom move pick modes 85 1 2 By the way unfix the molecules and do a Reset View from the Display menu to reset everything Load up the third structure deoxy pdb and give it the same selection as the other two molecules However color this one green Pull out Nature v 371 Oct 27 1994 and turn to page 740 With a bit of manipulation you should be able to recreate the image that appears there 3 7 Some Nice Represenations The following views are quite nice for d
141. connection to a remote simulation Turn on off labels for atoms bonds angles dihedral angles or springs Control the light sources used to illuminate graphical objects Turn on off logging a VMD session to a file or the console Create new material definitions and modify their settings Measure properties of moleculear structures Control or query the on screen GUI windows Load modify or delete a molecule Get information about a molecule or loaded file Change the current state mode of the mouse Start executing text commands from a specified file Output the currently displayed image scene to a file Rotate the current scene continually at a specified rate Rotate the current scene around a given axis by a certain angle Scale the current scene up or down Position a checkerboard stage on the screen Initialize and control external spatial tracking devices Translate the objects in the current scene Add new keyboard commands Tcl Get information about this version of VMD Create volumetric data based on molecular information Wait a number of seconds before reading another command Animation continues Sleep a number of seconds before reading another command Animation is frozen Table 9 1 Summary of core text commands in VMD 97 9 3 2 speed n Set animation speed to n style once Set to play animation once style loop Set to loop through animation continuously style rock Set to play animation forwar
142. copyunitcell True with simulations in the NPT ensemble the resulting unitcell information will be incorrect 10 5 8 label Python operations available from the label module used to create show hide and delete labels for atoms bonds angles or dihedrals e ATOM BOND ANGLE DIHEDRAL Label types defined by the label module for use as the first argument to the add listall show hide and delete methods e add type molids atomids Create a label of the given type molids and atomids must be tuples containing 1 2 3 or 4 integers for ATOM BOND ANGLE or DIHEDRAL labels respectively If the label already exists no action is performed Returns a dict corresponding to the referenced label that can be used in the show hide delete and getvalues methods e listall type Returns a list of labels of the given type The elements of the list are python dictionary objects with the following keys molid atomid value on The values for molid and atomid are tuples containing the molecule id and atom id for the label value is the numerical value of the geometry label or zero for ATOM labels on is 1 if the label is shown and 0 if the label is hidden e show type label Turn the given label on label must be a dictionary containing molid and atomid keys whose values are tuples If the tuples match the molecule ids and atom ids of the atoms in an existing label the label will be turned on Raises ValueError if the label doe
143. cs window in Draw Style mode Deleting a rep To delete a representation select the representation in the browser and press the Delete button Bear in mind that this does not delete the molecule it only deletes one of its graphical representations Hiding a rep To hide a rep double click its entry in the browser The text will turn pink to indicate that the rep is hidden Turn the rep back on by double clicking again on the same line Hidden reps will not recalculate their geometry if the animation frame changes until the rep is turned back on Selections Tab The Selections tab provides access to browsers which display the lists of atom names residue names and so forth for the selected molecule When the Selections tab is pressed several browsers appear in place of the drawing and coloring method controls These are used to list the available keywords macros and values for use in selecting atoms for the associated representation The top browser lists 44 v Graphical Representations LEL Selected Molecule 1 1e79 y Create Rep Delete Rep Style Color Selection NewCartoon Structure all YDW Name ions Lines ColorlD 0 water Selected Atoms ions Draw style Selections Trajectory Periodic and or not Apply Reset Keyword Value Singlewords Macro definition Figure 5 7 The Graphics window in Selections mode singlewords and macros such as all water and hydrophobic
144. ct to the root node on which NAMD initially started out IMD Using the Simulation window The Simulation window allows you to control the behavior of a molecular dynamics simulations which has been previously connected to through use of the Remote window This window contains controls to change parameters for the simulation and to affect how VMD displays the results of the simulation The window also contains informative displays which show the current status of the simulation connection and such things as the current energy temperature and timestep of the molecular system being simulated At the top of the window are two entry fields and a button for establishing a connection to a running MD simulation Enter both the hostname on which the simulation is running and the port on which the simulation is listening then press the Connect button to establish the connection See the text console for possible error messages and status updates Below the connection display is a browser used to set some connection parameters These include e Transfer Rate How often a timestep is transferred from the remote simulation program to VMD By default this is 1 which means every calculated timestep is sent If this is set to some value N then only every Nth step will send from the remote computer thereby decreasing the amount of network processing and rendering that needs to be done http www ks uiuc edu Research namd 55 e Keep Rate How ofte
145. ction for all the active molecules The primary use for this control is to prevent some molecules from being animated Inactive molecules will not animate when the play button is pressed e Drawn D If a molecule is Drawn then it is being displayed in the graphics display window This is useful for temporarily hiding a molecule from view without deleting it e Fixed F Fixed molecules do not undergo rotation translation or scaling Note that while it may seem that one molecule has been moved relative to another the difference is only apparent The internal coordinates do not change when a standard rotation is applied by using for example the mouse It is possible however to change the coordinates of atoms in a molecule using the text command interface and by using the atom move picking modes Changing the Molecule s Status The status of a given molecule can be changed by selecting the molecule in the browser and double clicking the appropriate flag Only one molecule can be top at any one time so the previous top molecule will change status when another is toggled Saving Trajectory Frames Using the Save Coordinates menu item you can write trajectory frames to a file in one of several file formats including PDB DCD Amber CRD etc This feature may be used to write out a new trajectory in a single file after assembling many frames from different sources such as PDB CRD DCD or Gromacs files or even from a remote simulation
146. ctive Ort hoBraplle VIEWS a a a as Ee 1 2 Monosc pic Modes isana aii entina aS a Se a a A A a 7 3 Stereoscopic Modes ee 7 3 1 Quad buffered tereo 7 3 2 Side By Side and Cross Eyed Stereo 2 0 0 0 0 e 7 3 3 DTI Side by side Stereo 7 3 4 Checkerboard Stereo 7 3 5 Column Interleaved Stereo aoo a 7 3 6 Row Interleaved Stereo e 7 3 7 Anaglyph Stereo 2 2 ee 7 3 8 Stereo Parameters 2 8 2 to Soke Rae A a ee a a 8 Scene Export and Rendering 8 1 Screen Capture Using Snapshot 2 a a e 8 2 Higher Quality Rendering aoaaa ee 33 Caveabss su Ve Begira AUS AAA ORR RE a Ge Behe a Bou 8 4 One Step Printing 8 5 Making Stereo Images eee 8 6 Making a Movie seoce moaca 22 ea aa a a a a ee eG 9 Tcl Text Interface 9 1 Using text commands esah kanda e tao ie ee Y CROW e AAA gti RE Ae Oe Oat eee Be ws 93 Tcl Text Commands 1 d iaa a a ai a a D a i a AS E R IM animate sis aotea SS eee SRE PA A a ERE Rh E EE aS 9 3 2 satomselett ia E Sk ek Bayes Ge eae OY BO RY OBO POROSE te es il Bek tes ok oe i IE oe do OA aE a a Ae ee se OS Aq lt COLOT 2 A A ak ae in ene gee es tenn pee A Mae gt A ae 03 0 COlOTINIO ta Be ehh aes A tet od te Eh tt eee sf 9 3 0 CAPA ci oe E ee A Bae A Bee as ee A he TS por be ndes es ih ca thee Reig Se ok ES ASE ona AE Let ae roe Eset oP R TA ene 86 86 86 86 87 87 88 88 88 88 88 89 90 90 90 91 92
147. cule and 3 pdb into a different molecule e m Load all subsequent files into separate molecules The f and m options may be specified multiple times on the command line in order to load multiple molecule containing one or more files e dispdev lt win text cave caveforms none gt Specify the type of graphical display to use The possible display devices include win a standard graphics display window text do not provide any graphics display window cave use the CAVE virtual environment for display windows are disabled caveforms use the CAVE virtual environment for display and with windows enabled This is useful with display machine 0 for remote display of the windows when the CAVE uses the local screen none same as text It is possible to use VMD as a filter to convert coordinate files into rendered images by using the dispdev text and e options e dist z Specify the distance to the VMD image plane e height y Specify the height of the VMD image plane e pos x y Specify the position for the graphics display window The position x y is the number of pixels from the lower left corner of the display to the lower left corner of the graphics window e size x y Specify the size for the graphics display window in pixels 186 e nt Do not display the VMD title at startup e eofexit Make VMD exit when EOF on stdin is reached for example when a script is redi rected to V
148. cule menu item deletes all the selected molecules There is no prompt verifying the deletion so take some care If a deleted molecule was the top molecule a new top molecule will be set from the remaining structures GUI Shortcuts There are a few useful mouse based shortcuts that can be used in the Molecule List browser Here is a list e Double clicking on a molecule s name brings up the Rename Molecule dialog box e Double clicking on a molecule s number of frames brings up the Delete Frames dialog box e Triple clicking on the T top in front of a molecule focusses on that molecule by making it the only molecule to be displayed D and active A Furthermore the view is reset and the molecule gets selected in the Representations window 5 4 3 Main Window Animation Controls Kalol HA HA 4 a zoom D Loop y step ij 1 1 speed Figure 5 2 The Main window animation controls Each molecule in VMD can contain multiple sets of atomic coordinates which may be animated to show its motion over time The coordinate sets can come from a molecular dynamics simulation or simply multiple versions of the same molecular structure The Main window contains controls for animated playback of these trajectories The controls contains several buttons which act like the buttons on a VCR or DVD player The buttons provide a way to play the trajectory step forward stop go to a specific frame and go to the beginning or end The status and fr
149. d with the orthogonal cell algorithm Further algorithm and corresponding list entris will be added in the future With the optional arguments delta default 0 1 and rmaz default 10 0 one can set the resolution and the maximum r value With the usepbc flag processing of periodic boundary conditions can be turned on With the selupdate flag enabled both atom selections are updated as each frame is processed allowing productive use of within selections The size of the unitcell has to be stored in the trajectory file or has to be set manually for all frames with the molinfo command The command uses by default only the current active frame for both selections Using an explicite frame range via first last and step is recommended for most cases hbonds cutoff angle selection selection2 Find all hydrogen bonds in the given selection s using simple geometric criteria Donor and acceptor must be within the cutoff distance and the angle formed by the donor hydrogen and acceptor must be less than angle from 180 degrees Only non hydrogen atoms are considered in either selection If both selection and selection2 are given the selection is considered the donor and selection2 is considered the acceptor If only one selection is given all non hydrogen atoms in the selection are considered as both donors and acceptors The two selections must be from the same molecule The function returns three lists each element in each list corresponds to
150. d and back continuously styles Return a list of the available styles goto start Go to first frame goto end Go to last frame goto n Go to frame n read file_type filename beg nb end ne skip ns waitfor nw molecule_number Read data for molecule_number from filename of type file type beginning with frame nb ending with frame ne with a stride of ns Return the number of frames read from this file if the file contains more than this number the remaining frames will be loaded during subsequent VMD display updates By default one frame will be loaded before the command returns The waitfor option allows you to specify how many frames to load before returning The waitfor parameter nw can be any integer or all choosing nw less than zero is the same as choosing all If frames from other files are still being loaded when the animate command is issued these frames will be loaded first write file_type filename beg nb end ne skip ns waitfor nw sel selection molecule_number Write data from molecule_number to filename of type file_type beginning with frame nb ending with frame ne with a stride of ns Return the number of frames written to this file if more frames have been specified than this number the remaining frames will be written during subsequent VMD display updates By default one frame will be written before the command returns The waitfor option allows you to specify how many frames to write before retu
151. decreasing size The last list contains the remaining yet unclustered frame indices e contacts cutoff selection selection2 Find all atoms in selection1 that are within cutoff of any atom in selection2 and not bonded to it If selection2 is omitted it is taken to be the same as selection1 selection2 and selection can either be from the same of from different molecules Returns two lists of atom indices the first containing the first index of each pair taken from selection1 and the second containing the second index taken from selection2 Note that the index is the global index of the atom with respect to its parent molecule as opposed to the index within the given atom selection that contains it e dipole selection elementary debye geocenter masscenter origincenter Com pute the dipole moment vector of the atoms in selection from their respective positions and charge values The result by default assumes charges given in units of an elementary charge and distances in angstrom By default the result is given in the same units same as using the elementary flag setting the debye flag will convert the output to units of Debye For selections that have a residual charge after summing up all individual charges the resulting dipole vector depends on the choice of center of the charge distribution By default the center will be the geometrical center of the selection sames as using the geocenter flag but using the selecti
152. des within VMD The Spaceball interface currently provides two methods of rotation and translation and a scaling mode The Spaceball interface currently uses Button 1 known as Function 1 in the SpaceWare driver to reset the view and Button 2 to cycle through the available Spaceball interface modes 5 2 1 Spaceball Driver VMD interfaces to the Spaceball in one of two ways either by communicating directly with the Spaceball using built in serial interface software or vendor provided drivers Unix and Mac OS X versions of VMD use the built in serial Spaceball driver At startup VMD checks for the existence of an environment variable VMDSPACEBALLPORT This environment variable must be set to the Unix device name of the serial port to which the Spaceball is attached The serial port device permissions must be set to allow the VMD user to open the device for reading and writing In typical usage this usually requires performing a chmod 666 dev somettyname on the appropriate device as root One restriction with the use of the built in Spaceball driver is that only one VMD process may safely use the Spaceball at a time If multiple VMD sessions are started on the same machine and all are set to open the Spaceball it will behave very erratically 31 Hot Key rock x spin about x axis rock x rock about x axis rock y spin about y axis rock y rock about y axis Zz spin about z axis Zz rock about z axis rock Z rock j Cntl n rotate rot
153. ding money on if one s intended use of VMD is primarily focused on visualization related tasks As an added bonus recent GPUs are now also capable of accelerating some of the computationally demanding tasks within VMD as will be discussed in more detail below Following the choice of graphics accelerator the amount of available system memory tends to have the next most significant impact on the performance and capability of VMD The more memory a machine has the more frames can be loaded at once from large molecular dynamics trajectory files For batch mode analysis tasks that consist primarily of scripting system memory is frequently the resource that limits feasability of many analysis tasks 2 2 Multi core CPUs and GPU Acceleration VMD makes full use of multi core processors and multiple GPUs for acceleration of the most computationally demanding visualization and analysis tasks Multi core CPUs accelerate features including interactive MD bond determination within atom selections and derivatives radial distribution functions and high quality renderings using the Tachyon and TachyonInternal ray tracing features VMD also supports GPU acceleration using CUDA and takes advantage of both multi core CPUs and GPUs for acceleration of electrostatics i e volmap coulomb and volmap coulombmsm implicit ligand sampling i e volmap ils and computation and rendering of molecular orbitals 16 Chapter 3
154. disp mol molinfo mol get drawn 169 turn everything off mol off all turn each molecule on then off again foreach mol molinfo list if disp mol mol on mol sleep 1 mol off mol turn the original ones back on foreach mol molinfo list if disp mol mol on mol The last loop which turns the originally drawn molecules back on doesn t turn them on at the same time That s because some commands those which use the command queue redraw the graphics when they are used This can be disabled with the display update see section 9 3 6 for more information Using this the final loop becomes turn the original ones back on display update off foreach mol molinfo list if disp mol mol on mol display update on Alternatively since the drawn option is settable you could do foreach mol molinfo list if disp mol molinfo mol set drawn 1 J However that won t set the flag to redraw the scene so you need to force a redraw with display redraw 12 2 Using the atomselect command Atom selection is the primary method to access information about the atoms in a molecule It works in two steps The first step is to create a selection given the selection text molecule id and optional frame number This is done by a function called atomselect which returns the name of the new atom selection the second step is to use the created selection to access the information about the atoms i
155. does not perform the endpoint fixup procedure described above for the regular Bonds 6 1 2 representation Instead it is intended to be used in concert with the VDW 6 1 6 representation to show bonds that are being created and destroyed during the course of a trajectory A bond is drawn if the atoms are within Distance Cutoff of eachother 6 1 4 HBonds The HBonds representation will draw a dotted line between two atoms if there is a possible hydrogen bond between them A possible hydrogen bond is defined by the following criteria Given an atom D with a hydrogen H bonded to it and an atom A which is not bonded to D a hydrogen bond exists between A and H iff the distance D A lt dist and the angle D H A lt ang where ang and dist are user defined Only the selected atoms are searched so both the donor and acceptor must be selected for the bond to be drawn Also you ll note that the above doesn t check the atom type of the donor or acceptor the only criterion is if it already has or doesn t have a hydrogen One downfall of the current implementation is that it does an n search of the selected atoms so you probably don t want to show all the HBonds of a very large structure Look for performance improvements in future versions of VMD If you choose an HBonds representation but fail to see any hydrogen bonds it may be because the default Angle Cutoff and Distance Cutoff criterion in VMD are too small s
156. e and put it in the newbeta list set dist veclength2 vecsub coord point lappend newbeta dist set the beta term sel set beta newbeta And here s one way to use it load pdb2plv ent using anonymous ftp to the PDB vmd gt mol new 2plv vmd gt set sel atomselect top all vmd gt betacolor_distance sel 0 0 0 Then go to the graphics menu and set the Coloring Method to Beta 12 4 RMS Fit and Alignment When one has two similar structures one often wants to compare them What s the difference between two X ray structures How much did the structure change during a simulation To answer these questions you must first figure out how to compare two structures which usually means that you must find the root mean square deviation RMSD Formally given N atom positions from structure x and the corresponding N atoms from struc ture y with a weighting factor w i the RMSD is defined as N lz uell 2 RMSD N x y ae Using this equation by itself probably won t give you the answer you are looking for Imagine two identical structures offset by some distance The RMSD should be 0 but the offset prevents that from happening What you really want is the minimum RMSD between two given structures the best fit There are many ways to do this but for VMD we have implemented the method of Kabsch Acta Cryst 1978 A34 827 828 or see file Measure C in the VMD source code This algorithm computes
157. e frame before returning The function will return the id of the newly created molecule or return an error if unsuccessful urlload lt file_type gt lt URL gt Load a molecule of file_type from a given URL address Return the id of the newly created molecule or an error if unsuccessful pdbload lt four_letter_accession_id gt Retrieve the PDB file with the specified accession code from the RCSB web site Returns the id of the newly created molecule or an error if unsuccessful list Print a one line status summary for each molecule list molecule_number Print a one line status summary for each molecule matching the molecule_number If only one molecule matches the molecule_number also print the rep resentation status for this molecule i e number of representations as well as the representa tion number coloring method representation style and the selection string for each of the representations color coloring method Change the default atom coloring method setting representation rep_style Change the default rendering method setting selection select_method Change the default atom selection setting clipplane center clipplane_id rep_number molecule_number vector clipplane color clipplane_id rep_number molecule_number vector clipplane normal clipplane_id rep_number molecule_number vector clipplane status clipplane_id rep_number molecule_number boolean 1 modcolor rep_number molecule_number coloring method Change
158. e joystick tool shows how a three dimensional input device can be used to supply relative differential coordinates instead of absolute coordinates e The Tug Tool is a tool that allows interaction with running molecular dynamics simulations Pressing the button connects the device with a simulated spring to the nearest atom and pulling on it adds a force to the simulation If a haptic device is being used the user will feel a force on his hand that is proportional to this force In this way the tug tool implements something like the click and drag that is commonly used with windowing systems If an atom selection is assigned to the Tools the the Tug Tool will apply a force to all the atoms in the selection The force applied will be proportional to the masses of the atoms in the selection so that all atoms experience the same acceleration When a Tool Selection has been assigned the Tug Tool will always affect that selection even if the button is pressed far from any atoms in the selection this is intended to make it easier for the user to apply forces only on those atoms he she intends to steer e The Spring Tool also allows interaction with running molecular dynamics simulations It works like the Tug Tool except that when the button on the tracker is released near an atom the simulated spring is connected to it See section 5 4 8 for information on viewing and modifying the list of active springs e The Pinch Tool is similar to the Tug
159. e mouse will update the settings of the sliders Conversely moving the sliders will change the definition of the the currently highlighted material in the browser Pressing the Default button will restore either of the first two materials Opaque and Transparent to their original settings 50 To create a new material press the Create New button in the upper right corner of the window A new material with a default name will be created and displayed in the browser window This name can be changed at any time to something more descriptive by typing in the input box to the right of the material browser and pressing enter note that the names of Opaque and Transparent cannot be changed You can now edit the properties of this material using the sliders at the bottom of the window All materials in the materials browser including those you create will appear in the Material pulldown menu in the Graphics window To experiment with the material settings first create a new material so that you can edit its values Next load any molecule change its drawing method to VDW representation and using the Material pulldown menu in the Graphics window change the representation s material to the material you just created Now go back to the Materials window highlight the new material in the browser and change some of the values in the sliders The effect of changing shininess should be especially dramatic 5 4
160. e oriented ribbon There may be some problems with the ribbon definition for nucleic acids as it is possible for the nucleic acid detection routine to label a residue as a nucleic acid even though it does not have phosphate oxygens Given the coordinates of each atom and the offset vector for the ribbon vector the drawing code finds the spline curves for the top and bottom of the ribbon The two splines are connected by triangles and both splines are drawn as small tubes As with the Tube representation the six ribbon segments nearest the given atom are drawn with the color assigned to that atom and the atom can be selected by clicking near the center of those six elements Bond Radius and Resolution modify the tubes that make up the top and bottom of the ribbon If the radius or resolution get too small the tubes are not drawn this speeds up drawing time by an appreciable amount The Width controls the width of the ribbon and make it look like everything from vermicelli to lasagna Additionally the sugars are drawn filled in with triangles This helps highlight the pucker Thanks to Ethan Merrit for the ribbon drawing algorithm taken from Raster3D 64 6 1 13 NewRibbons The NewRibbons representation is similar to Tube 6 1 11 in that it follows the a spline curve for both the protein and nucleic acids However it uses additional information the O of the protein backbone or some of the phosphate oxygens for nucleic acid
161. e representations can be added deleted or changed with the mol command See also sections on molinfo command 9 3 21 for more ways of retrieving information about the representations e new filename 1 options e addfile lt filename gt options mol new is used to create a new molecule from a file if the optional filename parameter is omitted a plain blank molecule is created with no atoms this can be used to create a canvas for drawing user defined geometry mol addfile is like mol new except that the structure and coordinate data are loaded into the top molecule whichever molecule was loaded last instead of creating a new one Both mol new and mol addfile accept the following set of options type lt type gt Specifies the file type psf pdb etc If this option is omitted the filename extension is used to guess the filetype otherwise it overrides what would be guessed from the filename first lt frame gt last lt frame gt step lt frame gt For files containing coordinate frames specifies which frames to load Frames are indexed starting at 0 A step of 1 means all frames in the range will be loaded a step of 2 means load every other frame waitfor lt frames gt For files containing coordinate frames specifies how many frames to load before returning the default is 1 If frames is less than the number of frames in the file the rest of the frames will be loaded in the back
162. e them entirely Also labels displaying geometrical data such as bond lengths may be graphically displayed using this window Label categories The Category chooser in the upper left is used to select which category of labels to manipulate The different label categories include e Atoms which are shown as a text string next to the atom listing the name and residue of the atom e Bonds which are shown as dotted lines between the atoms with the bond length displayed at the bond midpoint e Angles which are shown as dotted lines between the three atoms with the angle displayed at the center of the defined triangle e Dihedrals which are shown as dotted lines between the four atoms with the dihedral angle the angle between the planes formed by the first three atoms and the last three atoms shown at the midpoint of the torsional bond 47 e Springs which are shown as dotted lines between the atoms with the bond length displayed at the bond midpoint All the labels for the selected category which have been previously added are displayed in the browser in the center of the window The line itself contains from 1 to 4 atom names depending on the category the atom names have the form lt residue name gt lt residue id gt lt atom name gt followed by either on or off The last word indicates if the label is turned on or off Modifying or deleting a label A label can be turned on or off without deleting it by selecting the la
163. eb people sanner html msms home html faq http www ks uiuc edu Research vmd_ allversions vmd_faq html biocore http www ks uiuc edu Research biocore tachyon http www photonlimited com johns tachyon babel http www eyesopen com babel homepage http www ks uiuc edu Research vmd quickhelp http www ks uiuc edu Research vmd vmd_help html radiance http radsite lbl gov radiance HOME html maillist http www ks uiuc edu Research vmd mailing_list scripts http www ks uiuc edu Research vmd script library namd http www ks uiuc edu Research namd vrml http www web3d org rayshade http www graphics stanford edu cek rayshade rayshade html povray http www povray org plugins http www ks uiuc edu Research vmd plugins python http www python org software http www ks uiuc edu Research vmd allversions related_programs html tcl http www tcl tk userguide http www ks uiuc edu Research vmd vmd 1 8 1 ug ug html Table 9 2 On line Help Sources 9 3 12 imd Controls the connection to a remote simulation 108 connect host port connect to an MD simulation running on the machine named host and listening on port port This command will fail if a previously established connection has not yet been disconnected detach Disconnect from the simulation the simulation will continue to run kill Disconnect from the simulation and also cause it to halt pause lt on off toggle gt Pa
164. eg pil x amount rad deg pil y amount rad deglpi z amount rad deg lpi axis Lx y z amount rad deg pil bond x1 y1 z1 x2 y2 22 amount rad deg pi angle x1 y1 z1 x2 y2 22 4x3 y3 23 amount rad deg pi This command can do almost everything the other ones can do and then some It is designed to be the main function used for generating transformation matrices Using it correctly calls for understanding how it works internally There are three matrices centering rotation and offset The centering matrix determines where the center of rotation is located By default this is the origin but it can be changed to pivot about any point The rotation matrix defines the rotation about that centering point and the offset matrix defines the final translation after the rotation For example to rotate around a given point the transformations would be 1 the centering matrix to bring that point to the origin 2 the rotation about the center and 3 the final offset to return the origin back to its original location The different options for the trans command modify the matrices in various ways 166 center x y z Sets the centering matrix so that point x y z is brought to the origin offset x y z Sets the offset matrix so that the origin is brought to x y z origin x y z Sets both the centering and offset matrices to x y z axis x amount rad deg pi Adds a rotation about
165. ents i e to determine which residues are protein nucleic acids and waters etc A search is then made to connect these into larger fragments of the same type and summary information is printed to the screen An example output for BPTI is Info 1 Analyzing structure Info 1 Atoms 898 Bonds 909 Info 1 Backbone bonds Protein 231 DNA 0 Info 1 Residues 58 Info 1 Waters 0 Info 1 Segments 1 Info 1 Fragments 1 Protein 1 Nucleic 0 There are several types of fragments Protein and nucleic fragments are homogeneous either all proteins or all nucleic acids However it is possible for a protein to be connected to a nucleic acid or some other non protein When this occurs a warning message is printed as in Warning 1 Unusual bond between residues 1 and 2 These warnings will occur with terminal amino acids zinc fingers myristolated residues and poorly defined structures 4 3 Babel interface VMD can use the program Babel if installed to translate a wide variety of different molecular data files into the PDB format Not all of these have been tested for use with VMD so your results may vary VMD only uses Babel to read files and does not allow the use of Babel to save files to other formats The VMDBABELBIN environment variable 913 2 is used to specify the absolute path to the the Babel executable including the executable name For more information about Babel see http smog com chem babel1 VMD currently su
166. er describes the data files command line options and environment variables which are used to customize a VMD session These files control the initial appearance and behavior of VMD at the start and may be customized to suit each user s particular tastes Default versions of these files are placed in the VMD installation directory On Unix this is usually usr loca1 1ib vmd on Windows this defaults to C Program Files University of Illinois VMD Each user may specify their own versions of some of these files but unless this is done the commands and values in the default files are used In this way an administrator may customize the default behavior of VMD for all users while giving each user the option to change the default behavior however they choose Several configurable parameters may also be set in a number of ways including use of command line options or environment variables The order of precedence of these methods is as follows highest precedence to lowest 1 Command line options 2 Environment variable settings 3 Built in defaults as specified by compilation configurable parameters These are used only if no other values are specified by the other methods mentioned in this list The Installation Guide describes how to change these default values when compiling VMD 13 1 VMD Command Line Options When started the following command line options may be given to VMD Note that if a command line option does not start with
167. es vmd gt vecdist 1 5 5 5 7 0 vmd gt vecdist 0 O 0 3 4 0 5 0 vmd gt vecdist 0 1 2 3 4 5 6 6 5 4 3 2 1 0 15 8745 e vecinvert v Returns the additive inverse of v v Examples vmd gt vecinvert 11 1 11 1 vmd gt vecinvert 3 4 5 3 4 5 vmd gt vecinvert 0 1 2 3 01 23 11 2 Matrix routines Because matrices are rather large when expressed in text form the following definitions are used for the examples e transidentity Returns the identity matrix Example vmd gt transidentity 11 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 e transtranspose m Returns the matrix transpose of the given matrix Example vmd gt transtranspose 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 0 5 9 13 1 6 10 14 2 7 11 15 3 8 12 16 e C transmult m1 m2 m3 mn Returns the matrix multiplication of the given matrices 164 Examples vmd gt set mati 11 2 3 4 4 2 3 4 5 43 4 5 6 4 5 6 7 vmd gt set mat2 1 0 0 0 40 0 7071 0 7071 0 0 0 7071 0 7071 0 0 0 0 1 vmd gt set mat3 0 866025 0 0 0 0 1 O O 0 5 O 0 866025 0 0 0 O 1 vmd gt transmult mat1 transidentity 1 0 2 0 3 0 4 0 2 0 3 0 4 0 5 0 3 0 4 0 5 0 6 0 4 0 5 0 6 0 7 0 vmd gt transmult mat1 mat2 mat3 0 512475 3 5355 0 612366 4 0 0 7428 0 7071 4 28656 5 0 0 58387 0 7071 5 5113 6 0 7 35315 0 7071 6 73603 7 0 transaxis lt x y z gt
168. es can be used to draw a box around a molecule or an arrow between two atoms or place a text label somewhere in space The command syntax is graphics lt molid gt lt cmd gt where lt molid gt is a valid molecule id and lt cmd gt is one of the commands listed below To create a blank molecule use the Tcl command mol new See the draw 9 3 7 command for a possibly more convenient interface Also refer to the VMD script library for some examples of user defined graphics scripts As graphical primitives are added to the list they are assigned a unique increasing id The first object added is assigned 0 the second is assigned 1 etc The commands which add an item return its value e point zx y z Draws a point at the given position e line x1 yl z1 x2 y2 22 width u style lt solid dashed gt Draws either a solid or dashed line of the given width from the first point to the second By default this is a solid line of width 1 e cylinder x1 y1 z1 x2 y2 z2 radius r resolution n filled lt yes no gt Draws a cylinder of the given radius default r 1 from the first point to the second The cylinder is actually drawn as an n sided polygon If the filled option is true the ends are capped with flat disks otherwise the cylinder is hollow default width of the base The resolution parameter default n 6 determines the number of polygons used in the approxi mation e cone basex basey basez tipz tipy tipz
169. esigned to generate its images very rapidly to maximize interactivity which precludes the use of photorealistic rendering techniques that would slow down the operation of whole program Instead of producing high quality images directly VMD writes scene description files which can be used as input to several popular scanline rendering and ray tracing programs Tables 8 1 lists the currently supported output formats and where appropriate rendering software may be obtained Making the raster image is usually a two step process First you must make a scene description file suitable for the chosen rendering program and then execute the program using the new file as input to produce the raster image output The external rendering programs typically support different output file formats which may need to be converted to something more appropriate for you It is impossible to predict what that might be so we ll describe how to convert the different 90 file types to Targa and let you use the tools listed in Table 8 1 to get what you need Raster3D Tachyon and POV Ray can produce Targa files so you don t need to do anything but specify this output format Rayshade creates RLE image files which can be converted using ImageMagick Radiance generates an oct file which can be converted with the rview and rpict commands included in the Radiance distribution The free program display from ImageMagick see http www imagemagick org should be ab
170. estabilizes over the course of the simulation The animation controls are generally similar to what you d find on a DVD or CD player 19 3 5 An Introduction to Atom Selection In this section it is assumed that you have the myoglobin structure mbco pdb loaded and the views discussed in section 3 2 created If this is not true go back and repeat the process described there VMD has a powerful atom selection method which is very helpful when generating attractive informative and complex graphics In the previous section you used a few of these atom selection tools This tutorial assumes that you have already loaded the myoglobin molecule but it isn t necessary to recreate all the graphical representations To change which atoms are used to display each representation of the molecule shown in the display window open the Graphics window 5 4 7 and select the representation you want to change You can then either edit the different fields selection coloring method or drawing method or use the Delete button to delete the view entirely Try changing or deleting some of the views When finished delete all representations for the myoglobin structure To get the basic line drawing view back clear the atom selection text entry area enter all and press the Create Rep button Atoms may be selected on the basis of a property i e protein or not protein water or nucleic backbone They may also be selected by atom name such as atom C by residue
171. esults of the get gt gt gt from molecule import gt gt gt from AtomSel import AtomSel gt gt gt load alanin pdb gt gt gt CA AtomSel name CA gt gt gt CA name CA gt gt gt len CA 12 gt gt gt CA 0 5 11 17 23 29 35 41 47 53 59 65 gt gt gt resname resid CA get resname resid gt gt gt resname ACE ALA ALA TALA p TALA s TALA ALA ALA ALA ALA ZALA C BX gt gt gt resid 1 2 3 4 5 6 7 8 9 10 11 12 gt gt gt x y Z CA eet Cx y 5 z gt gt gt x 2 1840000152587891 1 4500000476837158 1 9809999465942383 0 54100000858306885 2 8090000152587891 5 9079999923706055 5 0440001487731934 4 5659999847412109 7 9340000152587891 9 7329998016357422 8 1689996719360352 9 2229995727539062 gt gt gt y 0 5910000205039978 0 0 3 6429998874664307 4 8410000801086426 2 5559999942779541 3 7860000133514404 7 4190001487731934 6 7989997863769531 5 0819997787475586 7 9559998512268066 10 515999794006348 8 5710000991821289 gt gt gt Z 0 9100000262260437 0 0 0 9089999794960022 2 3880000114440918 4 3920001983642578 2 5859999656677246 3 244999885559082 6 9559998512268066 7 2639999389648438 5 5669999122619629 7 8870000839233398 11 013999938964844 gt gt gt beta CA get beta gt gt gt CA set beta 5 gt gt gt CA set beta beta gt
172. etrical center is defined as the sum of the coordinate vectors divided by the number of elements and so far I have only calculated the sum of vectors I need the inverse of the number of elements which is done with the expression expr 1 0 selection num 172 The decimal in 1 0 is important since otherwise Tcl does integer division Finally this value is used to scale the sum of the coordinate vectors with vecscale which returns the new value which is itself returned as the result of the procedure The center of mass function is slightly harder because you have to get the mass as well as the x y z values then break that up into to components The formula for the center of mass is Y mizi gt gt mass proc center_of_mass selection Y some error checking if selection num lt 0 4 error center_of_mass needs a selection with atoms set the center of mass to 0 set com veczero set the total mass to 0 set mass 0 selection get x y z returns the coordinates x y z selection get mass returns the masses so the following says for each pair of coordinates and masses do the computation foreach coord selection get x y z m selection get mass sum of the masses set mass expr mass m sum up the product of mass and coordinate set com vecadd com vecscale m coord and scale by the inverse of the number of atoms if mass 0 error center_of_mass total ma
173. ffered stereo from the Display menu The image should switch to two images nearly superimposed but slightly offset 7 3 2 Side By Side and Cross Eyed Stereo Side by side stereo means that the normal display is divided into two halves a left view and a right view each occupying one half of the original display area Each view displays the current molecules from a slightly different perspective corresponding to the left and right eye of the viewer The images are separated however so to actually see a 3D object you must direct your eyes until the two images are on top of each other and then focus on the resulting image until you can see it as three dimensional There are two ways of placing the images In wall eyed stereo the left eye s image is located on the left side of the display and the right eye s image is on the right This is the standard method for displaying stereo images in publications as it works well when the display in this case the piece of paper is close to the eyes It is called wall eyed because your eyes are directed the same way they would be if looking at a distant wall In VMD this method is referred to as SideBySide stereo 87 In cross eyed stereo the left eye s image is located on the right side of the display and the right eye s image is on the left and hence the name cross eyed This is mostly used for distant displays such as overhead projections as it is much easier to cross eyes at that
174. found in either sell or sel2 sel Create a new atom selection using the atoms not found in sel len sel Returns the number of atoms in the selection sel 0 sel 0 3 Index and slice operations return the corresponding atoms in the selec tion center weight None Return the center of the selected atoms possibly weighted by weight which must be a sequence sasa srad samples 1 points None restrict None Returns the solvent accessible surface area SASA of atoms in the selection using the assigned radius for each atom ex tending each radius by srad to find the points on a sphere that are exposed to solvent If a restrict selection is given only solvent accessible points near that selection bill be consid ered The points parameter can be used to collect the points which are determined to be solvent accessible this must be a list variable getbonds Returns a list of the atoms bonded to each atom in the selection setbonds bonds Set the bonds for the atoms in the selection bonds must be a list of the same length as the selection each element in the list must be a sequence containing the indices of the atoms to which the atom has a bond 140 e minmax Returns the minimum and maximum coordinates of the atoms in the selection as a tuple of the form xmin ymin zmin xmax ymax zmax e rmsd sel frame None weight None Returns the root mean square distance of the atoms in sel from the selection If frame is gi
175. from two different perspectives one from the left eye and one from the right The images are made by finding the view that would be seen by someone located inside the scene The method uses two parameters to find the view the eye separation and the focal length The first defines the distance between the eyes and gives the parallax effect Setting the separation to 0 will result in a flat 2D image while setting it too large will give most people a headache The graphics model used by VMD assumes the eyes looking in front of the viewer and focusing at the same point the focal length away If the focal length is 0 the viewer s eyes are crossed and looking at each other A larger focal length will often help in creating a viewable image The two parameters can be changed with the text commands display focallength and display eyesep or using the Display Settings window 85 4 6 In general try to make the eye separation as large as possible without giving the viewer a migrane and try to vary the focal length to cut down on double images It may often help to translate the molecule forward or backward and also adjust the scaling since there is typically an optimum position for a molecule for a given set of stereo parameters 89 Chapter 8 Scene Export and Rendering One of the most common tasks performed by users of VMD is producing images which can be loaded into other programs or used in printed documents posters slides and transparencies
176. g 0 end 1 skip 1 waitfor 1 Read or write a file to from the specified molecule For reading if molid is 1 a new molecule will be created Optional arguments beg end and skip may be specified with keywords the default is to load save all coordinate frames New in VMD 1 8 The waitfor option will cause VMD to process the specified number of frames before returning If waitfor is negative all frames from the file will be processed before the function returns For reading files containing volumetric datasets set the volsets parameter to a list of set id s starting from 0 to specify which datasets to load add_volumetric molid name origin xaxis yaxis zaxis xsize ysize zsize data Add a volumetric data set to the given molecule origin xaxis yaxis and zaxis must be 3 tuples specifying the center and scale of the data xsize ysize and zsize give the number of elements along each dimension data must be a Python list of the correct size as indicated by the three sizes get_filenames molid Returns a list of filenames that have been loaded into this molecule get_filetypes molid Returns a list of filetypes corresponding to get filenames get_databases molid Returns a list of databases corresponding to get filenames get_accessions molid Returns a list of accessiosn corresponding to get filenames get_remarks molid Returns a list of remarks corresponding to get filenames delframe molid beg 0 end 1 skip 1
177. ground on subsequent VMD display updates If frames is 1 or all then all frames in all files still in progress will be loaded at once before the command returns Frames loaded this way will load faster than if they are loaded in the background If files are still being loaded in the background when the addfile command is issued frames from the files in progress will be loaded first volsets lt set ids gt For files containing volumetric data specifies which data sets to load lt set ids gt should be a list of zero based indices autobonds lt onloff gt Turn automatic bond calculation on off This can be useful for loading unusual non molecular coordinates for which VMD s bond finding algorithm is too slow e g if the point density is very high Default is on molid For addfile only The molecule id of the molecule into which the file should be loaded may be specified It must be the last option specified If omitted the default is the top molecule e load structure_file_type structure_file coordinate_file_type coordinate_file Load a new molecule from filename s using the given format If an additional coordinate file is specified load this file as well New in VMD 1 8 All frames from the coordinate file will be loaded before 120 the command returns If this is not desirable use the animate read command for more fine grained control over how coordinate files are loaded Previous version of VMD loaded only on
178. h a molecule of more than 40 residues use the scroll bars to scroll through the long list or use the Zoom controls to fit the data from a long list into a small space The Zoom slider and the Fit all Every Residue buttons zoom in and out of a long sequence list to allow viewing and selecting from the entire list all at once To represent more than 40 residues on the window the text list seems to skip residues but selections highlights and color coded data are still active for all residues By setting the Zoom slider to a value smaller than 1 0 or by pressing the Fit all button more or all of the sequence information for a large molecule can be seen at once To show a text line for every residue in the sequence zoom factor 1 0 click on the Every Residue button The Zoom 57 slider can be dragged with the left mouse button to re scale sequence smoothly or it can jump to a given value by clicking along the slider track with the middle button this is useful to work more quickly with very long sequences For a multi thousand residue protein with Fit all selected hundreds of residues can be selected at once and trends in B value and structure across the entire protein sequence can be detected In the screen shot above a section of 70 residues with lower B values than surrounding sequence is selected by dragging a rectangle around the green stretch in the B value column Other controls include e Toggle display of 3 letter and
179. he Resname category Residue type using the Restype category Residue identifier using the resid mod 16 for the color The one character chain identifier using the Chain category Segment name using the Segname category Molecule all one color using the Molecule category Helix sheet and coils are colored differently Use a user specified color index from 0 to 15 Color scale based on beta value of the PDB file Color scale based on the occupancy field of the PDB file Color scale based on the atomic mass Charge Pos Color scale based on the atomic charge Color scale based on the distance of each atom to the center of the molecule This is an interesting way to view globular systems Provides a single data value for each atom for each timestep Color scale is based on the atom index Due to the way the PDB file is organized this actually looks nice Backbone atoms green everything else is blue Animates colors through the active color scale based on wall clock time Color scale based on the current trajectory timestep frame User Index Backbone Throb Timestep Table 6 3 Molecular coloring methods 6 2 5 Materials VMD allows users to apply a materials property to the molecular models they create The material determines such things as how transparent an object is or how shiny or how large the specular reflections are Making objects semi transparent is a potentially powerful means of viewing multiple layers of the m
180. he vectors implementation is located at env VMDDIR scripts vmd test vectors tcl Since Tcl is slow at math some of these commands have been reimplemented in C The original definition is in the vmd script distribution but it is redefined later on inside VMD At times the speedup is a factor of 40 or more These commands are noted by C 11 1 Vectors e veczero Returns the zero vector 0 0 0 Example vmd gt veczero 000 e C vecadd v1 v2 v3 un Returns the vector sum of all the terms Examples vmd gt vecadd 1 2 3 4 5 6 7 8 9 11 11 11 147 vmd gt vecadd 0 1 0 2 0 4 0 8 1 1 2 3 3 1 4 1 4 1 2 2 6 4 4 8 vmd gt vecadd 4 5 9 e vecmul v1 v2 Returns the vector of a term by term multiply 161 Examples vmd gt vecmul 1 2 3 4 5 6 4 10 18 vmd gt vecmul 0 1 0 2 0 4 0 8 1 1 2 3 0 10 2 0 8 2 4 e C vecsub vi v2 Returns the vector subtraction of the second term from the first Examples vmd gt vecsub 6 3 2 2 8 vmd gt vecsub 10 9 8 7 0 1 0 0 1 9 99 8 7 1 vmd gt vecsub 1 2 3 4 5 6 7 8 9 10 bb b lt b 5 e C vecsum v Returns the sum of the elements in v Examples vmd gt vecsum 1 2 3 6 0 e C vecmean v Returns the mean of the elements in v Examples vmd gt vecmean 1 2 3 2 0 e C vecstddev v Returns the standard deviation of the elements in v Examples vmd gt vecstddev 123456789 10 2 87228131294 e C
181. hin 80 atoms distance between 21 plotting 49 atomselect command 97 98 169 170 axes 41 command 97 101 Python module 148 Babel 25 backface culling 41 batch mode 187 beta values 178 BioCoRE 14 bonds add or remove 28 determining 25 label 47 48 resolution 61 unusual 25 cachemode 41 callbacks Python 146 Tcl 135 136 center of mass 173 CHARMM files 24 38 chemical2vmd 192 clipping planes 42 user defined 121 color access definitions 102 assignment 21 background 49 category 49 71 72 102 184 command 71 97 101 id 43 71 in user defined graphics 107 index 102 map 49 material properties 107 names 71 102 properties 102 Python module 148 redefinition 49 183 revert to default 183 scale 50 72 74 101 182 changing 50 set minmax 123 155 window 21 49 71 72 color map 71 colorinfo command 97 102 coloring by category 71 by color scale 72 74 194 by property 184 methods 18 42 60 71 73 121 184 Command line options 185 contact residues 81 copyright 12 Coulomb potential volumetric data 130 culling 103 debug command 97 density volumetric data 129 depth cue 103 depth cueing 41 display ambient occlusion 103 antialiasing 103 backgroundgradient 103 command 97 103 device 186 Python module 149 update 104 170 183 window 40 distance volumetric data 130 distance between atoms 21 draw command 105 drawing method 18
182. ill do just that proc moveby sel offset foreach coord sel get x y z 4 lappend newcoords vecadd coord offset sel set x y z newcoords And to use this function in this case to apply an offset of x y z 0 1 2 8 9 to the selection movesel moveby movesel 0 1 2 8 9 However to simplify matters some options have been added to the selection to deal with movements these commands are also implemented in C and are much faster than the Tcl versions These functions are moveby moveto and move The first two take a position vector and the last takes a transformation matrix The first command moveby moves each of the atoms in the selection over by the given vector offset sel moveby 1 1 3 4 The second moveto moves all the atoms in a selection to a given coordinate it would be strange to use this for a selection of more than one atom but that s allowed Example sel moveto 1 1 4 3 The last of those move applies the given transformation matrix to each of the atom coordinates This is best used for rotating a set of atoms around a given axis as in sel move trans x 90 which rotates the selection 90 degrees about the x axis Of course any transformation matrix may be used A more useful example is the following which rotates the side chain atoms around the CA CB bond by 10 degrees 174 get the sidechain atoms CB and onwards set sidechain atomselect top sidech
183. implementations and to prevent VMD from using a GPU that s already oversubscribed by other processes running on the same machine VMDDISABLESTEREO Unix Prevents VMD from enabling stereoscopic display features This is normally only used as a workaround for buggy display drivers VMDPREFERSTEREO Unix MacOS X On Unix systems using X11 this environment vari able allows NVidia Quadro users to override the normal X11 visual search order skipping multisample capable visuals in favor of stereo visuals VMD still attempts to get the more complex visuals first but if it comes down to a choice between stereo and multisample as mutually exclusive options this variable provides the ability to force the use of stereo if avail able On MacOS X this environment variable tells VMD to create a a stereo capable display window even at the risk of terminating the program if the request is denied VMDSCRDIST Distance to the VMD image plane VMDSCRHEIGHT Height of the VMD image plane VMDSCRPOS Position of the VMD graphics window x y VMDSCRSIZE Size of the VMD graphics window x y VMD_EXCL_GL_EXTENSIONS Disable the use of named OpenGL extensions according to their official OpenGL extension names This is intended to be used only when one encounters severe stability problems caused by buggy display drivers VMDSHEARSTEREO Enable the use of an alternative perspective projection mode which may result in improved stereoscopic display Use
184. in one of several modes at any time the current mouse mode determines the effect of pressing and releasing mouse buttons or the mouse wheel while the mouse is in the graphics window 27 Each mouse mode except the lights mode see below sets the mouse cursor to a characteristic shape The mouse mode is selected via the Mouse menu The available mouse modes are as follows Rotate Mode hot key r When the mouse is in rotate mode holding the left mouse button down and moving the mouse rotates the molecules about axes parallel to the screen in a virtual trackball behavior To get a rotation around the axes coming out of the screen the z axis hold the middle button down and move the mouse left or right You can leave molecules rotating without continuously moving the mouse Start the molecule moving with the mouse as above then release the mouse button before you stop moving the mouse With some practice it becomes easy to impart a slight spin on the molecule or whirl it about madly To stop the rotation either press and hold the left mouse button down until the molecule stops moving or select Stop Rotation in the Mouse menu Also pressing the rotation hot key r or any of the other mouse mode hot keys causes rotation to stop Translate Mode hot key t When the mouse is in translate mode holding the left button down allows you to move the molecules parallel to the screen plane left right up and down
185. indow 85 4 4 We will load a PDB Protein Data Bank file containing the coordinates of the atoms in myoglobin compliments of Joel Berendzen of Los Alamos National Laboratory Select the Browse button in the files window to bring up a file browser Go into the proteins directory of the tutorial data set that you have downloaded from the VMD web site Once there select the file mbco pdb in the file browser and press the Load button in the molecule file browser button in the Files window Figure 3 1 shows an example of VMD displaying this protein You can use the mouse to manipulate the structure in the display window There are three basic mouse modes 85 1 1 rotation translation and scaling The mode can be changed from the Mouse menu in the main window or by pressing r t or s on the keyboard while the mouse is in the graphics window While experimenting note how the cursor changes to indicate the mouse mode In rotation mode the left mouse button controls rotation about axes parallel to the screen and the middle button controls rotation about the axis perpendicular to the screen In translation mode the left mouse button controls translation parallel to the screen while the middle button 17 Figure 3 1 Sample VMD session displaying myoglobin controls translation in and out of the screen Finally in scaling mode both the left and middle buttons control global scaling when the mouse is moved left or right but the middle but
186. ing is returned e add name create a new material with the given name The new material will start with the settings for Opaque If the name already exists no new material is created e add copy name create a new material copied from the selected material name e rename oldname newname rename the given material The command will fail if the name is already used e change property name value Change a material property of the material named name to the value value property must be one of the following ambient specular diffuse shininess opacity e delete name Delete the given material 9 3 17 measure The measure command supplies several algorithms for analyzing molecular structures In the following options selection refers to an atom selection as returned by the atomselect command described in section 9 3 2 The optional weight must be either none an atom selection keyword such as mass or a list of values one for each atom in the selection to be used as weights If weight is missing or is none then all weights are taken to be 1 When an atom selection keyword is used the weights are taken from selection e avpos selection first first last last step step Returns the average position of each of the selected atoms for the selected frames If no first last or step values are provided the calculation will be done for all frames e center selection weight weight Returns the geometric center of
187. ing to the selection s currently selected frame files types Returns a list of filenames and file types respectively for the files that have been loaded into this molecule numAtoms Returns the number of atoms in the molecule numFrames Returns the number of coordinate frames in the molecule setFrame frame Set the coordinate frame to the given value Must be in the range 0 numFrames curFrame Returns the current coordinate frame for the molecule delFrame first 0 last 1 step 1 Deletes the given range of frames dupFrame frame None Duplicate the given frame apending it to the end if frame is None then the current frame is used numReps Returns the number of molecular representations reps in the given molecule reps Returns a list of MoleculeRep objects one for each rep in the molecule addRep rep Add the given MoleculeRep instance to the Molecule Modifications to the rep will affect all Molecules to which the rep has been added Raises ValueError if the rep has already been added to this molecule delRep rep Removes the given MoleculeRep from the Molecule The rep is not affected and can be added to other molecules but changes to it will no longer affect this Molecule clearReps Removes all reps from this molecule autoUpdate rep onoff None If onoff is not None sets the auto update status for this rep and molecule note that a rep s auto update status may be different f
188. involved in interactions For instance protein within 5 of nucleic finds the protein atoms that are nearby nucleic acids Some selections may be sped up by short circuiting 6 3 3 A related atom selection construct is exwithin short for exclusive within The atom selection within 3 of protein and not protein is equivalent to exwithin 3 of protein The same lt keyword gt as lt selection gt finds all the atoms which have the same keyword as the atoms in the selection This can be used for selections like 80 same fragment as resid 35 which finds all the atoms attached to residue id 35 Any keyword can be used so selections like same resname as protein within 5 of nucleic are fine although weird The perhaps the most useful keyword for this command is residue so you can say same residue as Finding contact residues Suppose you want to view the atoms in A which are in contact with B Use the within lt distance gt of lt selection gt selection command For purposes of demonstration let A be protein B be nucleic and define contact as an atom in A which is within 2 A of an atom in B Then the selection command is protein within 2 of nucleic If you want to see all the residues of A which have at least one atom in contact with B use same residue as protein within 2 of nucleic 81 all none name type index serial atomicnumber element altloc chain residue protein nucleic
189. isplaying proteins and nucleic acids selection all drawing method tube coloring method segname or chain why This show the backbone of the protein and nucleic acid strands 21 selection protein and name CA or not backbone drawing method lines coloring method segname or chain why shows where the side chains are located but they are thin so the backbone is still visible and the scene is quickly drawn selection numbonds 0 and not waters drawing method vdw coloring method name why shows ions The not waters omits cases where a water s oxygen is known but not the hydrogen selection not waters or protein or nucleic drawing method lines coloring method name why shows whatever is left usually ligands and crystallizing agents 3 8 Saving your work After creating a set of attractive and informative representations of your molecule you may want to save your work so that you can regenerate the scene later There are two ways to do this in VMD e In the main menu press the Save State button found in the File menu this will bring up a browser window where you can enter a file name in which to save your work e In the text console type save_state filename where filename is the name of the file in which to save your work To restore your scene you also have three choices e Use the Load State item in the File manu to select and load a previously saved VMD session e From the command line
190. ist contains the id s of the atoms bonded to the corresponding atom in the selection setbonds Set the bonds for the atoms in the selection the second argument should be a list of bondlists one bondlist for each selected atom move 4x4 matrix Applies the given transformation matrix to the coordinates of each atom in the selection moveby offset move all the atoms by a given offset Imoveby offset_list move each atom by an offset given in the list 100 moveto position move all the atoms to a given location Imoveto position_list move each atom to a point given by the appropriate list element writeXXX filename write the selected atoms to a file of type XXX e g pdb dcd New in VMD 1 8 writepdb requires a filename omitting the filename no longer returns the PDB data as a string To get the PDB data as a string first write to a file then enter the following commands set fd open filename r set s read fd close fd The text will be contained in the variable s update Update the atom selection based on the frame for the selection the frame can be specified using the frame option as described above See section 12 2 for more on using atom selections for fun and profit as well as issues relating to speed of analysis scripts 9 33 axes The axes orthogonal vectors pointing along the x y and z directions can be placed in any of 5 locations on the screen or turned off e locations Return a
191. ition valueX value Y Set the position of the upper left corner of the display window to valueX x valueY pixels from the lower left corner of the screen shadows lt on off gt Turn shadow rendering on or off This only affects renderers that support control of shadow rendering It will have no visible effect on the interactive VMD dis play or on renderers that don t support it At present only the Tachyon and TachyonInternal renderers are capable of controlling the shadow rendering mode stereo mode Set the stereo mode to mode update Force a display update Used if the display update is off or to force a redraw This does not necessarily take care of resizing the display window or using the GUI while the display update is turned off update on Turn display update on update off Turn display update off By default VMD does the display updates constantly Sometimes it is beneficial to turn the turn the display updates off This prevents VMD from redrawing the scene as a response to every change thus saving time while doing changes of representations See the VMD script library for examples of use update status Return the display update status on or off update ui Similar to display update but also forces updates of the GUI windows The windowed interface is subject to the following behavior if the display update is set to off and actions such as e g iconify deiconify have been performed to the windows the windows do
192. k i ke ee 40 DA Graphics Window at ad a a eek a Dl Pea ds A a a G 42 4 8 Labels WINdOW 00 seam vd Ano ad iD ida a 47 HET Color Window lt p a ed ee CRA AE ae Soe ana ee ee a 49 9 4 10 Material Window lt lt dc kik Se ee Be a ae ee dae A 50 BAL Render Window a Ss ee A eA es Se AE bk 51 94 12 Tool Window See a Be he Oe a a ey ee ere es 52 5 4 13 IMD Connect Simulation Window 55 5 4 14 Sequence Window o 56 KEER ama POT vas ee pr o a Sina ee Be els la Le a 58 6 Molecular Drawing Methods 60 6 1 Rendering methods 0 0 00 0 2 ee ee 60 Oiled Liness sd Yen ao EVE eek ee Ace Dele Ee ea ee Be Se 61 012 CRON Sn at Te A Geet desea ce Snag A Seni Mee eae TE ae he asa 61 6 13 DynamieBonds aio prensa e ined Se A a Es 62 EN lA hooey Se ee dete OS ace nag ee Fa ten aes eee OA 62 Oslo POINGS as ts Seo Yel Men phe ea an ares be cherie 2 wiki de a ee E A 62 DED VID Ws ada le nee oii pt Oe ees ees Mees a A BA 63 Dlr OP Koa ode A wR ee eae ee A aie ae ale idee 63 61 37 ICOPICE Lil a a ae el Bae ty ee ee a hs ee Ge ees 63 6 19 Polyhedrd or te 2 ea ee A a A ce ae a ee BG 63 6 10 Trace ous os God es OR a oe oe Rin ees eh aS a ee Gs i ee 64 A A A le Meee E diel Le ee oe Se MP a E E 64 A A A A btn St oar he ed 64 6 1 13 NewRibbons dia a e A O Bete as A A 65 Gel 14 Cartoons a y a a UR A iS A da 65 61 15 Ne wCartoon sao Ai da a A A 66 6 1 16 PaperChaines As iN ii EA A A Bee aS 66 A hg ke Ps ee ee Oe oe ee Be a
193. l stay with the rep it was assigned to even when the order of the reps changes Use repindex to find the repid of the rep with the given name 1 is returned if no rep with that name exists e get_autoupdate molid rep e set_autoupdate molid rep onoff These two commands let you turn on off automatic updating of the atom selection for a given rep Automatic updating means the atom selection for the rep will be recalculated every time the coordinate frame of the molecule changes e get_colorupdate molid rep e set_colorupdate molid rep onoff These two commands let you turn on off auto matic updating of the color for a given rep Automatic updating means the color for the rep will be recalculated every time the coordinate frame of the molecule changes this is useful for coloring by Position or User e get_smoothing molid rep e set_smoothing molid rep n These two commands let you get set on the fly smooth ing of molecular representations Atom coordinates used to draw the given rep will be smoothed with a moving average window size of 2n 1 e get_scaleminmax molid rep e set_scaleminmax molid rep min max e reset_scaleminmax molid rep Get set the color scale range for this rep Normally the color scale is automatically scaled to the minimum and maximum of the corresponding range of data This command overrides the autoscaled values with the values you specify Omit the min and maz arguments to get the curren
194. lapping surfaces between non connected atoms becomes more apparent The second is Detail Level which should probably be renamed Density as it determines the surface density of the distributions The higher the detail the higher the density The final option is the Representation Method By default the surface is drawn as a collection of points but a point is a pixel in size regardless of the scale of the molecule so when scaled small the surface density appears high and when scaled large the density appears low Method 2 draws little plus signs instead of points which does scale better so the density appears more contant Method 3 draw lines between the surface points that are on the same atom but makes no attempt to connect the two spheres Thanks to Jan Hermans for implementation pointers and thanks again to Jon Leech for the code to compute the uniform point distributions That code was included as part of the 1 x distribution 70 6 2 Coloring Methods VMD maintains a database of the colors used for the molecules and other graphical objects which are visible in the display window It keeps track of e color name definitions its RGB value e mappings from a color category to color name so residue name MET is colored yellow e the current color scale red to white to blue and several related parameters There are 1057 colors available in VMD with color ids ranging from 0 to 1056 The first 33 are in order blue red gray o
195. lated at a lower resolution to improve interactivity to prevent this behavior you can use the middle or right button or the control shift alt modifier keys while dragging the slider e Draw This can be set to Points Shaded Points Wireframe or Solid Surface The default drawing mode is Points When viewing very dense isosurfaces of huge volumetric maps the Shaded Points drawing method can be an excellent compromise between the speed of the Points method and the quality of the Solid Surface method e Boundary Setting the boundary to Box causes the volume data bounding box and coordinate axes to be drawn rather than the isosurface for the data This is often useful when first working with volumetric data and checking that the coordinate systems of the volume data and the molecule match e Step This setting can be used to greatly reduce the resolution of the generated isosurface by skipping voxels e Size This sets the thickness of the point and line based isosurface representations This and other volumetric display features will be greatly expanded in forthcoming releases of VMD 6 1 23 FieldLines The FieldLines representation computes lines that trace the result of integrating the motions of massless particles advected by the volume gradient vectors associated with each location in a volumetric dataset VMD computes the volume gradient map when a volumetric dataset is initially loaded and the particle advection
196. lated thus the displayed atoms may not correspond to those that would be selected if the atom selection were performed for the new animation frame If the Update Selection Every Frame checkbox is highlighted by clicking on the checkbox then the atom selection for the current rep will be recalculated every time the animation frame changes Similarly if the Update Color Every Frame checkbox is activated the color will be recalculated for every frame Color Scale Data Range Several of the coloring methods available in Draw Style tab operate over data fields that have no specifically implied range of values It is often useful to highlight a very specific range of data values in order to accomplish this the color scale range can be manually set to a specific starting and ending values overriding the default behavior which is to autoscale from the minimum value to the maximum value This feature is particularly useful when displaying trajectories since the range of values of interest may be quite different from the autoscaled range for a single frame or all frames Draw Multiple Frames Draw multiple trajectory frames or coordinate sets simultaneously This setting allows the user to select one or more ranges of frames to display simultaneously The frame specification takes one of the following forms now frame_number start end or start step end Trajectory Smoothing The Trajectory Smoothing Window Size is used to control the application of a per
197. le to read and convert between all of these formats We suggest using Tachyon or Raster3D as they are generally the fastest programs These programs are easy to understand and are fast even when rendering very complex molecules The generated scene files are plain text so they are very easy to modify This is most often done to create a larger raster file though some have other global options which you may wish to change For instance by default the Raster3D file turns shadows on We suggest you consult the relevant renderer s documentation to determine what can be modified in the file To actually render the current image into an output file first set up the graphics in VMD just as you wish the output to appear Then either use the Render window 5 4 11 or the following text command to create the input file and start the rendering program going render method filename render command method is one of the names listed in the first column of table 8 1 and filename is the name of the file which will contain the resulting image processing program script Any text following this will be used as a command to be run to process the file If s appear in the command string they will be replaced with the name of the script file 8 3 Caveats When VMD creates the output file it will try to match the current view and screen size For the most part it does a good a job but there can be some problems The colors in the final raster image can someti
198. led with Tcl which add a complete scripting language including variables loops and conditionals along with a standard method for communicating with other programs via standard TCP IP sockets Versions 1 2 and later also include the Tk toolkit for creating menus with buttons bound to one s favorite actions Tcl short for Tool Command Language developed by John Ousterhout is an embeddable and extensible scripting language In other words Tcl sits inside VMD as a language interpreter where 1t can execute its standard language commands or the various VMD specific extensions VMD uses Tcl and Tk version 8 4 1 We refer you to http www tcl tk for more information about Tcl 9 3 Tcl Text Commands All Tcl commands in VMD are composed of one or more words or phrases separated by white space and terminated by a newline In Tcl a phrase is text surrounded by double quotes or by a matching set of open and close braces The first word of each command indicates the general purpose for the command and the following words specify the exact type of command to execute Table 9 1 summarizes the text commands in VMD by listing the first words and describing the general purpose for commands starting with those words The commands described in the following sections are listed by name and followed by a list of the available arguments If an argument is optional it is enclosed in s If only one of a list of arguments is needed the list is enclosed
199. list of possible locations e location Get the current location e location lt off origin lowerleft lowerright upperleft upperright gt Position axes Also though this may seem like a likely command for changing the color of the axes this function can only be performed from the Colors window or by the color command see below Future implementations of VMD may change this 9 3 4 color Change the color assigned to molecules or edit the color scale All color values are in the range 0 1 Please see the section on coloring 6 2 for a full description of the various options e category name color Set the color of the object specified by category and name to color e category name Get the color of the object specified by category and name e scale method lt scale_name gt Set type of scale to use for coloring objects by values They are RGB Red to green to blue BGR Blue to green to red RWB Red to white to blue BWR Blue to white to red RWG Red to white to green GWR Green to white to red 101 GWB Green to white to blue BWG Blue to white to green BIkW Black to white WBIk White to black scale midpoint x Set midpoint of color scale to x in the range 0 1 scale min zx Set minimum of color scale to zx in the range 0 1 scale max z Set maximum of color scale to zx in the range 0 1 change rgb color Reset rgb of color to defaul
200. ll for Windows systems The menu contains items for the VMD Quick Help page as well as the current User s Guide FAQ and links to various helpful information and programs 5 4 2 Main Window Molecule List browser The Main window shows the global status of the loaded molecules Any number of molecules may be displayed by VMD simultaneously Each molecule can separately be hidden from view or fixed in place e g prevented from being affected by mouse rotation commands The window contains controls to change the status of the molecules individually or in groups The browser displays information about each molecule A unique integer ID is assigned to each molecule by VMD when it is loaded The Molecule is the file name which contained the topology information Atoms shows the number of atoms in the molecule and Frames gives the number of frames associated with the file 34 Next to each molecule is a set of status flags which indicate the current Status of each molecule Each molecule has the following characteristics which can be on or off e Top T Top indicates the default molecule used in the text commands when nothing is specified for the mol text command It is also used in some forms like Graphics and Animate to determine certain values There can be only one top molecule at a time e Active A Several commands and actions in VMD operate on many molecules These commands unless specifically specified otherwise will do their a
201. mes look different from what is seen in the VMD graphics window This is because the external rendering programs use different shading equations and algorithms from what VMD uses Potential rendering discrepencies include e Geometry may look slightly different in VMD curved surfaces are polygonalized and drawn using a number of polygonal facets curved surfaces may be rendered entirely smoothly in the final output which is generally looked upon as an improvement e The rendered object colors or intensities may be slightly different due to different colormaps gamma values or lighting models This is particularly true with the material properties used for performing complex shading VMD s real time rendering of these material properties is often simplistic or limited compared to full fledged photorealistic renderers so there can potentially be big differences between implementations of transparency specular highlights etc e Many of the external renderers do not support true orthographic rendering This can be faked by translating the camera very far away from the molecule followed by zooming the camera so that the image size is acceptable again This will significantly decrease the perspective effect but is not a true orthographic projection 91 e The rendering commands do not currently support stereo output so even if the display is currently in stereo mode a non stereo perspective will be used for the rendering program input sc
202. mmands which may be put in this file Also section 5 1 3 discusses how to put commands into the vmdrc file to customize the behavior of the hot keys Here is an example of a startup file 190 add personalized keyboard shortcuts user add key E echo on user add key e echo off user add key g display reset user add key A stage location bottom user add key m mol list position the stage and axes axes location lowerleft stage location off position and turn on menus menu main move 5 196 menu display move 386 90 menu graphics move 5 455 menu files move 5 496 menu main on start the scene a rockin rock y by 1 13 4 Using VMD as a WWW Client for chemical documents Mosaic Netscape and possibly other browsers can be configured to use VMD as a helper application for viewing some chemical documents 13 4 1 MIME types When a web browser receives a document from a server it actually gets two pieces of information the header and the body The header contains information about the message and body One of the most important pieces of data called the MIME type specifies what the body of text describes For instance a GIF image is given the MIME type of image gif a JPEG image is image jpg and postscript is application postscript A class of types chemical has been created for chemical models so the MIME type for PDB files is chemical pdb for XYZ is chemical xyz etc Helper Applications The web browser uses
203. mol id of picked molecule name of pointer id of nearby mol id of nearby atom 1 if shift key down during pick 0 otherwise frame containing new coordi nates labeltype labelid labeltype labelid 1 Once an atom has been picked run the command mol_weight to get output like Mass of ALA 7 67 047 Since VMD sets the vmd_pick_event it can be traced The trace function is registered as trace add variable vmd_pick_event write mol_weight And now the residue masses will be printed automatically when an atom is picked Make sure to turn off the trace when you are done with it e g your plugin s window gets closed trace remove variable vmd_pick_event write mol_weight 137 Chapter 10 Python Text Interface VMD 1 6 and later contain an embedded fully functional Python interpreter The interpreter acts just like the Python command line you can import your own modules and run them from with the text console of VMD In addition VMD provides a number of modules for loading molecules and controlling their display Pre compiled VMD binaries currently use Python version 2 5 The current VMD source code has been tested to compile with Python versions 2 4 to 2 6 on a few platforms User contributed VMD rpm or deb packages can be thus be compiled against any of those versions 10 1 Using the Python interpreter within VMD When you start VMD the VMD text console normally uses the Tcl command interpreter to process wh
204. molid repid Choose only a single representation for tugging or SMD adddevice name toolid Add a device to a tool using a name found in the sensor configuration file removedevice name toolid Remove a device from a tool using a name found in the sensor configuration file callback on off Enable callbacks for the tools 9 3 31 translate Translate the objects in the current scene This does not change the atom coordinates by x y z Translate by vector x y z in screen units note that this does not change the atom coordinates to zx y z Translate to the absolute position z y z in screen units 128 9 3 32 user Add user customized commands e add key key command Assign the given text command to the hot key key When key is pressed while the mouse is in the display window the specified command will be executed e print keys Print out the current definition of the hot keys See section 5 1 3 for examples of the use of the user command 9 3 33 vmdinfo Tcl Returns information about this version of VMD e version Returns the version number e versionmsg Full information about this version e authors List of authors e arch architecture type in case you couldn t tell e options options used to compile VMD e www VMD home page e wwwhelp VMD help page This function is available without Tcl and the information is displayed to the screen 9 3 34 volmap The volmap command creates volumet
205. mples vmd gt set a 180 deg north 180 deg north vmd gt find_rotation_value a 3 14159 vmd gt set a north vmd gt set a 1 pi to eat 1 pi to eat vmd gt find_rotation_value a 3 14159 vmd gt set a to eat vmd gt set a 45 45 vmd gt find_rotation_value a 0 785398 vmd gt expr M_PI 3 0 2 0 4 71239 vmd gt set a 4 71238 radians 4 71238 radians vmd gt find_rotation_value a 4 71238 168 Chapter 12 Molecular Analysis 12 1 Using the molinfo command This section covers how to extract information about molecules and atoms using the VMD text command molinfo Examples Two functions one to save the current view position the other to restore it The position of the axis is not changed by these operations proc save_viewpoint 4 global viewpoints if info exists viewpoints unset viewpoints get the current matricies foreach mol molinfo list set viewpoints mol molinfo mol get center_matrix rotate_matrix scale_matrix global_matrix proc restore_viewpoint 4 global viewpoints foreach mol molinfo list puts Trying mol if info exists viewpoints mol 4 molinfo mol set center_matrix rotate_matrix scale_matrix global_matrix viewpoints mol Cycle through the list of displayed molecules turning each one on one at a time At the end return the display flags to their original state save the current display state foreach mol molinfo list set
206. mportant residues in the protein can be drawn as spheres or licorice bonds in other views When a molecule is first loaded it is given a default view which will draw all the atoms as lines and points coloring each atom by what kind of element it is 6 1 Rendering methods All of the different rendering methods have various parameters which determine how they are drawn For each method there are controls in the Graphics window which modify the associated parameters such as the line width and sphere resolution the graphical controls are described in section 5 4 7 Table 6 1 lists the available rendering methods and the following sections describe these methods and the parameters which modify their appearance 60 Representation styles Description Lines Bonds DynamicBonds HBonds Points VDW CPK Licorice Polyhedra Trace Tube Ribbons NewRibbons Cartoon NewCartoon PaperChain Twister QuickSurf MSMS Surf VolumeSlice Isosurface FieldLines Orbital Beads Dotted Solvent simple lines for bonds points for atoms lighted cylinders for bonds dynamically calculated distance based bonds display hydrogen bonds just points for atoms no bonds solid van der Waal spheres for atoms no bonds scaled VDW spheres with cylinders for bonds spheres for atoms cylinders for bonds same radius polyhedra connecting atoms within a cutoff radius connected cylindrical segments through Ca atoms smooth cylindrical tube
207. n VMD saves the timestep in its animation list instead of just dis carding it after displaying it By default this is 0 which means that VMD does not save any timesteps When this is 0 then when VMD receives a new timestep it replaces the last timestep in the animation list with the new timestep instead of appending it When it is set to some number N larger than 0 then every Nth timestep received from the remote simulation will be appended to the molecule Parameters may be changed by entering text into the appropriate entry field and pressing lt return gt When a new value is entered a command is sent to the remote simulation to change it There may be some delay between when the simulation gets commands acts on them and the results propagate back to VMD Connection state is shown in the center of the window The simu lation status text area displays energy values for the system being simulated kinetic electrostatic etc as well as the current timestep and the temperature It is updated each time a new coordinate set timestep is received by VMD The Stop Sim button will terminate the remote simulation but will not delete the molecule in VMD The Detach Sim button will sever the connection between VMD and NAMD but will allow the simulation to continue running 5 4 14 Sequence Window Close wind Figure 5 13 The Sequence window The Sequence window is used to list the residue sequences of proteins and the base seque
208. n specify the probe coordinates and VDW parameters probe atoms directly using the probecoor and probevdw options probecoor atomcoords Set the coordinates of the probe atoms in form of a list of triples zxo YO zo es rn UN zn probevdw parameterlist Set the tuple of van der Waals parameters for each probe atom in the form feo Rmin o 2 en Rmin y 2 They define the nonbonded interactions of the probe evaluated by the Lennard Jones potential 12 6 Uvpw y Eij 2 9 2 oe r atoms 2 9 1J where Rij Rmin Rmin j 2 and eij ye That s the same form as in CHARMM and AMBER parameter files Units of e are kcal mol and of Rmin 2 are ngstr m orient n Control the number of samples of different probe orientations for multiatom probes at each grid point The number n determines the angular spacing of probe orientation vectors and of the rotations around each of these vectors n 1 use 1 orientation only n 2 use 6 orientations vertices of a octahedron n 3 use 8 orientations vertices of a hexahedron n 4 use 12 orientations faces of a dodecahedron n 5 use 20 orientations vertices of a dodecahedron n 6 use 32 orientations faces vertices of a dodecahedron n gt 6 geodesic subdivisions of icosahedral faces with frequency 1 2 n 6 For each orientation a number of rotamers will be generated The angular spacing of the rotations around the orientation vectors is chosen to
209. n the selections Atom selection is implemented as a Tcl function The data returned from atomselect is the name of the function to use The name is of the form atomselect d where d is a non negative number such as atomselect0 atomselect26 The way to use the function created by the atomselect command is to store the name into a variable then use the variable to get the name when needed 170 vmd gt set sel atomselect top water atomselect3 vmd gt sel text water This is equivalent to saying vmd gt atomselect3 text The easiest way of thinking about this is that the atomselect command creates an object To get information from the object you have to send it a command Thus in the example above atomselect1 num the object atomselect1 was sent the command num which asks the object to return the number of atoms in the selection These derived object functions the ones with names like atomselect3 take many options as described in section 9 3 2 For instance given the selection vmd gt set sel atomselect top resid 4 atomselect4 you can get the atom names for each of the atoms in the selection with vmd gt sel get name NHCACBCO which remember is the same as vmd gt atomselect4 get name Multiple attributes can be requested by submitting a list so if you want to see which atoms are on the backbone vmd gt sel get name backbone N 1 H O CA 1 CB 0 C 1 40
210. name such as resname HEM or by many other identifiers Multiple atoms may be specified with one key word For example the selection name C CA N 0 will select the backbone atoms A similar effect may be obtained with the command protein backbone VMD can handle regular expressions so that name C will select all atoms with names starting with C VMD also understands the boolean operators and or and not so the selection resname HEM and not name N selects all non nitrogen atoms in the heme group of myoglobin Several more abstract selection criteria are available For instance the selection x gt 5 finds all atoms with an x coordinate greater than 5 while mass gt 12 and mass lt 14 selects all atoms with mass greater than 12 and less than 14 atomic mass units Many math functions 8 6 7 are also provided so the selection sqrt sqr x sqr y sqr z lt 10 will select atoms in a spherical region of radius 10 A centered about the origin of the coordinate space You can pick atoms nearby a selection with the phrase within lt distance gt of lt selection gt and all residues with the same property as a given selection as same lt property gt as lt selection gt See section 6 3 for a full description of the selection command 3 6 Comparing Two Structures Let s start from scratch by deleting everything use the text console and tye the command mol delete all and press enter This deletes all loaded molecules and i
211. nces of nucleic acids and to select residues bases from the sequence list for highlighting in the 3 D structure in the main VMD window When residues are selected in the main VMD window the corresponding residue is highlighted in the sequence list in this window Color coded protein structure information is displayed for amino acid residues and B factor information is displayed for all residues In this section residues refers both to amino acid residues in proteins and to nucleotide bases with associated backbone in DNA and RNA molecules Sequence information The Sequence window contains a vertical listing of the residue sequence of a loaded molecule The Molecule pop up menu control chooses which molecule to display the sequence of the current top molecule is displayed the first time the Sequence window is opened The name and molecule number of the sequence displayed is shown in the title frame of the Sequence window 56 For each residue displayed the window lists residue number residue name code and chain letter If no chain is specified chain letter is set to X To the right of this are two color coded columns B value and struct B value shows the contents of the B value temperature factor field The struct field shows protein secondary structure select Help Structure Codes from the window menu or see Table 5 5 for an explanation of the single letter codes in the color key Turn Exte
212. nded conformation Isolated bridge Alpha helix 3 10 helix Pi helix Coil Table 5 5 Description of secondary structure codes in the Sequence window Selecting residues from the Sequence window listing Click anywhere in the vertical listing with the left mouse button to highlight one residue Click and drag with the left mouse button to highlight multiple residues shift click to add a single residue to the current selection shift click and drag to add multiple residues to your selection right click to de select a residue Highlights appear as thick yellow Bonds representations these can be changed or turned off 5 4 14 Selecting residues by clicking on the 3 D structure Use the Mouse menu to enter Pick Atom mode or press 1 the standard keyboard shortcut Click on any protein atom or nucleic acid atom and its residue will highlight and the sequence list will scroll to display this residue Shift click works the same way but adds to the current selection Note that if the zoom factor is smaller than 1 0 the single residue sequence highlight will be shorter in height than a full line of text Once the Sequence window has been opened any Pick will create or add to selections until highlighting is turned off 5 4 14 Sequence Zooming Larger molecules contain thousands of residues too many to display in a linear text list all at once The sequence window can only list about 40 text lines to work wit
213. ne atoms in the pairs must be in the selection otherwise the first atom in each pair will be from the selection and the second will be from sel 10 3 3 An atom selection example In the first example we load the molecule alanin pdb and create an atom selection consisting of the alpha carbons Note that AtomSel is the name of the class which generates atom selection instances We show the string representation of the object by entering its name and pressing return this shows the text used in the selection Next we demenstrate how atom selections act like tuples we can get their length using the built in len command and return a copy of the selected atoms in a tuple by using the slice operator Finally we demonstrate the get and set operations The get operation takes any number of string arguments for each argument it returns a Python list of values corresponding to that string The set operation allows only one property to be changed at a time However you can pass in 141 either a single value which will be applied to all atoms in the selection or a tuple or list of the same size as the atom selection in which case values in the list will be assigned to the corresponding atom in the selection We take advantage of this behavior in the following example by first saving the current value of beta for the selection then setting the value of beta to 5 for all selected atoms and finally resetting the original values using the r
214. ne commands an alternate prompt appears and will not disappear until the command is finished Sometimes it is waiting for a close to a double quote open brace or open bracket while at other times it is waiting for a line that doesn t end in a backslash e Since you may not want to retype all the data in every time there are two ways to read the data in from a text file One is the play command This reads a line from the file executes it then updates the screen and checks for any changes in the mouse or window input so that VMD stays interactive during execution of the script The second way is the Tcl command source This reads the whole file before allowing the mouse and windows to respond to new input This is often more efficient when your script contains many lines e On Unix Linux platforms if the file vmdrc see section 13 3 3 exists in your home directory it is played at VMD startup If you don t have a vmdrc file VMD uses a default script in the VMD installation directory Similarly at startup the e command line flag can be used to specify an input file to be played after reading the vmdrc file The Windows version of VMD works similarly though the startup file is named vmd rc A good use of the vmdrc file is to specify which VMD menus you would like to have open when you start VMD and where they should be placed see section 9 3 18 for information on usage 95 9 2 Tcl Tk The standard distribution is compi
215. nnect to a simulation running on host host and listening for incoming connections on port port e pause If connected cause the simulation to pause 150 e detach If connected detach from the simulation The simulation will continue to run but no more frames will be received until a connection is re established e kil1 If connected terminate the simulation The connection will also be abolished e transfer rate Set get how often the remote simulation sends coordinate frames to VMD If rate is omitted or is negative no action is taken and the current value is returned A value of 1 corresponds to every frame being sent a value of 2 corresponds to every other frame etc e keep rate Set get how often received coordinates frames are kept by VMD as part of an animation If rate is omitted or is negative no action is taken and the current value is returned A value of 0 means no frames are saved A value of 1 corresponds to every frame being saved a value of 2 corresponds to every other frame etc e copyunitcell True False Control how unitcell information is passed to the new frame that recieved via IMD If set to False the default unit cell information would be taken from the IMD connection Since the IMD protocol currently has no provisions for communicating the unit cell information the unit cell dimensions are set to zero If set to True the cell information is copied from the previous frame WARNING when using imd
216. not cyclic residues named ALA GLY ILE LEU VAL atom s residue is an alpha helix a residue with atoms named C N CA and O residues named HIS PHE TRP TYR residues named ARG HIS LYS atoms for which numbonds gt 0 residues named ALA LEU VAL ILE PHE CYS MET TRP residues named CYT C GUA G basic or acidig residues named HIS PHE PRO TRP TYR Table 6 5 Atom selection keywords hetero hydrogen large medium neutral polar purine pyrimidine small surface rasmol alpha helix pi helix helix_3_10 helix extended_beta bridge_beta sheet turn coil structure phi psi within exwithin same ufx ufy ufz not protein or nucleic name 0 9 H protein and not small or medium residues named VAL THR ASP ASN PRO CYS ASX PCA HYP residues named VAL PHE GLN TYR HIS CYS MET TRP ASX GLX PCA HYP protein and not hydrophobic residues named ADE A GUA G residues named CYT C THY T URI U residues named ALA GLY SER protein and not buried translates Rasmol selection string to VMD atom s residue is in an alpha helix atom s residue is in a pi helix atom s residue is in a 3 10 helix atom s residue is in an alpha or pi or 3 10 helix atom s residue is a beta sheet atom s residue is a beta sheet atom s residue is a beta sheet atom s residue is in a turn conformation atom s residue is in a coil conformation single letter name for the secondary structure back
217. not get updated by just display update command whereas display update ui forces both updates to happen Tk does not seem to have this problem so this option will become obsolete after switching to Tk graphics user interface 104 9 3 7 draw VMD offers a way to display user defined objects built from graphics primitives such as points lines cylinders cones spheres triangles and text Since these are displayed in the scene just like all other graphics they can also be exported to the various ray tracing formats 3 D printers etc User defined graphics can be used to draw a box around a molecule draw an arrow between two atoms place a text label somewhere in space or to test a new method for visualizing a molecule The draw command is a straight Tcl function which is meant to simplify the interface to the graphics command as well as provide a base for extensions to the standard graphics primitives The format of the draw command is e draw command arguments The draw command is equivalent in most cases to graphics top command arguments in that it simply adds graphics primitives to the top molecule saving you the trouble of typing an extra argument However draw extends graphics in two ways First if no molecule exists draw creates one for you automatically Second draw can be extended with user defined drawing commands This is done by defining for a function of the form vmd_draw_ command If the function exists it is called
218. number and chain name These residues will be high lighted selected deselected together e B values can be user assigned To use the B value column to view arbitrary data use the selection set beta commands to change B values To refresh the displayed B value data re select the currently displayed molecule from the Molecule pop up menu 5 4 15 RamaPlot The RamaPlot window displays a Ramachandran plot for a selected molecule If you animate your molecule over a range of frames RamaPlot will update the Ramachandran plot automatically You can select a range of residues to be displayed in the plot Clicking on a point in the Ramachandran plot will show the trajectory of the selected residue in Ramachandran space over all frames Fields on the right of the window show the computed value of phi and psi for the most recently selected residue Finally you can create a PostScript image of the current Ramachandran plot RamaPlot functionality is summarized in Fig 5 14 58 Ramachandran plot for molecule 0 alanin pst Molecule a Selection all Segid MAIN Resname a Resid Je Phi 54 2731 595 Psi Jaa 50594325 Figure 5 14 The RamaPlot Window Using RamaPlot Start RamaPlot by typing ramaplot in the VMD text console or by selecting the ramaplot menu item in the Extensions menu The main window contains a Ramachandran graph with phi and psi running along the horizontal and vertical axis respectively from
219. nvironment variables and adds the vmd script directory to the Tcl autoindex path Most of the other files are referenced through the auto_path There are a few non Tcl scripts in this directory Currently these are perl scripts used for the urlload command and web client startup see section 9 3 19 and section 13 4 13 3 2 User Script Files A user written run time command file vmdrc on Unix vmd rc on Windows can be used with a list of initial VMD text commands to process This file may be changed to customize individual user s initial screen appearance and to set the proper display characteristics for displaying in stereo If it does not exist default values are used 13 3 3 vmdrce and vmd rc Files After everything is initialized VMD reads the startup file using the equivalent of the command play vmdrc This file contains text commands for VMD to execute just as if they had been entered at the VMD text console command prompt The file can contain any number of commands including blank lines and comment lines which begin with the character If an error is encountered while reading this file the command in error is skipped and processing of the file continues VMD searches for this file in three locations on Unix vmdrc HOME vmdrc and VMDDIR vmdrc On Windows VMD searches in vmd rc HOME vmd rc and VMDDIR vmd rc Only the first file found will be read in and processed See chapter 9 for a description of the VMD text co
220. o render in VMD in that FreeVR session The default value unless otherwise specified is 80 Megabytes Values of 200MB to 512MB are commonly needed for large molecular systems containing several hundred thousand atoms VMDFORCECONSOLETTY Unix only intended only for clusters This environment variable forces VMD to treat the text console as an interactive terminal despite what the operating system says This is only useful for running an interactive VMD session on a Clustermatic or Scyld Linux cluster node VMDGDISPLAY Unix only The name of an X Windows display that VMD will use to display the graphics window This environment variable is only used on Unix systems Through the use of the the DISPLAY and VMDGDISPLAY envrironment variables the VMD graphics window can be placed on a separate screen from the windows and menus This is particularly useful when giving 3 D demonstrations using a projector The windows and menus can be kept on a different screen from the graphics so that they do not distract the audience VMDGLSLVERBOSE OpenGL Shading language compiler diagnostic errors only printed only when this environment variable is set VMDHTMLVIEWER The name of a command that will run a web browser in the background Netscape Mozilla Firefox or whatever you prefer that VMD should use to display HTML documents such as this help file By default on UNIX this is mozilla usage examples in Tcl set env VMDHTMLVIEWER mozilla rem
221. o arguments will create a new empty molecule in VMD Passing a valid molecule id will make the Molecule instance mirror the state of the corresponding molecule in VMD e _int_ Casting a Molecule to an int returns the molecule ID e rename self newname Changes the name of the molecule e name Returns the name of the molecule e delete Deletes the molecule corresponding to this Molecule instance The object can no longer be used e load filename filetype None first 0 last 1 step 1 waitfor 1 volsets 0 Load molecule data from the given file The filetype will be guessed from the filename ex tension this can be overrideen by setting the filetype option first last and step control which coordinates frames to load if any volsets indicates which volumetric data sets to load from the file Raises IOError if the file cannot be loaded 157 save filename filetype None first 0 last 1 step 1 waitfor 1 sel None Save timesteps to the given file The filetype will be guessed from the filename extension this can be overridden by setting the filetype option first last and step control which timesteps to save Returns the number of frames written before the command completes Pass an AtomSel instance as sel to write only a selection of atoms to the file Note that this differs from the AtomSel write method in that Molecule save writes a range of timesteps while AtomSel write writes only the coordinates correspond
222. o you might want to try increasing the angle value from 20 to 30 degrees and the distance value from 3 to 4 The HBonds are drawn as dotted lines of a given width The default Line Thickness is 1 but you should probably increase that to 2 On most SGIs you can t make it any wider than that as described in the man page for linewidth The bond is colored by the color associated with the acceptor 6 1 5 Points Points draws each atom as a point and does not draw any of the bonds This option is useful when rendering very large molecules containing millions of atoms particularly for rendering water or other structures for which geometric detail may not be necessary The Size of the points can 62 be changed When the VMD rendering mode is set to GLSL the Points representation will render space filling spheres with a size proportional to the Size parameter and with performance on par with the non shaded points drawn in other rendering modes 6 1 6 VDW VDW draws the atoms as spheres The Sphere Scale used is the van der Waals radius multiplied by a user selectable scaling factor The Sphere Resolution determines how finely to tessellate the spheres that are drawn when using rendering modes and external rendering tools that can only draw polygonal geometry The performance of polygonal sphere rendering varies inversely with the number of triangles produced by tessellation into triangles The number of triangles per sphere varies pr
223. ociated with that name e Chain if the coordinate file contained data in the Chain field for this atom then that data is given here e Segname the name of the segment to which this atom belongs e Index the internal VMD index used to identify the atom this is useful for specifying selection syntax to generate different representation styles for particular atoms For PDB files Index corresponds to the atom number listed in the file minus 1 so that the index starts with 0 e Value the calculated length of bonds angles or geometric measurements performed by the selected label 48 Plotting a labels value If the label has a numeric value such as a bond length geometry monitor it is easy to graph the change of the value over time for multiple frames in an animation The Graph button calls a Tcl script to plot the data for the selected labels You can create your own script to handle label plotting simply by creating a Tcl proc named vmd_labelcb_user The proc should accept three arguments Have a look at the default scripts in the VMD scripts directory found in the VMD installation directory under scripts vmd graphlabels tcl If no supported graphing program is available a dialog box will be presented which will allow you to save the values of the labels to a file 5 4 9 Color Window Color Controls Assign colors to categories Categories Names Colors Figure 5 9 The Color window VMD maintains a database
224. of 176 hardware requirements 16 help 34 command 97 108 topics 108 highlight 57 hot keys 30 129 animation control 33 customizing 30 menu control 32 mouse control 31 rotation and scaling 32 hydrogen bonds 62 113 image lighting controls 28 41 shading and material properties 50 IMD 55 imd command 97 108 Python module 150 requirements 55 implicit ligand sampling volumetric data 130 Interactive Molecular Dynamics 55 interpolation volumetric data 130 joystick using 33 label command 97 109 Python module 151 labels 20 categories 47 109 delete 48 hide 48 picking with mouse 28 plotting 49 136 show 48 text 105 window 47 light command 97 110 controlling with mouse 28 toggle 41 logfile command 97 110 disable from GUI 22 disable from text 110 enable from GUI 22 enable from text 110 logging tcl commands 22 110 mask volumetric data 130 mass center of 173 of residue atoms 135 total 175 material changing 121 command 97 110 methods 42 Python module 152 material properties 107 matrix routines alignment 165 identity 164 inverse alignment 165 196 list of 164 multiplication 164 rotation 165 trans command 166 translation 166 transpose 164 MDTools 15 measure command 97 111 175 176 menu command 97 119 menus 119 molecular surface 66 68 molecule active 35 36 analysis 175 best fit alignment 180 command 97 119 123
225. ohn E Stone for the Tachyon ray tracer WorkForce threading and timer routines hash table code and Spaceball drivers and Ethan Merrit for one of the ribbon drawing algorithms 1 5 Copyright and Disclaimer Notices VMD is Copyright 1995 2009 Theoretical and Computational Biophysics Group and the Board of Trustees of the University of Illinois Portions of this code are copyright 1997 1998 Andrew Dalke The terms for using copying modifying and distributing VMD are specified by the VMD License The license agreement is distributed with VMD in the file LICENSE If for any reason you do not have this file in your distribution it can be downloaded from http www ks uiuc edu Research vmd current LICENSE html Some of the code and executables used by VMD have their own usage restrictions e ACTC ACTC the triangle consolidation library used in some versions of VMD is Copyright C 2000 Brad Grantham and Applied Conjecture all rights reserved 12 Redistribution and use in source and binary forms with or without modification are permit ted provided that the following conditions are met 1 Redistributions of source code must retain the above copyright notice this list of condi tions and the following disclaimer 2 Redistributions in binary form must reproduce the above copyright notice this list of con ditions and the following disclaimer in the documentation and or other materials provided with the distribution 3 All
226. ol selection text frame frame2 set coords2 sel2 get x y z and compute the rmsd values set rmsd 0 foreach coordi coords1 coord2 coords2 set rmsd expr rmsd veclength2 vecsub coord2 coord1 divide by the number of atoms and return the result return expr rmsd selection num 0 0 The following uses the frame_rmsd function to list the rmsd of the molecule over the whole trajectory as compared to the first frame vmd gt mol new alanin psf vmd gt mol addfile alanin dcd vmd gt set sel atomselect top all vmd gt for set i 0 i lt molinfo top get numframes incr i puts list i frame_rmsd sel i 0 oy 0 0 0 1 0 100078 2 0 291405 3 0 523673 97 20 0095 98 21 0495 99 21 5747 177 The last example shows how to set the beta field This is useful because one of the coloring methods is Beta which uses the beta values to color the molecule according to the current color scale This can also be done with the occupancy field Thus redefining the beta values allows you to color the molecules based on your own definition One useful example is to color the molecule based on the distance from a specific point for this case coloring a poliovirus protomer based on its distance to the center of the virus 0 0 0 helps bring out the surface features proc betacolor_distance sel point Y get the coordinates foreach coord sel get x y z 4 get the distanc
227. olecule simultaneously Imagine a protein on the surface of and extending part way into a membrane One way to visualize the extent of the penetration is to represent the lipids as Bonds and make them transparent That will show the membrane without completely obstructing the view of the protein VMD maintains a database of materials which can be applied to any representation in the system much like the database for colors There are two default materials Opaque and Trans parent which cannot be modified Each material is defined by five settings as follows material is e Opacity a number 0 0 to 1 0 describing the transparency 1 is solid 0 is transparent By default transparent objects are drawn with Opacity set to 3 e Ambient a value describing how strongly the material reflects ambient light Ambient light provides a uniform illumination of objects with a background lighting of the object color e Diffuse Diffuse reflections are independent of the viewing direction but depend on the 73 Method small red middle green large blue small blue middle green large red small red middle white large blue small blue middle white large red small red middle white large green small green middle white large red small green middle white large blue small blue middle white large green small black large white small white large black Table 6 4 Available Color Scale Gradations run Component
228. on s center of mass through the masscenter flag is available as well as using the origin via the origincenter flag Using masscenter is recommended but not made default as it depends on the mass value to be correctly set for all atoms e fit selection1 selection2 weight weight order index list Returns a 4x4 transformation matrix which when applied to the atoms in selection 1 minimizes the weighted RMSD between selection and selection2 See section 12 4 2 for more on RMSD alignment The optional flag order takes as argument a list of 0 based indices specifying how to reorder the atoms in selection Example To reverse the order of atoms in a selection containing 10 atoms one would use order 9 8 7 65 4 3 2 1 0 e gofr selection selection2 delta value rmax value usepbc boolean selupdate boolean first first last last step step Calculates the atomic radial pair distribution function g r and the number integral fj pg r r dr for all pairs of atoms in the two selections Both 112 selections have to reference the same molecule and may be identical In case one of the selections resolves to an empty list for a given time step and empty array is added to the histograms The command returns a list of five lists containing r g r f pg r r2dr the unnormalized histogram and a list of frame counters containing currently 3 elements total number of frames processed the number of skipped frames and the number of frames handle
229. on finds all rings up to a user defined maximum size by walking the molecular topology then proceeds to render each ring by fitting a polyhedron to the involved atoms and the ring centroid The rings are drawn as bipyramids with a user controlled height The rings are colored by pucker using the Cremer Pople pucker amplitude which is defined for all rings of three atoms or greater 6 1 17 Twister The Twister representation traces glycosidic bonds with a flat ribbon that twists according to the relative orientation of successive sugar residues The concept is similar to the familiar ribbon representations VMD uses for proteins The paths connecting oriented rings are connected by thin ribbons with user adjustable width and thickness and with adjustable geometric resolution and the representation handles branched structures 6 1 18 QuickSurf The QuickSurf representation computes an isosurface extracted from a volumetric Gaussian den sity map computed from atoms or particles in the neighborhood of each lattice point The density map generation algorithm accumulates Gaussian densities on a uniformly spaced 3 D lattice defined within a bounding box large enough to contain all of the atoms or particles that are selected as part of the rendered surface sufficient padding at the edges of the volume ensures that the extracted surface is not clipped off The density map generation algorithm satisfies N ae 77 12 p T Fia PN doe
230. on should work as ex pected so that 8 is between 1 and 11 in a numeric context but not in a string one This may lead to some peculiar problems Some keywords such as segname can take on string values but can also be used by some people as a number field Suppose someone labeled the segname field with the numbers 1 through 12 on the assumption that they are numbers That person would be rather confused to find that segname 1 to 11 only returns two segments Also strings will be converted via atof to a number so if the string isn t a number it will be given the value of 0 It is possible to force a search to be done in either a string or numeric context using the relational operator discussed in 6 3 6 Selections can be combined with the boolean operators and and or collected inside of paren thesis and modified by not as in name CA or name CB and mass 12 to 17 which selects all atoms name CA or CB and have masses between 12 and 17 amu this could be used to distinguish a C alpha from a calcium VMD has operator precedence similar to C so leaving the parentheis out of the previous expression as in name CA or name CB and mass 12 to 17 actually selects all atoms named CA or those that are named CB and have the appropriate mass 6 3 1 Definition of Keywords and Functions The keywords available for selecting atoms in VMD are listed in tables 6 5 and 6 6 at the end of this chapter If a keyword definition is foll
231. onal style color selection and material properties MoleculeRep objects also have attributes with the same names as the above keywords these can be used to query the state of the rep Don t set these attributes directly use the change methods below instead e changeStyle style e changeColor color e changeSelection selection e changeMaterial material Set the draw style color atom selection and material for this rep If the rep is assigned to any molecules the molecule rep will be updated accordingly style must be a valid draw style see the Style functions below In the following example we load a molecule add a new transparent VDW rep to the molecule then change the atom selection for the rep to name CA gt gt gt from VMD import gt gt gt from Molecule import gt gt gt bR Molecule gt gt gt bR load proteins brH pdb 159 lt snip gt gt gt gt reps bR reps gt gt gt reps 0 style Lines gt gt gt vdw MoleculeRep style VDW material Transparent gt gt gt bR addRep vdw gt gt gt vdw changeSelection name CA 10 6 3 Draw Style Methods The syntax for changing the draw style in the MoleculeRep changeStyle method is fairly simple and easy to remember as long as the default values for each style are used however remembering that rep changeStyle CPK 0 5 0 5 8 is the way to set the bond radius sphere scale and sphere resolution for CPK is
232. oportionally with the Sphere Resolution parameter value squared For rendering modes such as GLSL and for external rendering tools that can directly represent spheres and other quadric surfaces the Sphere Resolution parameter has no effect Note Due to variations in atom naming conventions in rare instances VMD may improperly assign VDW radii to specific atoms since VMD determines each atom type based on the first letter forming its name For example VMD would assume an atom named HG to be a hydrogen rather than a mercury If this happens you are always free to redefine the radii using a syntax much like that below set sel atomselect top name HG sel set radius 1 9 6 1 7 CPK CPK is a combination of both Bonds 6 1 2 and VDW 6 1 6 in that it draws the atoms as spheres and the bonds as cylinders The resolution and radius can be modified independently The size of the sphere drawn in CPK mode is by default the scaled down VDW radius but this scaling factor can be changed by adjusting the Sphere Scale parameter Since a sphere is drawn for each atom it will always be slower than the VDW option If the radii for a sphere or bond are too small they will not be drawn 6 1 8 Licorice Licorice draws the atoms as spheres and the bonds as cylinders The difference between this and CPK 6 1 7 is that the sphere radius is not controllable instead it is made the same size as the
233. or different molecules Returns the reps auto update status ssRecalc Recalculate the secondary structure for this molecule Examples gt gt gt from VMD import gt gt gt from Molecule import gt gt gt bR Molecule gt gt gt bR load proteins brH pdb 158 lt snip gt lt Molecule Molecule instance at 0x406d878c gt gt gt gt bR name gt molecule gt gt gt bR rename bR lt Molecule Molecule instance at 0x406d878c gt gt gt gt bR name bR gt gt gt bR numAtoms 3762 gt gt gt bR dupFrame lt Molecule Molecule instance at 0x406d878c gt gt gt gt bR numFrames 2 10 6 2 MoleculeRep The MoleculeRep class defined in the Molecule module is designed to make it easy to keep track of the reps in a molecule and to update reps in many molecules simultaneously The way it works is to create a MoleculeRep instance then add it to as many molecules as you want using the Molecule addRep method The only operations on MoleculeRep objects is to change their properties when this occurs all molecules to which the rep has been added will be updated Deleting a MoleculeRep instance has no effect A list of MoleculeRep instances for a given molecule can be gotten from the Molecule reps method The MoleculeRep class provides the following methods e _init_ style defStyle color defColor selection defSelection material defMaterial Initialize the Rep object with opti
234. ormap name Returns a dictionary of name color pairs for the given color cate gory set_colormap name dict Change the color definitions for the colors in the given color category The keys in dict must come from the keys listed by get_colormap for that color category though not all keys need be listed The values must be legal color names get_colors Returns a dictionary whose keys are all the legal color names and whose corresponding values are the RGB values of the color represented as a 3 tuple set_colors dict Changes RGB values for colors in VMD Keys must be chosen from the keys returned by get_colors Values must be 3 tuples of floats scale_method Returns the current color scale method scale_methods Returns a list of all available color scale methods scale_midpoint Returns the current color scale midpoint scale_min Returns the current color scale minimum scale_max Returns the current color scale maximum set_scale method midpoint min max Change the color scale method midpoint min imum or maximum All properties may be set using keyword arguments 148 10 5 4 display Python operations available from the display module used to control the VMD camera as well as screen updates e update Force a display update without checking the VMD FLTK menus e update_ui Update the display as well as any other user interfaces e update_on Tell VMD to regularly update the display and the FLTK menu
235. ote openURL s set env VMDHTMLVIEWER mozilla s amp VMDIMAGEVIEWER The name of the external program to use for displaying VMD snapshots or other images in various formats 188 VMDIMMERSADESKFLIP Enable a special reversed reflected stereo projection mode for use with experimental displays based on LCD panels phase plates and beam splitters VMDVMDMACENABLEEEXTENSIONS Enable performance oriented OpenGL rendering extensions which are disabled by default These extensions have been observed to trigger instability on some MacOS X systems VMDMSECDELAYHACK Add in a user specified delay which causes VMD to sleep for specified number of milliseconds each time it renders the molecular scene on the display This feature is meant as a workaround to poor performing display drivers which make the windowing system unresponsive if VMD is allowed to run unrestricted at maximum drawing rate VMDMSMSUSEFILE Force VMD to communicate with MSMS through the filesystem rather than with the socket based network interface This option can be used when the socket interface isn t working properly for some reason This is the default behavior when using VMD on Windows VMDNOCUDA Force VMD not to use CUDA based GPU acceleration even if CUDA support was compiled in and CUDA capable devices are detected at startup This can be used in cases where a GPU or GPU drivers prove to be unreliable for computation for benchmarking vs CPU only
236. owed by bool it is either on or off If followed by str it takes a value in the string context If followed by num it takes a value in the number context 76 Table 6 7 lists the built in functions which may be used in atom selection expressions with keywords which take on a numeric value Table 6 8 lists the built in atom selection keywords which may be used in atom selection ex pressions to query the values of an underlying volumetric map in the same molecule These are read only 6 3 2 Boolean Keywords Some selections take no values For example backbone selects the backbone atoms of the protein and nucleic acids and protein selects protein atoms Giving options to these selections is an error The selections can be used in the same way as other selections as in protein and backbone nucleic or protein In addition if neither and nor or are located after a boolean keyword then an implicit and is inserted so that the following are valid protein name CA same as protein and name CA nucleic backbone 6 3 3 Short Circuiting The boolean logic in VMD does short circuit evaluation on an element wise basis For instance given one atom if X is true then X or Y will be true regradless of the value of Y so there is no need to evaluate it Similarly if X is false then X and Y will also be false so Y again need not be evaluated Knowing how short circuit selections work can speed up several types of selections Consider a system
237. panel displays 8 Row interleaved also known as line blanking stereo works with compatible shutter glasses and LCD panel displays 7 3 1 Quad buffered Stereo Quad buffered aka CrystalEyes stereo is the name used within VMD for the quad buffered frame sequential stereo display mode found on professional graphics workstations Quad buffered stereo generally yields the highest quality output and is therefore the most desirable stereo mode to use when available Since quad buffered stereo requires more video memory and special display synchronization circuitry this mode is usually only available on professional grade GPUs such as AMD FireGL NVidia Quadro FX and similar products Typically this mode is used to drive LCD shutter glasses with a CRT display 120Hz LCD panels or various high end stereo capable projection systems Quad buffered stereo mode provides separate left and right eye frame buffers It allows the a window display in stereo while all other windows appear as normal The display must be set in a stereo capable mode before starting VMD On SGI workstations one must use either the setmon or xscreen utilities to configure the display mode On Sun workstations this is done using the fbconfig utility HP systems use the sam utility for display configuration Microsoft Windows uses the Display Properties tab to control video board display mode settings Once set in the proper display mode start VMD as normal and select QuadBu
238. per redraw for n steps reverse and repeat 9 3 27 rotate Rotate the current scene around a given axis by a certain angle This does not change atom coordinates e stop Stop all rotation similar to rock off but it also stops mouse rotations as well e lt x y_ z gt by angle Rotate around the given axis angle degrees e lt x y z gt to angle Rotate the given axis to the absolute position angle e lt xlylz gt lt by to gt angle step Rotate at a rate of step degrees per redraw 9 3 28 scale Scale the current scene up or down This does not change atom coordinates e by f Multiply scene scaling factor by f e to f Set scene scaling factor to f 127 9 3 29 stage Position a checkerboard stage on the screen location lt off origin bottom top left right behind gt Set the location location Get the current location locations Get a list of possible locations panels n Set number of panels in stage up to 30 panels Get the number of panels in use 9 3 30 tool Initialize and control the tools that are controlled by external tracking devices create Create a new tool change type toolid Change the type of a tool scale scale toolid 1 Change the scale of the coordinates reported by a tool scaleforce scale toolid Increase or decrease the force on a force feedback device offset x y z toolid 1 Add a vector to a tool s position delete toolid Remove a tool rep
239. played in the Materials menu delete id Deletes the graphics primitive with the given id delete all Deletes all graphics primitives replace id Causes the next graphics primitive to replace the one with the given id Subse quent graphics primitives will be added to the end of the list as usual exists id Returns whether the primitive with the given id exists list Returns a list of valid graphics id s info id Returns the text of a Tcl command which will recreate the graphics primitive with the given id 107 9 3 10 gettimestep Retrieve the specified molecule s timestep as a Tcl byte array which can be used for high efficiency analysis calculations by compiled Tcl plugins e lt molid gt lt timestep gt retrieve timestep as a Tcl byte array for use in compiled analysis plugins 9 3 11 help Display the on line help file with an HTML viewer See Chapter 13 for information on how to change the default viewer which is Netscape e subject Jump to help corresponding to subject Presently subject can be any one of the following words which launches the associated URL To guarantee that the help system will work correctly you will probably want to start up your web browser before choosing one of these options After you do this VMD will properly direct the browser to the pages mentioned below Associated URL raster3d http www bmsc washington edu raster3d msms http www scripps edu pub olson w
240. pports version 1 6 of Babel 25 4 4 Raster3D file format In addition to the molecular file formats VMD can read the input file for Raster3D Raster3D converts an input file into a shaded raster image for use in making high quality pictures It is often used with MolScript The ability to read Raster3D allows users to view MolScript files in 3D and incorporate special images into the display without having to edit the VMD code The file format which is part of the Raster3D documentation describes a simple collection of triangles spheres and cylinders with either flat or spherical ends Each shape is colored by an RGB triplet Certain newer Raster3D objects are ignored such as quadrics Also nearly all of the header information is ignored most notably the viewing matrix Raster3D uses many cylinders with spherical rounded ends VMD deliberately omits these rounded ends since the resultant image would be very slow to render interactively VMD uses a fixed size palette of colors each triplet is converted into its nearest indexed color T his may cause images to be colored slightly differently than expected 26 Chapter 5 User Interface Components VMD provides several methods for the user to control and interact with the molecular display The primary methods are by using the mouse either in the graphics window or in the different graphical user interface GUI forms provided by the program In addition to the mouse VMD also
241. radius r resolution n Draw a cone with the center of the base at the first point and the tip at the second The radius default r 1 determines the width of the base As with cylinder the resolution default n 6 determines the number of polygons used in the approximation e triangle x1 y1 z1 x2 y2 23 x3 y3 23 Draws a triangle with endpoints at each of the three vertices e trinorm x1 y1 z1 x2 y2 23 23 y3 23 nal y1 z1 nz2 ny2 nz3 nx3 ny3 nz3 Draws a triangle with endpoints at each of the first three points The second group of three values specify the normals for the three points This is used for making a smooth shading across the triangle The normals must be normalized to unit length for proper display e tricolor x1 y1 z1 x2 y2 23 x3 y3 23 nal y1 z1 nx2 ny2 nz3 nz3 ny3 nz3 cl c2 c3 Draws a triangle with endpoints at each of the first three points The second group of three values specify the normals for the three points The last three integers indicate the colors thttp www ks uiuc edu Research vmd script_library 106 to apply to each vertex This is used for making a smooth shading across the triangle The normals must be normalized to unit length for proper display sphere xz y z radius r resolution n Draws a sphere of the given radius default r 1 centered at the vertex The resolution default n 6 determines how many polygons are used in the approximation of a sphere text x y z
242. range yellow tan silver green white pink cyan purple lime mauve ochre iceblue black yellow2 yellow3 green2 green3 cyan2 cyan3 blue2 blue3 violet violet2 magenta magenta2 red2 red3 orange2 and orange3 The next group of 1024 colors from 33 to 1056 are colors used in the color map These can be set to one of several ranges with the Color window or the color text command red green blue red white blue or black white etc There are no names for the specific colors The color map will be discussed in more detail in a section to follow 6 2 1 Color categories VMD maintains a database of the colors used for the molecules and the other graphical objects in the display window The database consists of several color categories each color category contains a list of names and each name is assigned a color For example there is a Resname color category and within this category there are many names one for each of the available residue names Some of these are ALA CYS and PRO Each name can be assigned a color from a list of 33 available colors called the color map The RGB value of each color can be modified directly in the Color window 85 4 9 To color items in a gradation manner there are additional 1024 colors used in the color scale 6 2 4 The different color categories in VMD are listed in table 6 2 The Color window can be used to change the assignment of colors to the names in each of these categories
243. range than use the wall eyed method you are already looking at the wall In VMD this method is referred to as CrossEyes stereo This mode is supported by all GPUs 7 3 3 DTI Side by side Stereo This stereo mode is the same as the regular side by side stereo mode except that the aspect ratio of the displayed image is adjusted to work correctly on DTI stereo flat panel displays This mode is supported by all GPUs 7 3 4 Checkerboard Stereo Checkerboard stereo works by interleaving the left and right eye views on every other pixel in the display in a checkerboard pattern This type of stereoscopic display mode is compatible with a range of DLP projectors and TV s in combination with shutter glasses The only special requirements for the graphics accelerator are that it provide a stencil buffer which is used to generate the alternating columns in the final image This mode is generally supported by low cost gaming GPUs 7 3 5 Column Interleaved Stereo Column interleaved stereo works by interleaving the left and right eye views on every other vertical column in the display The stereo hardware either separates them into two separate displays or blanks the even or odd columns in sync with shutter glasses or otherwise makes them visible only to one or the other eye in the case of autostereoscopic displays The only special requirements for the graphics accelerator are that it provide a stencil buffer which is used to generate the altern
244. re all relative to the top molecule 5 4 2 Looping Styles When the animation is playing forward and reaches the end of the data available for the top molecule one of three possible actions takes place as specified in the style chooser The default is Loop which will reset the active molecules to the first frame and continue playing forward Once will stop the animation when it reaches the last frame and Rock reverses the direction of animation The actions are symmetrical when the animation is playing in reverse 5 4 4 Molecule File Browser Window lt Molecule File Browser BE Load files for New Molecule y Filename 1e7za Browse Determine file type Web PDB Download v Load Frames Volumetric Datasets First Last Stride jo F 1 Load in background Load all at once Figure 5 3 The Molecule File Browser window The Files window is used to load a file from disk into a new or existing VMD molecule It can be brought up by choosing New Molecule from the File menu or by hilighting a molecule in the Main window5 4 1 and choosing the Load Data Into Molecule menu item Once the window appears select the file you want by using the file browser or by typing the filename into the text entry area By default VMD will try to guess the type of file you are loading by matching the filename extension with one of the file reader plugins in the file type list the available file types are
245. re name is the name that VMD will use to refer to the device and USL is the device s USL e Options tell VMD how to use the most recently listed device Currently there are four supported options scale x scales the position of a tracker by a factor x offset x y z adds a constant vector to the position of a tracker rot right left Ago 401 433 multiplies the orientation matrix returned by a tracker on either the right or the left by the matrix A forcescale x multiplies the force applied to a force feedback device by the amount zx Here is a simple example showing some of the things you can do with a sensor configuration file for a more complete example please refer to the vmdsensors file that came with your VMD distribution Sensable PHANTOM via VRPN http www sensable com The Phantom haptic device connected to the computer odessa device phantomtracker vrpntracker odessa Phantom0 scale 10 rot left 00 1010100 device phantombuttons vrpnbuttons odessa Phantom0 device phantomfeedback vrpnfeedback odessa Phantom0 Using Tools There are several different tools each of which can be used with any of the input devices e The Grab Tool mimics a pair of tweezers and can be used to move molecules around on the screen without any keyboard or mouse commands Pressing a button connects the 3d cursor to the nearest molecule Then moving or rotating the tracker
246. recall is that sel1 is the selection for the backbone atoms You really want to move the whole fragment to which it is attached or even the whole molecule This is where the discussion earlier comes into play So you need to make a third selection containing all the atoms which are to be moved and apply the transformation to those atoms molecule O is the same molecule used for sel1 set move_sel atomselect 0 al1 move_sel move transformation_matrix As a more complicated example say you want to align all of molecule 1 with molecule 9 using only the backbone atoms of residues 4 to 10 in both systems Here s how compute the transformation matrix set reference_sel atomselect 9 backbone and resid 4 to 10 set comparison_sel atomselect 1 backbone and resid 4 to 10 set transformation_mat measure fit comparison_sel reference_sel apply it to all of the molecule 1 set move_sel atomselect 1 al1 move_sel move transformation_mat A simulation example script Here s a longer script which you might find useful The problem is to compute the RMSD between each frame of the simulation and the first frame Usually in a simulation there is no initial global velocity so the center of mass doesn t move but because of angular rotations and because of numerical imprecisions that slowly build up the script aligns the molecule before computing its RMSD Prints the RMSD of the protein atoms between each timestep and
247. returns the distance Similar things are true for measure angle dihed and imprp The following options can be specified molid lt default molid gt The default molecule to which an atom belongs unless a molecule number was explicitely specified for this atom in the atom list Further all frame specifications refer to this molecule Default is the current top molecule frame lt frame gt By default the value for the current frame will be returned but a specific frame can be chosen through this option One can also specify all or last instead of a frame number in order to get a list of values for all frames or just the last frame respectively first lt frame gt Use this option to specify the first frame of a frame range Default is the current frame last lt frame gt Use this option to specify the last frame of a frame range Default is the last frame of the molecule In case you specified the molecule IDs in the atom list then all frames specifications will refer to the current top molecule unless a default molecule was set using the molid option Since the top molecule can be different from the molecules involved in the selected atoms it is generally a good idea to specify a default molecule Here are a few examples of usage measure bond 3 5 Returns the bond energy between atoms 3 and 5 of the current frame of the top molecule measure bond 3 5 molid 1 frame all Returns the bond energy
248. ribose atoms can be given names like C5 or C5 depending on the age of the PDB record The lexer in VMD has been modified so that C5 0 and N can be used without quotes but it cannot handle an unquoted asterisk conflicts with multiplication and the parser is not able to resolve the difference Some examples are name 05 segname A name 05 Quotes may also be used to get around a reserved selection word like x The selection command segname x will give an error because x is another keyword Instead use segname x There is an escape mechanism for including single quotes inside a single quoted string which uses a backslash NV before the single quote This allows unusual names like C to be quoted as C segname x lt error conflicts with the x keyword segname x name 05 Also double quotes discussed in the next section can be used as in C gt or C Xx 6 3 5 Double Quotes and Regular Expressions Double quotes around a string are used to specify a regular expression search compatible with Perl 5 005 using the Perl compatible regular expressions library written by Philip Hazel If you don t know how to use them try consulting the man pages for ed egrep vi or regex If not read the Perl docs or get any one of a number of books including the O Reilly and Associates Sed and Awk book The following examples show just a few ways that regular expressions can be used wi
249. ric maps 3D grids containing a value at each grid point based on the molecular data which can then be visualized in VMD using the Isosurface and VolumeSlice representations or using the Volume coloring mode Also note that the VolMap plugin accessible from the VMD Extension menu provides a graphical front end to many of the volmap command s capabilities To create a volumetric map the volmap command is run in the following way where the atom selection specifies the atoms and molecule to include in the calculation and where the maptype specifies the type of volumetric data to create volmap lt maptype gt lt atom selection gt optional arguments For example to create a mass density map with a cell side of 0 5 A averaged over all frames of the top molecule and add the volumetric data to the top molecule on would use volmap density atomselect top all res 0 5 weight mass allframes combine avg mol top The various volumetric data map types currently supported by volmap are listed as follows Please note that when a map type description refers to an atoms radius or beta field etc that these values will be read directly from VMD s associated fields for that atom In certain cases you may want to adjust the atom selections fields such as radius beta etc before performing the volmap analysis 129 e density creates a map of the weighted atomic density at each gridpoint This is done by replacing each atom in the
250. ript Rendering in stereo is accomplished by setting the display mode to left then rendering an image followed by right and rendering again This will yield a stereo pair to the best of VMD s ability with the external rendering program e The near and far clipping planes are ignored by all external renderers e Text is generally not available as a graphics primitive in the renderer scene languages so label text will not appear although the lines of bond angle etc labels will be drawn The only exception is in Postscript output which supports text output e Dotted spheres are not drawn with dots e The background color may be black as not all output formats support a background color other than black 8 4 One Step Printing A frequently asked question is How can I quickly get a printout of the VMD Display There are several one step solutions to this problem a few are listed below e Choose the snapshot option and type convert s eps 4s ps lpr s ps in the render command box This assumes that you have the ImageMagick tools available in your PATH setting e Asan example of how to directly print a Raster3D file choose the Raster3D option in the Ren der 5 4 11 window and type render lt s sgi s rgb convert s rgb eps s ps lpr s ps in the render command box e Choose the PostScript output option in the Render window and type lpr s in the render command box 8 5 Making Stereo Images Stereoscopi
251. rmally come with a Python distribution you must tell Python where to find the libraries There are two primary means of doing this The PYTHONHOME environment variable points to 138 the location where Python is installed the version installed at this point must match VMD s version 2 5 Thus if you have Python libraries in usr local lib python2 5 adding the line set env PYTHONHOME usr local to your startup script or vmdrc file will do the trick If you have additional modules that you want to use within VMD use the PYTHONPATH environ ment variable to tell Python where to find them Please note that any of these modules have to be compiled against matching versions of the Python package and its subpackages that are distributed with the pre compiled VMD binaries If you want to use the native Python and its packages you will have to compile VMD from source code or install a user contributed package that matches your OS See any Python book and the instructions for compiling VMD from source code for more information if the Tkinter module is found in the Python installation VMD will load it at Python startup in order to make Tkinter windows work in harmony with windows created from within Tk In addition if you have Numeric Python installed in your system a submodule called vmdnumpy will become available within the VMD module see below for details 10 3 Atom selections in Python 10 3 1 The built in atomsel type NEW IN VMD 1 8 6 The
252. rning The waitfor parameter nw can be any integer or all choosing nw less than zero is the same as choosing all Pass the name of an atom selection as selection to write only the selected atoms to the file delete beg nb end ne skip ns molecule_number Delete data for molecule number beginning with frame nb ending with frame ne and keep frames with a stride of ns a stride of 1 implies to keep all frames atomselect Atom selection is the primary method to access information about the atoms in a molecule It works in two steps The first step is to create a selection given the selection text molecule id and optional frame number This is done by a function called atomselect which returns the name of the new atom selection the second step is to use the created selection to access the information about the atoms in the selections list Return a list of all undeleted atom selections 98 e keywords Return a list of all recognized keywords in an atom selection text e macro name selection Create a new singleword atom selection out of existing atom selections name must be a single word starting with a non numeric character and contain no spaces or special characters selection can be any valid atom selection and can even contain other macros You should ensure that your macros do not contain themselves either directly or through a chain of other macros If VMD detects this situation it will abort the evaluation of the atom
253. rted to C 0 and matches anything starting with a C or ending with an O A regular expression is similar to wildcard matching in X PLOR Table 6 10 is a list of conver sions from X PLOR style wildcards to the matching regular expression 6 3 6 Comparison selections Comparisons can be used in VMD to do atom selections like mass lt 5 which selects atoms with mass less than 5 amu and name eq CA which is another way of choosing the CA atoms The underlying idea for the comparison selection is also based on the concept that every atom has a property as specified by a keyword When the keyword is given in the expression the array or vector of the corresponding values is constructed and the size of the array is the same as the number of atoms in the molecule If a single number or string is given instead of a keyword the array consists of copies of that given value The operations like addition multiplication string matching and comparison are then applied element wise along the array This type of selection is similar to the vector statement in X PLOR Take the example mass lt 5 when applied on water which has an oxygen of mass 15 9994 and two hydrogens of mass 1 008 VMD sees the keyword mass and constructs the array 15 9994 1 008 1 008 then sees the 5 and makes the array 5 5 5 It then compares each term of the array and returns with the boolean array False True True since 15 9994 is not less than 5 but 1 008 i
254. s e update_off Tell VMD not to regularly update the display The display will be updated only when display update is called e stereomodes Returns a list of the available stereo modes e PROJ_PERSP PROJ_ORTHO String constants defined in the display module for setting the projection keyword in the set method e set keywordlist e get key set and get control various display properties The following keywords ac cept return floating point values eyesep focallength height distance nearclip farclip The following keywords accept boolean values for on or off respectively antialias depthcue culling stereo should be one of the values returned by stereomodes projection should be one of the PROJ constants defined in this module size should be a list of two integers corresponding to the width and height of the display in pixels 10 5 5 evaltcl The evaltel method provides access to the main VMD Tcl interpreter from Python It takes a string with Tcl commands as an argument and evaluates it Its main purpose is to provide the Python interpreter with access to functionality that is only available from Tcl and for which no equivalent implementation yet exists in Python for example the Tcl based plugins Usage Examples from VMD import evaltcl versionid evaltcl vmdinfo version evaltcl play somescript tcl 10 5 6 graphics Python operations available from the graphics module used to create custom 3 D o
255. s This final boolean array is then used to determine which atoms are selected in this case the hydrogens More complicated comparison selections can be constructed either from arithmetic operations or by using some of the standard math functions the functions are listed in Table 6 7 Probably the most often used function will be sqr which squares each element of the array Thus the command to select all atoms within 5 A of a point x y z 3 4 5 in space is sqr x 3 sqr y 4 sqr z 5 lt sqr 5 6 3 7 Comparison Operators There are two types of comparison operators numeric and string which allow the user to specify the appropriate comparison function Suppose the segment name which takes on a string value contains the names 11 and 8 VMD cannot figure out if 8 should be less than 11 in 79 the numeric sense or greater than 11 in the lexographical sense Instead of trying to resolve this problem through some sort of internal heuristics VMD leaves it up to the user so that 8 lt 11 but 11 1t 8 Perl users should recognize this solution The numeric comparisons are the standard ones lt lt or gt gt and The corresponding string comparisons are 1t le eq ge gt and ne As in perl there is a match operator so that ICA Cle segname VP 1 4 matches VP1 VP2 VP3 and VP4 present in some virus structures are valid No distinction i
256. s to find a normal for drawing an oriented ribbon There may be some problems with the ribbon definition for nucleic acids as it is possible for the nucleic acid detection routine to label a residue as a nucleic acid even though it does not have phosphate oxygens The NewRibbons representation uses the alpha Carbons as control points for a spline which defines the ribbon backbone The ribbon is drawn by extruding a two dimensional cross section along the length of the spline orienting it by referencing the positions of the Oxygens on the protein backbone As with the Tube representation the six ribbon segments nearest the given atom are drawn with the color assigned to that atom and the atom can be selected by clicking near the center of those six elements The Aspect Ratio parameter controls the width of the ribbon relative to the thickness value as a multiplicative factor An aspect ratio of 1 0 yields a Tube like representation The Resolution parameter controls the degree to which the ribbon surface is tesselated with triangles Higher settings yield nicer looking images at the expense of interactive rendering performance Points can be interpolated with either a Catmull Rom or B Spline by changing the value of Spline Style Note that the B Spline does not always pass through the Ca positions as it is a smoother spline 6 1 14 Cartoon The Cartoon option produces a simplified representation of a protein based on its secondary struc
257. s your two eyes see slightly different images because they are located at different viewpoints Your brain puts the images together to generate a stereoscopic viewpoint When generating a single image for the computer display the default calculations mode Stereo Off assume there is one eye centered between where two eyes would be For stereo the left and right eye views need to be generated independently Choosing mode Left produces the left eye viewpoint while Right produces the right eye viewpoint The left and right monoscopic modes are most useful when exporting scenes to external ray tracers 7 3 Stereoscopic Modes Molecules may be rendered in stereo which can greatly enhance the appearance and visual content of the displayed systems There are several stereo formats available 1 Quad buffered stereo aka CrystalEyes in older versions which requires a stereo capable monitor quad buffered stereo video board or GPU stereo emitters and stereo glasses equipped with liquid crystal or polarized lenses 2 Above Below stereo 86 3 Side by side stereo 4 DTI Side by side stereo for DTI stereo flat panel displays 5 Anaglyph stereo requires stereo capable monitor quad buffered stereo video board and red blue horror movie style stereo glasses 6 Checkerboard also known as line blanking stereo works with compatible shutter glasses and DLP projectors 7 Column interleaved works with compatible shutter glasses and LCD
258. s made between single and double quotes 6 3 8 Other selections sequence VMD supports selection based on the one letter amino acid sequence with the sequence selection keyword This allows selections of the form sequence APD sequence C C might be used to pick out zinc fingers sequence AATCGGAT Unlike the other string selection commands which take one of three types of strings all the strings for sequence are taken as regular expressions though strings with non alphanumerics must still be quoted to get past the input parser The method works by taking each of the protein and nucleic acid fragments pfrag and nfrag in turn and constructing the one letter amino acid sequence If a regular expression matches any of the sequence the atoms in the matching residues are selected Multiple matches are allowed though they cannot overlap As is usual with regular expressions the largest possible match is made so take care with expressions like C C within and same Two useful types of selection mechanisms available in VMDare within lt number gt of lt selection gt and same lt keyword gt as lt selection gt The first selects all atoms within the specified distance in A from a selection including the selection itself Therefore the command within 5 of name FE selects all atoms within 5 A of atoms named FE One common use for this command is to limit the region of atoms shown on the screen Another is to find atoms that may be
259. s not exist e hide type label Turn the given label off label must be a dictionary containing molid and atomid keys whose values are tuples If the tuples match the molecule ids and atom ids 151 of the atoms in an existing label the label will be turned off Raises ValueError if the label does not exist e delete type label Delete the given label label must be a dictionary containing molid and atomid keys whose values are tuples If the tuples match the molecule ids and atom ids of the atoms in an existing label the label will be deleted Raises ValueError if the label does not exist e getvalues type label Returns a list of values of the given label for each coordinate frame in the label If the atoms in the label belong to different molecules only the coordinates of the first molecule will be cycled If the labels don t have values like atom labels None is returned 10 5 9 material Python operations available from the material module used to create and modify material prop erties of molecular representations e listall Returns a Python list of the names of all available materials e settings name Returns a Python dictionary of the material settings for material with the given name e add name None copy None Create a new material with the given name Optionally copy the properties from material copy into the new material If no name is given a new one will be provided e delete name Delete the materi
260. s often more convenient then selecting them and deleting them all one by one Alternatively you could highlight each molecule in the molecule browser and use the Delete Molecule item in the Molecule menu to remove them one by one Begin by loading the mbco pdb structure with the Files window Turn on just the heme CO and histidines by using the selection commands resname HEM CO or resid 64 93 The dot probably green in the middle is the iron and you can verify that by picking it with the mouse Do this by changing the Object Mode pull down to Pick and selecting Atoms for the pick mode in the Mouse menu The label HEM154 FE should appear both on the display and in the text console Change the pick mode in the Mouse menu to Bonds To get the distance between the iron and the oxygen of the CO click with the left mouse button first on the iron and then on the oxygen The first click turned the FE label on and the second turned the O label on and drew 20 a line between the two atoms with the distance drawn in the middle and a bit to the right The distance between the two atoms is 2 94 as compared to 2 93 in the paper not bad However picking the distance between the FE and the C of the CO reveals a distance of 1 91 as compared to 1 85 in the paper The difference is that the structures in the VMD distribution are actually preliminary structures obtained before the final coordinates were determined In order
261. s the shear matrix stereo formulation rather than eye rotation 189 e VMDSIMPLEGRAPHICS Forces VMD to use absolutely minimalistic graphics features with no use of OpenGL extensions Essentially nothing but bread and butter vertex arrays and immediate mode rendering will be used This mode is intended to be used only when one encounters severe stability problems caused by buggy display drivers e VMDWIREGL This environment variable disables several graphics features which are unsup ported or poorly supported by WireGL and Chromium This variable will be superceded with a more general implementation in a future release 13 3 Startup Files 13 3 1 Core Script Files In the following the value of VMDDIR is the vmd installation directory During the original in stallation this is the value of INSTALLLIBDIR It can also be found by looking at the first few lines of the vmd startup script head which vmd or by starting VMD and using the command set env VMDDIR As mentioned elsewhere VMD uses the Tcl interpreter VMD read Tcl scripts at initializa tion which are contained in VMD distribution The locations of the scripts is determined by the TCL_LIBRARY environment variable which is set in the vmd startup script to VMDDIR scripts tcl In addition VMD has its own directory of core Tcl routines The most important of these is VMDDIR scripts vmd vmdinit tcl This file sets up the basic Tcl initialization commands defines some e
262. s varname restrict restrictedsel samples numsamples Re turns the solvent accessible surface area of atoms in the selection using the assigned radius for each atom extending each radius by srad to find the points on a sphere that are exposed to solvent If the restrictedsel selection is used only solvent accessible points near that selec tion will be considered The restrict option can be used to prevent internal protein voids or pockets from affecting the surface area results The points option can be used to see where the area contributions are coming from and then the restrict flag can be used to eliminate any unwanted contributions after visualizing them The varname parameter can be used to collect the points which are determined to be solvent accessible e sumweights selection weight weights Returns the sum of the list of weights or data field to use for the weights for all of the atoms in the selection e bond atom_list options Returns the distance of the two specified atoms The atoms are specified in form of a list of atom indexes Unless you specify a certain molecule through molid molecule number these indices refer to the current top molecule If the atoms are in different molecules you can use the form atomid1 molid1 atomid2 molid2 where you can set the molecule ID for the individual atoms Note that measure bond does not care about the bond that are specified in a psf file or that are drawn in VMD it just
263. scussed in detail in chapter 9 but to give you a flavor for their use here are a couple of examples that you may find useful right away Most things can be done with color 89 3 4 and colorinfo 9 3 5 commands 12 5 1 Changing the color scale definitions Suppose that of the 1024 colors the first 511 should be red then 2 whites and finally 511 blues You can use the color command to modify the color scale values accordingly proc tricolor_scale 4 set color_start colorinfo num 182 display update off for set i 0 i lt 1024 incr i if i 0 1 set r 1 set g 0 set bo if i 511 set r 1 set g 1 set b1 if i 513 set r 0 set g 0 set bl color change rgb expr i color_start r g b display update on tricolor_scale 12 5 2 Creating a set of black and white color definitions To map grayscale on the color ids 0 16 0 black 16 white proc make_grayscale display update off set coloridcount colorinfo num set colordiv expr coloridcount 1 0 for set i 0 i lt coloridcount incr i 4 set val expr i colordiv color change rgb i val val val display update on Note that the display updates are switched off for the time of redefinition so that the screen would not be redrawn every time one color is changed This way the procedure works faster The only bad thing about this idea is that black becomes white and white changes too so the names
264. selection with a normalized gaussian distribution of width standard deviation equal to its atomic radius The gaussian distribution for each atom is then weighted using an optional weight see the weight argument and defaults to a weight of one i e the number density The various gaussians are then additively distributed on a grid e interp creates a map with the atomic weights interpolated onto a grid For each atom its weight is distributed to the 8 nearest voxels via a trilinear interpolation The optional weight see the weight argument defaults to a weight of one e distance creates a map for which each gridpoint contains the distance between that point and the edge of the nearest atom In other words each gridpoint specifies the maximum radius of a sphere cnetered at that point which does not intersect with the spheres of any other atoms All atoms are treated as spheres using the atoms VMD radii e coulomb Creates a map of the electrostatic field of the atom selection made by comput ing the non bonded Coulomb potential from each atom in the selection in units of kgT e The coulomb map generation is optimized to take advantage of multiple processors and pro grammable graphics board if they are available e ils Creates a free energy map of the distribution of a weakly interacting monoatomic or di atomic gas ligand throughout the system using the Implicit Ligand Sampling ILS technique See additional information about I
265. set View This menu item can be used to force VMD to reset the scene back to the default viewing orientation and scale as is done when a molecule is first loaded e Stop Rotation This menu item stops autorotation of the scene The scene can be au torotated by quickly dragging the mouse while briefly depressing and releaseing the mouse button leaving the scene spinning until it is stopped either by this menu item or by further mouse interactions e Perspective The view of the scene can be Perspective or Orthographic In the perspec tive view the default objects which are far away are smaller than those near by In the orthographic view both objects appear at the same scale Note that several of the sup ported external rendering programs do not support orthographic rendering As such it may be necessary to fake it by translating the scene far away from the camera and apply a zoom factor This has the effect of significantly reducing the perspective while not truly an orthographic view 40 Antialiasing Turns antialiasing on or off Antialiasing helps smooth out the jagged ap pearance of displayed geometry resulting from the inherently discrete pixels on the display device The antialiasing feature is only available on platforms which support full screen an tialiasing sometimes known as multisample antialiasing Several SGI and Sun graphics systems fully support this feature On platforms lacking the multisample c
266. set gc veczero selection get x y z returns a list of x y z values one per atoms so get each term one by one foreach coord selection get x y z sum up the coordinates set gc vecadd gc coord and scale by the inverse of the number of atoms return vecscale expr 1 0 selection num gc With that defined you can say assuming sel was created with the previous atomselection example vmd gt geom_center sel 0 703168 4 45868 2 43667 Pll go through the example line by line The function is named geom_center and takes one param eter the name of the selection The first line sets the variable gc to the zero vector which is 0 0 0 On the second line of code two things occur First the command selection get x y z is executed and the string is replaced with the result which is 0 710000 4 211000 1 093000 0 026000 3 700000 0 697000 0 541000 4 841000 2 388000 0 809000 4 462000 2 976000 1 591000 4 371000 3 381000 2 212000 5 167000 4 085000 This is a list of 6 terms one for each atom in the selection and each term is a list of three elements the x y and z coordinate in that order The foreach command splits the list into its six terms and goes down the list term by term setting the variable coord to each successive term Inside the loop the value of coord is added to total sum The last line returns the geometrical center of the atoms in the selection Since the geom
267. settings list List the available rendering methods hasaa method Query whether or not a renderer has controllable antialiasing feature aasamples method samples Query or set the number of antialiasing samples to be used by this renderer if supported aosamples method samples Query or set the number of ambient occlusion lighting samples to be used by this renderer if supported formats method List a renderer s available image output formats modes format method format Set a renderer s active image output format mode method filename Render the global scene to filename using method and execute the default command where method can be one of the following ART Gelato POV3 PostScript Radiance Raster3D Rayshade Renderman snapshot STL Tachyon TachyonInternal VRML 1 126 VRML 2 Wavefront e method filename command Render the global scene to filename then execute command Any s in command are replaced by the filename up to 5 e options method Get the default command string e options method command Set new default command e default method Get the original default command 9 3 26 rock Rotate the current scene continually at a specified rate e off Stops rocking e lt xlylz gt by step Rock around the given axis at a rate of step degrees per redraw e lt xlylz gt by step n Rock around the given axis at a rate of step degrees
268. shift key and the left mouse button while moving the mouse will rotate the atoms in the rep about the selected atom If the middle mouse button is held down instead the atoms in the rep will rotate about a line drawn through the picked atom and parallel to a line coming directly out of the screen This behavior is similar to the usual Rotate mode except that coordinates of atoms are changed 5 1 3 Hot Keys When the mouse is in the graphics window many commands are accessible via programmable hot keys Hot keys allow you to do things like change mouse modes or advance the animation by a frame by simply pressing a key There are a number of predefined hot keys as listed in tables 5 1 5 2 5 3 and 5 4 They can be printed out with the command user print keys The commands listed are the text commands which are executed when the hot key is pressed these text commands are explained in section 9 3 To add or modify a hot key use the command user add key key command The key parameter must be a single character If command contains more than one word it must be enclosed in braces so that the subsequent command words are not ignored When that key is pressed while the mouse cursor is in the graphics display window the associated command will be executed Once you have a set of commands which are particularly useful and familiar for you you will want these hot key commands automatically available every time you run VMD This can be done by placing the
269. sions of VMD will greatly enhance the user interfaces and capabilities of this feature The following selectors control the VolumeSlice representation e Data Set This controls which volume data set is referenced in the representation since multiple volumetric data sets can be loaded for a single molecule e Slice Offset The slice setting indicates the position of the volume slice along the chosen axis in the coordinate system of the volumetric data range 0 to 1 68 e Slice Axis The orthogonal axis along which the slice plane moves can be X Y or Z e Render Quality The quality can be set to either Low or Medium The Low setting causes the slice texture map to be rendered using the color nearest the sample point A quality level of Medium indicates that the slice texture map will be rendered using bilinear interpolation 6 1 22 Isosurface The Isosurface representation computes and draws a surface within a volumetric data field on a 3 D surface corresponding to points with a single scalar value There are several settings which control how the isosurface is displayed e Data Set This control selects which volume dataset is used for the isosurface calculation since a given molecule can contain multiple volumetric data sets e Isovalue The Isovalue control selects the value for which the isosurface will be computed In the GUI when dragging the isovalue slider the drawn isosurfaces are temporarily calcu
270. ss is fairly robust and can handle molecules whose coordinates deviate to a certain extent from the ideal symmetry The closest match with the highest symmetry will be returned Options tol lt value gt Allows one to control tolerance of the algorithm when considering wether something is symmetric or not A smaller value signifies a lower tolerance the default is 0 1 nobonds If this flag is set then the bond order and orientation are not considered when comparing structures verbose lt level gt Controls the amount of console output A level of 0 means no output 1 gives some statistics at the end of the search default Level 2 gives additional info about each stage and 2 3 4 yield even more info for each iteration idealsel lt selection gt The symmetry search will be performed on the regular selection but then the found symmetry elements will be imposed on the selection given with this option an the search is repeated with this second selection This method allows for example to perform the symmetry guess on a selection without hydrogens which might point in random directions for rotable groups but still get the ideal coordinates and unique atoms for the entire structure The selection specified here must be a superset of the selection used for the symmetry search I Instead of guessing the symmetry pointgroup of the selection determine if the se lection s center off mass represents an inversion center
271. ss is zero The 1 0 can t be 1 since otherwise integer division is done return vecscale expr 1 0 mass com vmd gt center_of_mass sel Info 0 912778 4 61792 2 78021 Y ie ae E The opposite of get is set Many keywords most notably x y and z can be set to new values This allows for instance atom coordinates to be changed the occupancy values to be updated or user forces to be added You can also change the resname segid and so forth which may be easier to do within VMD than for example editing a PDB file by hand set sel atomselect top index 5 sel get x y z 1 450000 0 000000 0 000000 set set x y z 111 6 0 O 173 Note that just as the get option returned a list of lists the set option needs a list of lists which is why the extra set of curly braces were need Again this must be a list of size n containing elements which are a list of size i The exeception is if n is 1 the list is duplicated enough times so there is one element for each atom get two atoms and set their coordinates set sel atomselect top index 6 7 sel set x y z 5 0 0 7 6 5 4 3 2 In this case the atom with index 6 gets its x y z values set to 5 0 0 and the atom with index 7 has its coordinates changed to 7 6 5 4 3 2 It is possible to move atoms this way by getting the coordinates changing them say by adding some offset and replacing it Following is a function which w
272. ss the Create Rep button and enter resid 93 64 to select the two histidines and render them as CPK If you followed all that then congratulations you have made a nice image of myoglobin With further experimentation you should be well on your way to learning how to use VMD 3 3 Rendering an Image Find an interesting view of the molecule from the previous tutorial Suppose you want to publish this view in a journal and want a high quality image or you want to make a large poster Taking the image from a screen capture often results in a rather grainy image as the size of the pixels becomes apparent so you want something with more resolution There are several programs available which can render a high quality raster image based on an input script VMD has the option to create input scripts for many of these image processing programs which may then be processed to create a higher quality image of the scene displayed by VMD at the time the script was created See Chapter 8 on rendering for a further description of how this works Open the Render window 5 4 11 and select Tachyon from the Render Using menu Both of the text boxes will be filled with default values which should not need to be changed for the purposes of this tutorial Press the Start Rendering button After a few moments of processing you sould see the message Info Rendering complete in the VMD text console If everything worked correctly you will end up with an
273. ssary to have a molecular dynam ics program that supports the IMD communication protocol To date two such programs exist NAMD developed at University of Illinois and Protomol developed at Notre Dame The rest of the discussion in this chapter assumes you are using NAMD See the NAMD home page for information on obtaining NAMD Interactive Molecular Dynamics IMD works by establishing a TCP connection between VMD and the molecular dynamics simu lation program NAMD or whichever MD program is being used acts as the server In order to prepare NAMDto accept VMD s IMD connection request NAMDmust be configured to listen for incoming connections on a network port Once NAMD has started up may wait for the user to connect through that port When VMDconnects to NAMDsuccesfully the simulation commences Before connecting to the remote simulation the VMDuser must first load a molecule corresponding to the system being simulated The structure file should correspond to the same structure file used by NAMD Once the molecule is loaded and NAMD has been started and is listening for a connection you are ready to connect to the simulation and start receiving coordinates To establish a connection open the Simulation window enter the hostname on which NAMD is running and the port on which NAMD is listening for incoming connections then press the Connect button to establish the connection If NAMD is running on several distributed nodes VMD must conne
274. st match all except the chars in the list next token must be the first part of string prev token must be the last part of string match 0 or more copies of prev char or regular expression token match 1 or more copies of the prev token match either the Ist token or the 2nd combines multiple tokens into one Table 6 9 Regular expression methods 84 X PLOR Wildcard Regular Expression matches any string matches a single character matches any digit matches any number Table 6 10 Regular expression conversions 85 Chapter 7 Viewing Modes There are many different viewing modes available These show the scene in orthographic or per spective views and in several mono and stereo graphic displays The stereo mode can be changed using the stereo entry in the Display menu or the text command display stereo mode 7 1 Perspective Orthographic views In the perspective view the default objects which are far away are smaller than those nearby In the orthographic view all objects appear at the same scale Since some prefer one over the other both options are available Perspective viewpoints give more information about depth and are often easier to view because you use perspective views in real life Orthographic viewpoints make it much easier to compare two parts of the molecule as there is no question about how the viewpoint may affect the perception of distance 7 2 Monoscopic Modes When you normally look at object
275. such as PDB CRD DCD or Gromacs files The new coordinate sets are appended to the end of the stored frames for the selected molecule Loading coordinate data is like loading any other file select it with the file browser make sure the file type is set correctly for the file being loaded and then press the Load button By default VMD will load all of the frames contained in a coordinate or trajectory file Sometimes you may not want to read in a whole coordinate or trajectory file For example you may only want the last frame or every tenth frame You can do this by changing the options in the Frames control of Files window The Frames controls consist of three numeric input fields labeled First Last and Stride These make it possible to use a subset of the frames starting at frame First and selecting every Stride frames until the Last is reached For instance to select every fifth frame between frames 14 and 98 set e First to 14 e Last to 98 e Stride to 5 Remember that frame numbers in VMD start at 0 so frame 0 is the first frame The value 1 is a special number setting First to 1 is the same as starting at the first frame Last 1 is the same as ending at the last frame and Stride 1 is the same as taking one step 5 4 5 Mouse Menu The Mouse menu indicates and controls the behavior of the mouse when the mouse moves and clicks within the graphics window Mouse clicks and drags can affect VMD in one of two ways It
276. t be set to send button events as Function 1 and Function 2 at a minimum Once set it should be possible to cycle through the various VMD Spaceball operational modes as described below 32 Hot Key animate next move to next frame animate prev move to previous frame animate forward play animation forward animate reverse play animation reverse animate reverse play animation reverse animate pause stop animation Table 5 4 Animation hot keys 5 3 Using the Joystick in the Graphics Window The Windows version of VMD provides support for the Windows joystick driver and will enumerate all available joystick devices at startup time The joystick interface employed in VMD is quite simple allowing the use of three control axes to translate rotate and scale the molecule The joystick interface assumes a device with at least two buttons The first joystick button resets the view in the display window and the second button cycles through each of the available joystick modes When VMD first attaches to each of the joysticks they are initially disabled so that miscalibrated joysticks do not adversely affect the VMD session Each joystick is initially enabled by pressing its second button to switch modes All joysticks are independently controlled such that multiple joysticks can control different control axes and multiple users could interact with the program with separate controls 33 5 4 Description of each VMD window VMD uses se
277. t value change rgb color r g b Set the RGB of color to r g b restype resname restype Set the residue type for resname to restype If the restype parameter is omitted the current residue type is returned add item category name colorname Adds colors for the named color category item name using the colorname color See the colorinfo 9 3 5 command for additional ways to query VMD s color settings See the graphics 9 3 9 command for how to change color of a user defined graphics object 9 3 5 colorinfo Tcl This command provides access to the color definitions For information on the color properties see the chapter on Coloring 6 2 colorinfo categories returns a list of available categories colorinfo category category returns a list of names for the given category colorinfo num returns the number of base solid colors 33 colorinfo max returns the total number of colors available 1057 colorinfo colors returns a list of the named solid colors colorinfo index rgb lt name value gt returns the index or rgb of the given name or color id colorinfo scale lt method methods midpoint min max gt returns the information about the color scales Examples find out what color corresponds to which id set i 0 foreach color colorinfo colors puts i color 102 incr i also get a list of RGB values set i 0 foreach color colorinfo colors lassign colorinfo rgb
278. t values Use reset_scaleminax to rescale the color scale to the maximum range again e get_visible molid rep e set_visible molid rep onoff These two commands let you show or hide a selected molecular representation and retrieve the visibility status of a given rep 10 5 12 render Python operations available from the render module used to export the scene to a file that can be read by external rendering programs e listall Return a Python list of the names of all supported rendering methods One of these should be the first argument to the render operation below 155 render method filename Using the the given rendering method export the current scene to the file filename method should be one of the values returned by listall O 10 5 13 trans Python operations available from the trans module used to change the view of the rendered scene rotate axis angle Rotate the scene about the specified axis by the given angle axis gt E should be x y or z angle is measured in degrees translate x y z Translate the scene by the given x y and z values scale factor Scale zoom the scene by the given factor resetview molid Sets the center scale rotation for all molecules so that the viewpoint is centered on the molecule with the given id get_center molid set_center molid vector Get set the coordinates of the center of the given molecule as a Python list get_scale
279. terial E GR A A AB ek Te OR oe ek 152 LO 5 LO molecular be alk A eee ba ee es Bed is Sk ne ee a 152 E Ne See 154 TOS AD Trender hor Glass ce maty in Ayah oe hes We oe Sat uae A ee Be ee 155 TOSS TRANS 453 oe nad Ly te ein de BE eS Raed Ge as ean ER A pay chee assed Bes 156 10 514 vimdnumipy ara et Re AAA A Pea te a 156 10 6 High level Python Interface 2 20 20 2000 e 157 10 61 Molecules it Aid ea AN hh a es A oP ON eee Bh 157 10 6 2 MoleculeRep a i022 i marani eri a Ve eee A ee A 159 10 6 3 Draw Style Methods aa a 160 10 6 4 Saving and Restoring Molecule State 0048 160 11 Vectors and Matrices 161 TLELDOEVECOLS LR A A E as A EA AA E ee dS Beis 161 112 Matrix TORMES Li eda cas BY hes eee ath Aad ses aoa ed 164 11 3 Multiplying vectors and matrices 2 2 e 167 11 4 Misc functions and values 2 167 12 Molecular Analysis 169 12 1 Using the molint o comimiarid ti A es a A A 169 12 2 Using the atomselect command 170 12 3 Adal YSIS SCLID S A A A o A a 175 12 4 RMS Fit and Alignment 2 a a 178 12 4 1 RMS Fit and Alignment Extension 179 12 42 RMS and Scripting 20 ac Aw eal AB Sn OO le le bee ral he PG 180 12 5 VMD Script Commands for Colors ooa a 182 12 5 1 Changing the color scale definitions 00 000 000 182 12 5 2 Creating a set of black and white color definitions 183 12 5 3 Revert all RGB values to defaults 0 0 0 0 a a 0 00
280. tes a new atom selection object gt gt gt sel AtomSel name CA 1 Selects the alpha carbons of molecule 1 e select selection Change the selected atoms gt gt gt sel select resid 5 e list Return a copy of the selected atom indices 139 frame value 1 Set get the coordinate frame for the selection Nonpositive values will return the current value of the frame without changing it gt gt gt sel frame 5 gt gt gt sel frame 5 get attri attr2 Takes any number of string arguments which should correspond to a valid atom property such as name x or water Returns a list of the value of the property for each atom in the selection For boolean properties such as water the returned value will be 1 if true and 0 if false gt gt gt x y z sel get x y z set attr val Set the atom property corresponding to attr using the values in val The number of elements in val should be either 1 or the number in the atom selection gt gt gt len sel 12 gt gt gt sel set beta 3 gt gt gt sel set beta 1 2 3 4 5 6 7 8 9 10 11 12 write filename filetype None Write the atoms in the selection to filename Filetype is guessed from the filename or can be specified with filetype sell amp sel2 Create a new atom selection using the atoms found in both sel1 and sel2 sel1 sel2 Create a new atom selection using the atoms
281. the color scale which is a list of 1024 smoothly changing colors There are many color gradations available All of them consist of transformations of three colors For instance RGB colors the smallest value red values near the middle of the scale are green and the largest values are blue Colors in between are linear mixes of the two colors The list of available gradations is given below The minimum of the range of values is linearly scaled and shifted to start at 0 and end at 1 Assume the color scale is RGB For a given value of x in the scale range 0 1 the RGB value is found first from a linear scaling based on the midpoint If x 0 R is 1 for maximum red This continues linearly until x midpoint at which point R is 0 and stays 0 The green component is 0 at both x 0 and x 1 and is 1 at the midpoint Linear scaling occurs in between The blue component is 0 for x lt midpoint and 1 for x 1 An additional term min is added to each of the component terms before they are merged This shifts the final colors more towards white or black Min can take on values from 1 to 1 There is only one color scale used at a time so it is impossible to display objects colored by multiple different color scales 72 Method Name Type ResName ResType ResID Chain SegName Molecule Structure ColorID Beta Occupancy Mass Atom name using the Name category Atom type using the Type category Residue name using t
282. the other for nucleic acids The protein tube is a smooth curve through the selected Ca positions and the nucleic acid tube is a smooth curve through the backbone phosphates The protein tube is a spline curve that passes through all the Ca atoms in a protein fragment Five evenly spaced interpolation points are found along the curve to break the curve connecting the two Ca atoms into six line segments If the first Ca is selected the first three segments are colored by the color assigned to that Ca If the second Ca is selected the last three segments are colored by the color of the second Ca The nucleic acid tube is constructed in the same manner except that the phosphate atoms are used The two controls set the spline radius and resolution and have the same meaning as they did in the Bond 6 1 2 control However if the bond s Radius becomes 0 or Resolution is 2 or less then the spline is drawn as a simple line This make moving and rotation the image much faster It is possible to pick with the mouse the Ca which defines the tube by clicking near the middle of the six tube segments which are associated with that atom 6 1 12 Ribbons The Ribbons representation is similar to Tube 6 1 11 in that it follows the same spline curve for both the protein and nucleic acids However it uses additional information the O of the protein backbone or some of the phosphate oxygens for nucleic acids to find a normal for drawing th
283. the same as Lines 6 1 1 except that instead of drawing a bond as a line between two atoms a cylinder is drawn instead To be more specific it draws an n sided prism where the number of sides is determined in the Graphics window 85 4 7 by the Bond Resolution control and the radius is given by the value of Bond Radius in Angstroms If the radius or number of sides gets too small the bonds are drawn as lines In order to fine tune the bond representation VMD does a small amount of trickery to the 61 prisms That is imagine two hollow cylinders coming together so that the center of the face of one cylinder is in the same position as the center of the face of the other cylinder Also suppose these two cylinders come together at 90 degrees Although most of these two cylinders will overlap there will appear to be a gap at their intersection To correct for this problem VMD extends both cylinders somewhat so that the far ends touch If one looks closely this produces more of an overlap but it is much nicer looking than the gap When three or more bonds join at one atom VMD chooses the lowest numbered bond and extends all other bonds to meet with that one It then extends that lowest numbered bond to meet with the second lowest numbered one 6 1 3 DynamicBonds The DynamicBonds representation will automatically perform a distanced based bond search for the active atom selection and active trajectory frame This representation
284. the transformation needed to move one structure onto another in order to minimize the RMSD With the mathematical prerequisites behind us we still need to be able to specify how to choose the atoms to compare If you want to compare all the atoms in both structures and they both 178 have the same number of atoms then the problem is easy N is everything This occurs most often in MD simulations when the only thing different between two structures are the coordinates But what about homologous sequences In this case the number of atoms differ because while the number of residues is the same the sidechains have different numbers of atoms The usual solution is to determine the RMSD based solely on the backbone atoms or in some X ray structures where only the Ca atoms have been determined based on the Ca atoms VMD allows you to fit and align based on any valid atom selection as long as the atom selection specifies the same number of atoms in each molecule being compared 12 4 1 RMS Fit and Alignment Extension To get started with RMS fitting and alignment open the RMSD item from the Extensions menu You should now have a new window titled RMSD Tool We ll describe the RMSD calculator function first RMSD calculation xj RMSD Tool Jresidue 5 to 85 RMSD Align W Backbone only History 4 Top Average Selected ID Molecule RMS deviations 0 test 7 793957 70073 1 mystructure 0 0 Total RMSD 7 79
285. the x axis by the given amount to the rotation matrix axis y amount rad deg pi Adds a rotation about the y axis by the given amount to the rotation matrix axis z amount rad deg pi Adds a rotation about the z axis by the given amount to the rotation matrix axis x y 2 amount rad deg pi Adds a rotation of the given amount about the given vector to the rotation matrix bond x1 y1 z1 22 y2 22 amount rad deg pi Sets the center and offset transforma tions to the first point and defines a rotation about the bond axis by the given amount angle x1 y1 z1 x2 y2 22 x3 y3 23 amount rad deg pi Sets the center and offset transformation to the second point and defines a rotation about the axis perpendicular to the plane made by the three points the vector is computed from the cross product of the vector connecting the first two points with that connected the last two 11 3 Multiplying vectors and matrices There are two commands to multiply a matrix and a vector vectrans and coordtrans They assume the vector is in column form and premultiply the matrix to the vector If the vector contains four numbers the two commands are identical If the vector has three elements a fourth is added a 0 for vectrans and a 1 for coordtrans The difference is that vectors are not affected by translations during transformations while coordinates are e C vectrans m v Multiple the matrix m
286. thin VMD Selection of all atoms with a name starting with C name C Segment names containing a number segname 0 9 Multiple terms can be provided on the list of matching keywords This example selects residues starting with an A the glycine residues and residues ending with a T As with a string a regular expression in a numeric context gets converted to an integer which will always be zero resname A GLY T Selections containing special characters such as or must be escaped with the character In order to select atoms named Na one would use the selection name Na 78 In brief a regular selection allows matching to multiple possibilities instead of just one char acter Table 6 9 shows some of the methods that can be used There are many ways to do some selections For example choosing atoms with a name of either CA or CB can be done in the following ways name CA CB name CA CB name C AB name C A B Several caveats for those who already understand regular expressions VMD automatically prepends and appends to the selection string This makes the selection 0 match only O and not OG or PRO On the other hand putting and into the command won t really affect anything selections that match on a substring must be preceded and followed by as in 0 x and some illegal selections could be accepted as correct but strange as in C 0 which gets conve
287. through the Cg atoms flat ribbon through the Ca atoms smooth ribbon through the Ca atoms cartoon diagram cylinders and ribbons based on secondary structure smooth cartoon diagram smooth ribbons based on secondary structure display ring structures as polygons colored by ring pucker flat ribbon tracing glycosidic bonds with twists oriented by sugar residues molecular surface Gaussian density surface molecular surface as determined by the program MSMS molecular surface as determined by SURF display a texture mapped slice from a volumetric data set display an isovalue surface from a volumetric data set field lines generated by integrating particles by volume gradient vectors molecular orbital selected by wavefunction type spin excitation and orbital ID per residue approximate bounding spheres dotted van der Waals spheres for atoms no bonds dotted representation of the solvent accessible surface Table 6 1 Molecular view representation styles 6 1 1 Lines The default representation is Lines which is also known as wireframe It draws a line between each atom and the atoms to which it is bonded Both atoms have to be selected before the bond will be drawn The first half of each bond is colored appropriately for the first atom while the color of the final half corresponds to the second atom The only parameter for the lines representation is the line Thickness 6 1 2 Bonds Nearly everything about this option is
288. tion Use the provided selection to align all trajectory frames to the first frame If you don t use this option you should make sure that you aligned all frames yourself before running volmap ils e transform matriz Suppose you want to align your trajectory to a reference frame from a different molecule In this case you should align the first frame of your trajectory to the reference and provide the according alignment matrix as returned by measure fit using the transform option volmap ils will take care of the rest e pbc This flag signals that you want a periodic boundary aware ILS calculation Depending on the desired target grid size image atoms from neighboring PBC cells are taken into account for the computation The atoms used for the calculation are chosen from a box that exceeds the target grid size by the interaction cutoff in each direction Note If your molecule rotated or drifted from the PBC center during your MD simulation then the structure alignment will rotate or shift the PBC cell so that your map might not lie entirely inside the PBC cell anymore This will lead to ill defined fringes of the map and you might want to consider rewrapping the coordinates Rewrapping cannot undo the rotation but unless you have a very oblonged PBC cell removing the shift by rewrapping will in most cases yield a map without or with little boundary effects See the pbc wrap command from the PBCtool plugin Warning If you use pbc DO NOT
289. to experiment with more complex picking modes consider the angle made by the O of the CO with the FE of the heme and the NE2 of residue 93 you can click on the atoms to find which ones are which Using the Mouse menu change the pick mode to Angles This should cause the cursor to become a red crosshair Click on each of the three atoms using the left mouse button After the third pick a shallow angle will appear indicating an 8 71 degree angle between the three atoms Now load the intermediate star pdb file which can also be found in the proteins directory of your distribution Again use the Files window to do this Both of the molecules will be loaded side by side Go to the Graphics window and change the selection so it the same as the first i e resname HEM CO or resid 64 93 The two molecules are almost atop each other making it hard to distinguish the two so change the colors to simplify things First in the Graphics window change the Coloring method to Molecule Use the Selected Molecule chooser to change the mbco pdb Coloring method to Molecule as well Open the Color window 5 4 9 and scroll the Category browser down until the line Molecule is visible Click on it then click on the line which says mbco pdb There may be two mbco lines if the file had been loaded before in this session Scroll the Colors browser up to click on blue This should change one of the molecules in the display to blue Next cli
290. ton causes larger changes By default molecules are displayed in a lines representation colored by atom type Suppose you would like to view the myoglobin structure with its protein backbone represented as a tube the heme represented as licorice the SO4 ion and CO molecule represented as van der Waals spheres and histidines 64 and 93 represented as CPK models First open the Graphics window 85 4 7 by selecting the Representations item in the the graphics menu of the VMD Main window Type backbone in the Selected Atoms text entry area and press enter to select the myoglobin backbone All of the protein except for the backbone will disappear Choose NewCartoon in the drawing method chooser to display the backbone as a tube and choose Structure in the coloring method chooser to color the tube with the predefined secondary structure color Press the Create Rep button This creates a new representation in the browser identical to the original one The new representation can be changed without affecting others so clear the atom selection text area and enter resname HEM to select the heme At this point the heme isn t visible because it cannot be drawn as a cartoon so choose the Licorice drawing method to make it appear Click on 18 Create New again to make a new view and enter resname S04 CO to select the SO ion and the CO molecule and choose the drawing method VDW to render them as Van der Waal spheres Once again pre
291. ture Helices are drawn as cylinders beta sheets as solid ribbons and all other structures coils and turns as a tube If the secondary structure has not yet been determined it will be calculated automatically by the program STRIDE A helix cylinder is constructed by finding the least squares linear fit along the coordinates of the helix s Ca atoms If a given residue s Ca is selected the small cylinder found by linear interpolation along the line of best fit is drawn with radius determined by the radius parameter Because this method computes a best fit a helix must have at least 3 residues before it is drawn those helicies with one or two residues are drawn as a coil It is possible to pick the Ca for each cylinder segment but they are at the location of the Ca which is not near the axis cylinder Interesting results occur when the whole protein is defined to be a helix and drawn as a cartoon The solid beta ribbon is constructed by building a spline along the center points between each beta sheet residue Again the spline is linearly interpolated to find the start and end points for each residue Those are extended to construct the corners for a ribbon with rectangular cross section the amount of extension is determined with the thickness parameter A ribbon segment is used if the corresponding Ca atom is selected Note that since this method assumes the protein is in a beta conformation it draws a much smoother ribbon than the standard
292. ularly useful for animating trajectories 6 1 26 Dotted Same as VDW 8 6 1 6 except that the spheres are drawn dotted instead of solid That is a dot is placed at each of the vertices of the triangle making up each sphere This can be used for instance to imitate a surface representation 6 1 27 Solvent This method is similar in spirit to the Dotted 6 1 26 representation in that it gives a quick estimate of the molecular surface with a collection of dots However it goes above and beyond the Dotted option by giving a more uniform coverage of the surface The method that VMD uses to check for overlaps isn t technically correct but it is fast and works quite well A technical descrip tion of the algorithm is as follows For each point of the surface distribution of radius r atom radius probe radius of atom 1 check each of the atoms j to which it is covalently bound If the point is too close to 7 don t display it Also if the point is too close to any neighbor k of j k 4 i then don t draw it This is fast since there aren t that many neighbors to check but it doesn t omit parts of the surface in contact with atoms which aren t one or two bonds away This can be considered a good thing since you might get a better idea of the contact surface There are three parameters for this option One is the Probe Radius which was mentioned in the description If the probe radius is too large the problem of over
293. ult this is tmp or usr tmp on Unix systems and C on Windows e VMDCUSTOMIZESTARTUP Unix only The name of a C shell script to source prior to running the actual VMD process This shell script can contain any commands necessary for performing machine specific spaceball graphics and other customizations necessary to run VMD This can be anything from a simple script that sets the right serial port for a Spaceball based on the hostname or it can be a complex script for turning on a projection system logging demos configuring multi display stereo framelock features etc e VMDBABELBIN The complete path and filename for the program babel which is used by VMD to convert molecular structure coordinates files into PDB files which VMD can actually understand If this is not set explicitly the VMD startup script will attempt to find babel in the current path If Babel cannot be found or is not installed VMD will not be able to read molecular file formats other than PDB PSF and binary DCD files e VMDFILECHOOSER Specifies which file chooser to use for loading and saving files from the GUI At present this should be either FLTK which uses Fltk s platform independent file chooser or TK which uses Tk s file chooser The Tk file chooser is the default and uses a 187 native Windows interface on Windows platforms The Fltk file chooser looks the same on all platforms supports tab completion but not drive letters and is probably most
294. umber from 0 to 16 Changing a rep To change a representation select it in the representation browser The atom selection for that rep will appear in the Selected Atoms text area and the controls will update to reflect the current settings Changing the settings will immediately affect the displayed representa tion if the Apply Changes Automatically check box is selected When it is disabled updates will only occur when the Apply button is pressed Changing the drawing method brings up method specific controls and defaults If you go back to the previous draw style VMD restores any changes that you may have made to the settings Pressing the Default button will restore the default settings The display will be updated after every change Adding a rep To add a new representation of the molecule enter the selection into the Atom Selection text area or keep what is there and press Create Rep This adds the representation to the currently selected molecule 43 y Graphical Representations Je JJ Selected Molecule 1 1e79 y Create Rep Delete Rep Style Color Selection NewCartoon Structure all YDW Name ions Lines ColorlD 0 water Selected Atoms ons Draw style Selections Trajectory Periodic Coloring Method Material Name y Opaque y Drawing Method vow y Default Sphere Scale alij 1 0 nL Sphere Resolution ajaj 12 DL Apply Changes Automatically Apply Figure 5 6 The Graphi
295. ur GUI windows for you 10 5 Controlling VMD from Python Commands for controlling VMD from Python are organized into modules which roughly correspond to Tcl commands Importing all the commands in a module is not recommended as some of the functions e g listall overlap All commands are listed below with the name of the module given by the section heading 10 5 1 animate Python operations available from the animate module used to control which coordinate frames are displayed e forward e reverse forward and reverse causes VMD to start animating frames automatically in order of increasing or decreasing frame number respectively e once e rock e loop once rock and loop control how frames are cycled when VMD is animating a series of frames once causes VMD to stop when it reaches the first or last frame rock causes VMD to reverse direction each time it gets to the beginning or end loop causes VMD to continue from the beginning when reaches the last frame or from the last frame if it gets to the beginning e style Returns either Once Rock or Loop corresponding to the animation mode VMD is currently in e goto frame Set the animation to the given frame and pause the animation e prev Step to the next lowest frame then pause e next Step to the next highest frame then pause e pause Stop animating frames e speed value Get set the relative rate at which
296. urn a light off e light_number status Return the pair on off highlight unhighlight e light_number rot lt x y z gt angle Rotate a light at infinity angle degrees about a given axis e light numer pos Return current position e light numer pos default Return default position e light numer pos x y z Set light position 9 3 15 logfile Turn on off logging a VMD session to a log file This will create a log file with commands for all the actions taken during the session The log file may be played back later by using the play command or the Tcl source command The only actions recorded are those which change the state of the VMD display so straight Tcl commands are not saved All of the core VMD commands will write to the log e filename Turn on logging to filename e console Turn on logging and direct it to the VMD text console window e off Turn off logging To write log information to the file off use the file name off 110 9 3 16 material This set of commands is used to create new material definitions and modify existing ones e list Return a list of the available materials e settings name Return a list of the five material settings for the material of the given name These settings take on floating point values between 0 and 1 The values are returned in the following order ambient specular diffuse shininess opacity If the specified material has not been defined noth
297. urns the currently active frame selection text 122 smoothrep molecule_number rep_number n Get set the window size for on the fly smooth ing of trajectories Instead of drawing the specified rep from the current coordinates VMD will calculate the average of the coordinates from the n previous and subsequent timesteps If n is zero then no smoothing is performed Note that this smoothing does not affect any label measurements and does not change the values of the coordinates returned by atom selections or written to files it only affects how the rep is drawn Smoothing can be especially useful in visualizing rapidly fluctuating molecules or making movies scaleminmax molecule_number rep_number min max auto Get set the color scale range for this rep Normally the color scale is automatically scaled to the minimum and maximum of the corresponding range of data This command overrides the autoscaled values with the values you specify Omit the min and maz arguments to get the current values Use auto instead of a min and max to rescale the color scale to the maximum range again showrep molecule_number rep_number on off Get set whether the given rep is shown or hidden Hidden reps cannot be picked and do not show any graphics volume molecule_number lt volumeset_name gt lt Origin gt lt a gt lt b gt lt c gt a b c lt Data gt Add a volumetric data set to the current molecule Origin a b and c are vectors setting the
298. use unpause or toggle the paused state of the remote simulation transfer rate Set the rate at which new coordinates are sent by the remote simulation to VMD to the specified value keep rate Set the keep rate i e the frequency at which VMD saves simulation frames to memory to the specified value copyunitcell lt on off gt Enable or disable copying unit cell information from the pre vious frame when updating or saving frames through IMD This can be useful when using periodic display with IMD since the IMD protocol currently doesn t support communicating the unitcell information or when using a IMD client that does not provide this information after the protocol has been extended WARNING when using imd copyunitcell on with simulations in NPT ensemble the resulting unit cell information will be incorrect The default setting is off 9 3 13 label Turn on or off labels for the four categories atoms bonds angles or dihedral angles create and destroy simulated springs Once a label is created given the list of associated atoms it can be turned on or off until it is deleted Also the value of the label over the trajectory can be saved to a file and viewed with an external program such as xmgrace In the following category implies one of Atoms Bonds Angles Dihedrals list Return a list of available categories list category List all labels in the given category add category molID1 atomID1 molID2 atomID
299. values If only a single attribute is given a list of corresponding attributes values will be re turned If a list of attributes is given then a list of sublists will be returned each sublist will contain the values for the corresponding attributes See Tables 6 5 6 6 and 6 8 for the recognized attribute keywords set attribute_list values_lists Set the attributes in the attribute list with the values gven in the values lists If there is only one attribute then values_lists can be either a single value or a list of values one for each selected atom If there is more than one attribute then values_lists must be a list of sublists the number of sublists must equal the number of selected atoms and the number of items in each sublist must equal the number of attributes Example set sel atomselect top all set mass sel get mass set xyz sel get x y z sel set beta 0 all values are set to zero sel set beta mass copy mass to beta set occupancy to x mass to y beta to z sel set occupancy mass beta xyz It is an error to set integer or floating point keywords using non numeric values If floating point values are passed to integer keywords they will be converted to integers and vice versa The set command immediately updates all representations of the selected molecule If speed is an issue delete all representations of the molecule before setting the values getbonds returns a list of bondlists each bondl
300. ven the coordinates from the corresponding frame will be used see the example If weight is given the computed RMSD will be weighted using the values in weight e align ref None move None frame None weight None Finds the transformation that aligns the atoms in the selection with the atoms in ref with optional weights weight and applies this transformation to the atoms in move The following default values for all arguments are provided ref Same molecule and atoms as selection but always using the align ref None move None frame None weight None Finds the transformation that aligns the atoms in the selection with the atoms in ref with optional weights weight and applies this transformation to the atoms in move The following default values for all arguments are provided ref Same molecule and atoms as selection but always using the first timestep in the molecule move All atoms in the selection molecule frame overrides both the selection s frame and the move frame but does not affect the ref frame x weight Defaults to uniform weights on all atoms in selection first timestep in the molecule move All atoms in the selection molecule frame overrides both the selection s frame and the move frame but does not affect the ref frame weight Defaults to uniform weights on all atoms in selection e contacts cutoff sel None Returns pairs of of atoms within cutoff of each other If sel is No
301. veral different GUI windows each designed to control a specific aspect of the molecular display e g to control the appearance of the graphics display window or to change the colors of displayed objects The following sections give a brief description of the windows available in VMD the remaining chapters in this manual describe the actions which these windows make available in greater detail 5 4 1 Main Window VMD Main File Molecule Graphics Display Mouse Extensions Help A D F Molecule Atoms Frames Vol 26318 ADF 1e79_autopsf_modified 51246 1 0 A D F 1e79_autopsf_modified 51246 1 0 Halo HA HA 4 la zoom O Loop y step i 1 1 speed Da Figure 5 1 The Main window The Main window is the main way to access other windows load and save files control trajectory playback change various global program settings access help and to quit the program Many of these actions can also be performed with the menu shortcut keys described in Table 5 3 The Quit menu item exits VMD This will bring up another window which verifies that you do indeed wish to exit Press Yes to quit or No to return to VMD Help The Help menu items each start a web browser to display on line VMD help documents The browser is designated by the environment variable VMDHTMLVIEWER 13 2 Selecting a help item multiple times may start multiple browsers The default web browser is Mozilla for Unix systems and the built in Explorer she
302. w controls how molecules are drawn Molecules are represented by reps which are defined by four main parameters the selection 6 3 the drawing method 6 the coloring method 6 2 and the material 6 2 5 The selection determines which part of the molecule is drawn the drawing method defines which graphical representation is used the coloring method gives the the color of each part of the representation and the material determines the effects of lighting shading and transparency on the representation 42 4 3 SCRHEIGHT i e 8 0 ewe SCRDIST Viewer s Si SEE ee x Le 2 0 Eye Position SON o SCRHEIGHT i e 6 0 A Figure 5 5 Relationship between screen height SCRHEIGHT screen distance to origin SCRDIST and the viewer Draw Style Tab Select a molecule for editing using the Selected Molecule chooser at the top of the window The browser below this chooser lists the reps available for the molecule Each line of the browser summarizes information about the drawing method the coloring method and the selection Below this browser choosers and a text input filed reflect the current state of the rep and provide controls for changing the properties of the rep Each drawing method has specific controls which will appear when it is selected When the ColorID coloring method is selected a text entry box is shown allowing you to specify the index of a color to use for the selection which may be a n
303. whether or not the three sliders will move together as a unit Color definitions are immediately updated in the graphics window so you can see the result of your editing right away Color Scale Several of the coloring methods in the graphics window e g Beta Index Position are used to color a range of values as opposed to a list of names The actual coloring is determined by the color scale 6 2 4 The color scale used to assign these colors is set in the Color Scale tab of the color menu Choose one of the ten color scales from the chooser and adjust the Offset and Midpoint sliders until the color scale shown at the bottom of the tab is as desired 5 4 10 Material Window Default GlassBubble GlassBubble os J Ambient os J Difuse roo JSpecuar roo JShininess oo J Opacity oo Outline foo E OutineWidth M Angle Modulated Transparency Figure 5 10 The Material Window This window is used to create and modify material definitions The material definitions created here will show up in the pulldown menu in the Graphics window allowing you to apply a material to a given representation The upper left corner of the Materials window contains a browser listing all the currently defined materials Below this browser is a set of five sliders which indicate the current materials settings for the material highlighted in the browser Highlighting a different material in the browser by clicking with th
304. will cause the molecule to move or rotate around on the screen The tools have been designed to allow VMD to use haptic devices Most of the tools can give force feedback to the user but none of them require haptic devices in order to operate 53 e The Rotate Tool is a tool for precisely rotating molecules with haptic devices When a button is pressed and released the cursor is again connected to the molecule With this tool however the center of the molecule is fixed and the end of the haptic pointer is forced to lie on the surface of a sphere about this center Moving the device around the surface of the sphere rotates the molecule and another button click releases the molecule There are detentes like the clicks commonly felt in a 2d dial on the surface of the sphere arranged so that the user can rotate the molecule to precise 90 degree points If the user holds down the button for a while initially he can feel the sphere and the detentes but do not affect the molecule This preview mode allows the user to find a good point from which to start the rotation e The Joystick Tool is the three dimensional equivalent of a Joystick for haptic devices Pressing the button creates a virtual spring holding the device to its current location If it is pushed away from this point in some direction the selected molecule starts sliding in that direction with a velocity that is proportional to the displacement of the device Th
305. with a large number of waters and a protein The expression protein and segname lt 10 is faster than segname lt 10 and protein since in the first selection only the atoms which are proteins have the segname converted to a number while in the second selection all the segment names are converted The within selection has its own form of short circuiting The command can be interpreted as find the atoms of A which are withing a given distance from B and if A isn t given search all the atoms The search done in VMD takes a time roughly proportional to the number of atoms in A multiplied by the number of atoms in B so reducing the number of atoms in A i e by not testing every atoms make the search faster Using the system with a lot of water and a protein compare the selection protein within 5 of resid 1 to within 5 of resid 1 and protein The first is very fast as it does a distance search between all the protein atoms and all the atoms in resid 1 However the second selection searches through all the atoms for those which are within 5 A of resid and then finds which of those are protein atoms 6 3 4 Quoting with Single Quotes VMD allows two types of quoting mechanisms single and double quotes Single quotes are used to include spaces and other non alphanumeric characters Believe it or not there are some residue names with a space in them so they can be referenced as for example 77 resname A 1 More importantly
306. with the first parameter as the molecule index and the rest as the arguments from the original draw call Here s an example which extends the draw command to include an arrow primitive proc vmd_draw_arrow mol start end an arrow is made of a cylinder and a cone set middle vecadd start vecscale 0 9 vecsub end start graphics mol cylinder start middle radius 0 15 graphics mol cone middle end radius 0 25 After entering this command into VMD you can use a command such as draw arrow 0 0O O 41 1 1 to draw an arrow In addition to defining new commands user defined drawing commands can also be used to override existing commands For example if you define vmd_draw_sphere then draw sphere 0 0 0 will call your sphere routine not the one from graphics Here s a quick way to add your own label to an atom selection 86 3 This function take the selection text and the labels that atom in the top molecule with the given string It returns with an error if more anything other than one atom is selected proc label_atom selection_string label_string set sel atomselect top selection_string if sel num 1 error label_atom selection_string must select 1 atom get the coordinates of the atom lassign sel get x y z coord and draw the text draw text coord label_string 105 9 3 8 exit Quit VMD 9 3 9 graphics The graphics command draws low level graphics primitives These primitiv
307. with the vector v length 4 returns a vector e coordtrans m v Multiple the matrix m with the coordinate v length 3 returns a vector Examples vmd gt vectrans transaxis z 90 1 0 0 3 67321e 06 1 0 0 0 vmd gt vectrans transvecinv 3 4 12 3 4 12 13 0 1 8e 05 5 8e 05 11 4 Misc functions and values Several other terms are added to the vectors package The first is the variable M_PI which contains the value of pi 167 Examples vmd gt set M_PI 3 14159265358979323846 vmd gt expr 90 M_PI 180 1 5708 The functions trans_from_rot trans_to_rot trans_from_offset and trans_to_offset are used to get or set a transformation matrix from either a 3x3 rotation matrix or offset vector As currently designed these assume there is no scaling in the matrix The trans_from_offset is identical to transoffset and is present for completeness The last is find_rotation_value varname which takes a variable name and extracts from the beginning of it those terms which describe an amount of rotation The rest of the data in the variable remains and the amount of rotation in radians is returned This is used by those functions which need a rotation The valid values are a number followed by one of rad radian or radians for a value in radians the word pi to give the rotation in factors of pi or one of deg degree or degrees for a value in degrees If no units are given the value is assumed to be in degrees Exa
308. wly created atom selection is a Tcl proc which takes the following options num Return the number of atoms in the selection list Return a list of the atom indices in the selection BTW this is the same as get index text Return the text used to create this selection molid Returns the molecule id used to create this selection frame Returns the animation frame associated with this selection The result will be either now last or an integer corresponding to the frame When the frame is now the atom selection will use atomic coordinates from the current frame for its associated molecule If the frame is last the atom selection will always use coordinates from the 99 last frame If the frame is a specific integer the selection will always use coordinates from that frame even if the current animation frame changes Note that if a nonexistent frame is specified the atomic coordinates will reference the last frame frame frame Set the frame for the selection frame should be either now last or an integer delete Delete this object removes the function global Moves the object into the global namespace Atom selections created within a Tcl proc that are not made global are deleted when the proc exits uplevel level Moves the object to a new level in the namespace stack Works the same as the Tcl function uplevel get attribute_list Given an attribute or a list of attributes returns the attribute
309. y over a network Caching cannot be performed while animating trajectories so the Al performance benefit is only possible interactive rotation and zooming of static molecular structures Rendermode The Rendermode chooser controls which low level rendering method VMD uses The Normal rendering mode is the default VMD rendering algorithm based on standard fixed function OpenGL The GLSL rendering mode uses OpenGL Programmable Shading Language to implement real time ray tracing of spheres alpha blended transparency and high quality per pixel lighting for all geometry On machines with high performance graphics boards supporting programmable shading the GLSL rendering mode provides quality on par with many of the external software renderers supported by VMD but at interactive display rates Clipping Planes Near Clip and Far Clip These controls are found in the Display Settings window Only those parts of the scene between the near and far clipping planes are drawn The display clipping planes also set the depth cueing start and endpoints Objects at the near clipping plane are distinct and crisp objects at the far clipping plane will be blended into the background Clipping planes positions are changed with the Near Clip and Far Clip controls It is not possible for the near clip to be farther away than the far clip When using stereo it may be useful to set the near clip plane much lower than the default value This makes the geometry
310. ypes or may have different meaning for different map types e cutoff cutoff Specifies a cutoff distance For the distance maps specifies the largest distance that will be considered large number is better but slower For the mask maps specifies the distance from each atom which will be considered part of the mask e points For the occupancy map type Treat atoms as point particles instead of as spheres e radscale factor For the density map type Sets a multiplication factor that multiplies all the VMD atomic radii for the purpose of the calculation e weight lt field name value list gt For the density map type Sets a per atom weight to be used when computing the density This can be the name of any VMD numerical atomic field such as mass charge beta occupancy user radius etc or else a Tcl list of numbers of the same length as the number of atoms Implicit Ligand Sampling volmap ils command This command computes a map of the estimated potential of mean force in units of kgT at 300 K of placing a weakly interacting gas monoatomic or multiatomic ligand at every gridpoint These results will only be valid when averaging over a large set of frames Note that if you have a CUDA enabled GPU then your ILS calculation will run about 20 times faster than on a CPU Please refer to and cite Cohen J A Arkhipov R Braun and K Schulten Imaging the migration pathways for O2 CO NO and Xe inside myoglobin Biophysi

VMD User's Guide

Contents

Download Pdf Manuals

Related Search

Related Contents