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PyMOL User's Guide

1. Set Origin of Rotation An abbreviated version of this table the Mouse Matrix is always displayed in the Internal GUI in order to help you remember which key and mouse button performs which action When using PyMOL on a laptop it may be necessary to attach an external mouse or reassign the particular mouse controls you plan to use onto the reduced set of buttons that you have available internally see reference on the button command Virtual Trackball Rotation Virtual Trackball Rotation 14 PyMOL s Virtual Trackball Virtual trackball rotation works as if there is an invisible ball in the center of the scene When you click and drag on the screen it is as if you put your finger on the sphere and rotated it in approximately the same manner If you click outside the sphere then you get rotation about the Z axis only Generally the view will be easiest to control by either clicking in the center of the scene and moving outwards mostly XY rotation or by clicking and draging around the edge of the screen and moving in a circular fashion Z rotation Virtual Trackball Rotation 15 Moving Clipping Planes PyMOL s clipping plane control is somewhat unusual and may take a few minutes to get used to Instead of having separate controls for the front and back clipping planes controls are combined into a single mode where up down mouse motion moves the front near clipping plane and left right mouse motion controls
2. 1 0 controls the ambient light intensity for both OpenGL and the ray tracer e ambient_scale float controls the relative ambient intensity between OpenGL and the ray tracer e antialias 0 or 1 generate a smooth image best quality but takes 4X as long e direct 0 0 1 0 the planer light intesity originating from the camera Ray Tracing 46 e gamma 0 1 2 0 gamma transformation applied after rendering is complete e light vector the position of the light e reflect 0 0 1 0 the planer light intesity originating from the light source e spec_reflect 0 0 1 0 intensity of the specular reflection from the light e spec_power 1 100 how localized is the specular reflection higher smaller Saving Images png All images ray traced or not can be saved in PNG format using the png command This format is directly readable by PowerPoint and can be easily converted into other formats using a package like ImageMagick You can also save images using the Save Image option in the File menu Images are always saved at the same resolution as the viewer window ray png my_image png Saving Images 47 Stereo Introduction PyMOL can supports several different stereo graphics options Supported Stereo Modes Crosseye Stereo Walleye Stereo Hardware Stereo Generating Stereo Figures Stereo figures are often used in molecular graphics illustrations in order to provide the reader with a three dimension
3. http www python org MacOS X Installation 6 Recommendations e Mac OS 10 2 x or 10 3 x e Dual 2 0 Ghz GS system e GeForce4 or Radeon 9x00 OpenGL accelerator e 1 GB of RAM Minimial Requirements e Mac OS X 10 2 x e Single 833 Mhz G4 system will run on less but performance is poor e 3D OpenGL graphics acceleration e 512 MB of RAM 1 GB recommended If you use Fink PyMOL is part of the Fink ports collection sudo s apt get pymol install should be sufficient to get a functioning instance on your system However it may not be the most recent version We also highly recommend installation of Apple s X Server which enables PyMOL to access your accelerated graphics hardware If you do not use Fink Option 1 MacPyMOL At the request of various Macintosh users as well as Apple itself we have created MacPyMOL a special native Aqua version of PyMOL for the Macintosh The latest version of MacPyMOL can be downloaded from http delsci com macpymol However note that this version is an Incentive Product only available to PyMOL sponsors but students and teachers are exempt from this requirement For more information on MacPyMOL contact support delanoscientific com Option 2 PYMOL X11 Hybrid This version of PYMOL includes a native Aqua based OpenGL window and an X11 based Tcl Tk external GUI graphical user interface Before launching the PyMOL X11 Hybrid you must have Apple s X11 server install
4. operator formal charge value an integer fc C 33 Details of the atom and residue name formats can be found in the official guide to PDB file formats http www rcsb org pdb docs format pdbguide2 2 guide2 2_frame html Selection Algebra Selections can be made more precise or inclusive by combining them with logical operators including the boolean and or and not The boolean and selects only those items that have both or all of the named properties and the boolean or selects items that have either or any of them Venn diagrams show that and selects the areas of overlap while or selects both areas AorB Operators Selection operators and modifiers are listed below The dummy variables s1 and s2 stand for selection expressions such as chain a or hydro Short Operator Effect form Selects atoms that are not included in sl not sl Isl PyMOL gt select sidechains bb Selects atoms included in both s1 and s2 sl and s2 sl amp s2 PyMOL gt select far_bb bb amp farfrm_ten Selects atoms included in either s1 or s2 sl or s2 sl s2 PyMOL gt select all_prot bb sidechain Selects atoms in s1 whose identifiers PERS slins2 Pame resi resn chain and segi all match atoms in s2 PyMOL gt select same_atms pept in prot Selects atoms in s1 whose identifiers s1 like 52 sil so name and resi match atoms in s2 PyMOL gt select similar_atms pept like prot Selects all atoms whose van der Waals radii are sepa
5. refer to atoms in that object will no longer work But when named selections are deleted the data are still available under the object name Disabling objects eliminates them from the viewer but disabling named selections just turns off the pink dots that highlight them in the viewer Atom selections named or not can span multiple objects EXAMP LE PyMOL gt load PYMOL_PATH test dat fc pdb PyMOL gt load SPYMOL_PATH test dat pept pdb PyMOL gt select alpha_c name ca The named selection alpha_c is created it includes atoms in both fc and pept objects PyMOL gt color red name ca CA atoms in both objects Named Atom Selections 29 EXAMPL PyMOL gt PyMOL gt load SPYMOL_PATH test dat pep select bb name c o n ca PyMOL gt count_atoms bb PyMOL gt remove resi 5 PyMOL gt count_atoms bb EXAMPLE PyMOL gt load SPYMOL_PATH test dat pep PyMOL gt select static_demo pept PyMOL gt count_atoms static_demo PyMOL gt h_add PyMOL gt count_atoms static_demo PyMOL gt count_atoms EXAMPL PyMOL gt select bb name c o n ca PyMOL gt select c_beta_bb bb or name are colored red Named selections will continue working after you have made changes to a molecular structure pdb The named selection is created bb PyMOL counts 52 atoms in bb All atoms in residue 5 are removed from the object pept Now PyMOL
6. residue identifier range PyMOL gt select nterm resi 1 10 alternate conformation identifier list list of single letters PyMOL gt select altconf alt a chain G chain identifier list list of single letters or sometimes numbers Single word Selectors 32 PyMOL gt select firstch chain a segment identifier list list of up to 4 letter identifiers segi PyMOL gt select ligand segi lig ag number a single integer from 0 to 31 PyMOL gt select f1 flag 0 type number a single integer PyMOL gt select typel nt 5 type string a list of up to 4 letter codes text_type PyMOL gt select subset text_type HA HC fla g d internal index number a single integer PyMOL gt select intid index 11 secondary structure type list of single letters external index number i id a single integer PyMOL gt select idno id 23 idx Ss PyMOL gt select allstrs ss h s 1 Other property selectors select by comparison to numeric identifiers Numeric Argument eee amp Example NN comparison operator b factor value a real number formal_charge PyMOL gt select doubles comparison operator partial charge value a real number partial_charge p PyMOL gt select hicharges pc gt 1 Single word Selectors PyMOL gt select fuzzy b gt 10 comparison operator occupancy value a real number PyMOL gt select lowcharges q lt 0 50 comparison
7. the third as an identifier to chain and so on It may take any of the following forms object object name segi identifi name segi identifi object name segi identifi object name segi identifier object name r chain identifier resi identifier nam r chain identifier resi identifier r chain identifier identifier EXAMPLES PyMOL gt zoom pept PyMOL gt show spheres pept lig PyMOL gt show cartoon pept lig a PyMOL gt color pink pept lig a 10 PyMOL gt color yellow pept lig a 10 ca If the macro does not begin with a slash it is interpreted differently In this case PYMOL expects to find the fields ending with the bottom of the hierarchy Macros that don t start with a slash may take the following forms resi identifier name identifier chain identifier resi identifier name identifier segi identifier chain identifier resi identifier name identifier object name segi identifier chain identifier resi identifier name identifier EXAMPLES PyMOL gt PyMOL gt PyMOL gt PyMOL gt zoom 10 cb show spheres show cartoon color pink pept enz c 3 n a 10 12 ca lig b 6 8 cto You can also omit fields between slashes Omitted fields will be interpreted as wildcards as in the following forms resi identifier resi identifier nam chain identifier object name chain identifier EXAMPLES PyMOL gt zoom 142 PyMOL gt show spheres 15
8. 50 54 and 58 is colored green PyMOL gt color yellow resi 60 90 The representation of residues numbered 60 through 90 is colored yellow PyMOL gt color blue akeeper Residues numbered 1 10 which were collected in the named selection akeeper are colored blu PyMOL gt color red ss h The representations of helical residues are colored red PyMOL gt color yellow ss s The representations of Coloring Objects and Selections 21 beta sheet residues are colored yellow PyMOL gt color green ss 1 The representations of loop and unassigned residues are colored green In the last three examples the selector ss chooses secondary structures specified by h for helix s for beta sheet strand and 1 for loops and unspecified structures Turning Objects and Selections On and Off PyMOL can hold several objects in memory at the same time The commands disable and enable allow you to eliminate representations of objects from the viewer while still controlling their properties with commands SYNTAX nable object nam EXAMP LE PyMOL gt load PYMOL_PATH test dat fc pdb PyMOL gt load SPYMOL_PATH test dat pept pdb PyMOL gt disable pept All representations of pept are removed from view PyMOL gt color yellow name cto ntca Backbone atoms in both fc and pept are colored yellow but pept atoms are still not visible PyMOL gt enable pept pept atoms are visible an
9. PyMOL commands in very brief examples The section titled Simple Examples shows other commands that combine representations selections and property changes More complicated examples appear in the section titled Cookbook and Complex Examples and a comprehensive listing of typed commands appears in the section titled Command and API Reference To see a list of the keyword commands that are available in PyMOL on your computer screen type help and enter Typing TAB and enter will work too Add the keyword if you want help on a particular command SYNTAX help keyword EXAMP LE PyMOL gt help load PyMOL responds by displaying the manual page that discribes the command in the PyMOL viewer Command line completion works inside of help so if you don t remember the full keyword type help the first character or so of the keyword and hit TAB Python will display a list of possible help topics Click inside the viewer and hit escape to toggle back and forth between the display of the manual page or the list of commands and the molecules you have loaded in PyMOL All the keywords that PyMOL understands are listed alphabetically and described in the Reference section PyMOL commands run on top of the Python programming language and may contain Python statements After you type in a command and hit return Py MOL will check whether the first word is one of its keywords or if it can be extended into a keyword If not PYMO
10. Viewer Window The PyMOL Viewer represents the heart of the PyMOL system This is a single OpenGL window where all 3D graphics are displayed and where all direct user interaction with 3D models takes place Names Panel Mouse Matrix Frame Indicator Movie Controls _ Command Line y PyMOL Viewer window with Internal GUI enabled Default PyMOL s Windows 11 The Internal GUI contained within this window right allows you to perform actions on specific objects and specific atom selections From top to bottom it contains an object list a mouse button configuration matrix a frame indicator and a set of VCR like controls for working with movies The Viewer also contains a command line bottom which can be used to enter PyMOL commands It is also possible to view PyMOL text output in the Viewer window you can hit the ESC key anytime to toggle between text and graphics mode inside the Viewer window The PyMOL Viewer can be run all by itself and it provides the complete capability of the PyMOL core system If desired the Command line and Internal GUI can be disabled Many tasks can be made easier and more efficient through use of standard menus and controls For the most part such gadgets are currently found in an External GUI window The External GUI Window ioii file Got Foyet Readue Mowe Rendering Dery Settna Mose Caton Weed Scupting Demo tep Enter help for a list of commands all fest Enter help lt
11. a series of images in RAM and to play them back at a much higher rate than they could be rendered originally This is most useful for ray traced images but it can also be used with OpenGL images cache frames The cache_frames option controls whether or not PyMOL saves frames in memory Its usage is demonstrated in the following script NOTE caching images takes a tremendous amount of memory so you should use the viewport command to shrink the window before utilizing this option viewport 320 240 load test dat pept pdb orient hide show sph mset 1 x30 util mrock 1 30 3 1 1 set ray_trace_frames 1 set cache _frames 1 mplay mclear Once you have loaded a set of frames into RAM the frames will remain there until you run the mclear command even if you manipule that model You can also press the mclear button on the external GUI window mclear flushes the frame cach Saving movies Complex Examples 51 mpng You can save movie images to numbered PNG format files with a common prefix If you want each frame to be ray traced you should turn on raytracing of frames turn off caching and clear the cache see the Movie Menu or use the following commands set ray_trace_frames 1 set cache_frames 0 mclear You can save the movie using the mpng command or you can save it from the File menu Either way you must provide a prefix which will be used to create numbered PNG files mpng mov will create mov0001
12. allows you to edit conformations naturally Sculpting allows the molecule to adapt to your changes e Expandability The PyMOL Python API provides a solid way to extend and interface Weaknesses e User Interface Development has been focused on capabilities not on easy of use for new users e Documentation Only recently has any documentation become available e Object Orientation There is a single monolithic functional API e Electrostatics PyMOL is not yet a replacement for Delphi Grasp e No Mechanics Engine Although PyMOL sports potent molecular editing features you can t yet perform any clean up This chapter last updated January 2004 by Warren L DeLano Ph D Strengths 3 Introduction Welcome to PyMOL Over the years PYMOL has become a capable molecular viewer with support for animations high quality rendering crystallography and other common molecular graphics activities It has been be adopted by many hundreds perhaps even thousands of scientists spread over thirty countries However PyMOL is still very much a work in progress with development expected to continue for years to come Is PyMOL Free Software Yes but PyMOL is Copyrighted software that is Free for all parties to use modify and redistribute Because of PyMOL s unusual status you can be confident that the time you invest today in learning the package will provide you with long term utility no matter where your career happens to takes
13. counts the remaining 48 atoms in bb Named selections are static Only atoms that exist at the time the selection is defined are included in the selection even if atoms which are loaded subsequently fall within the selection criterion t pdb The named selection static_demo is created to reference all atoms PyMOL counts 107 atoms in static_demo PyMol adds hydrogens in the appropriate places PyMOL still counts 107 atoms in static_demo even though it counts 200 atoms in pept Named selections can also be used in subsequent atom selections An atom selection named bb is made consisting of all atoms named C 0 N or CA cb An atom selection named c_beta_bb is made consisting of all atoms named C 0 N CA or CB Note that the word or is used to select all atoms in the two groups bb and cb The word and would have selected no atoms because it is interpreted the subsection on Selection Algebra below Named Atom Selections in its boolean logical sense not its natural language sense See 30 Single word Selectors The very simplest selection expressions are single word selectors These selectors do not take identifiers they are complete by themselves Selector Selector a E none none No atoms empty selection hydro h Al hydrogen atoms currently loaded into PyMOL All hydrogen atoms currently loaded into PyMOL hetatm het All atoms lo
14. different when all smoothing features are turned off For instance with smoothing enabled set cartoon_flat_sheets 1 set cartoon_smooth_loops 1 Cartoon Representations 39 the image differs substantially from set cartoon_flat_sheets 0 set cartoon_smooth_loops 0 which more accurately reflects the true path of the peptide backbone Cartoon Representations 40 To facilitate beautiful imagery smoothing is enabled by default just like Molscript NOTE THIS MAY CHANGE BEFORE VERSION 1 0 Just be sure to turn it off when you want to study structures at atomic resolution remember real life is a bit more complicated than what you see in cartoons Customization Cartoon Types Best results will be obtained when secondary structure information has been defined for each residue in the molecule Under these conditions PyMOL will do extra processing to insure that good normals have been calculated for helical regions and perform smoothing of loops where desired Also under such conditions in automatic mode cartoon representations will be assigned according to the secondary structure type However you can instruct PyMOL to ignore such information and manually control when and where various cartoon representations are employed show cartoon cartoon automatic default Customization 41 42 Customization cartoon cartoon cartoon cartoon cartoon cartoon tube tube 1 49 arrow 50 loo
15. expression is missing PyMOL will apply the command to all We ll keep our selection expressions short in this section If you name the selection you will be able to manipulate it any number of times Object and selection names may include the upper or lower case characters A a to Z z numerals 0 to 9 and the underscore character _ Characters to avoid include CS MEN E O A O O A ME o First name the selection SYNTAX select selection name selection expression EXAMPLES PyMOL gt select akeeper resi 1 10 Select the residues and name them akeeper Then use it SYNTAX zoom selection name hide representation selection name show representation selection name EXAMPLES PyMOL gt zoom akeeper Zoom in on them in the viewer PyMOL gt hide everything akeeper Hide their representation in the viewer PyMOL gt show spheres akeeper Show them in a different representation spheres this time When you create a selection name PyMOL puts it in the control panel so you can apply control panel functions to the selection using your mouse See the section titled PyMOL Command Language Named selections such as akeeper are manipulated like PyMOL objects but objects and named selections are fundamentally different Py MOL creates an object name to locate data when you load a data file Making selections is a way of pointing to a subset of that data To distinguish s
16. large maps of this format and then display arbitrary bricks of density within these maps about atom selections load PyMOL expects XPLOR CNS map files to have a xplor extension This requirement can be avoided by supplying an explicit type of xplor to the load command load 2fofc xplor mapl type inferred from the extension load 2fofc map map1 1 xplor type explicitly provided See help load or the reference section for additional information isomesh and isodot Map objects are used to store the data and are represented by a wire frame brick in space indicating the extent of the map An arbitrary number of mesh or dots objects can be created from a given map using the isomesh and isodot commands isomesh msh1 map1 1 0 display an isosurface mesh at level 1 0 over the entire map object mapl isomesh msh2 map1 1 0 chain A 3 0 display isosurface mesh at 1 0 in a brick about chain A with a border of 3 0 Angstroms See help isomesh or the reference section for additional information Electron Density Maps 56 Compiled Graphics Objects CGOs and Molscript Ribbons Introduction Although PyMOL uses OpenGL for all real time rendering the simple ray tracing engine inside of PPMOL is incapable of understanding arbitrary OpenGL calls Thus any graphics scene must be translated into a set of primitives spheres cylinders and triangles that can be provided to the ray tracer in order to generate high q
17. much easier While PyMOL can read Molscript output directly see the chapter on Molscript this is no longer necessary or as convenient as utilizing PyMOL s built in cartoon ribbon capability PyMOL built in ribbons molauto nice molscript r gt Molscript s cartoons are slightly more ideal but PyMOL comes pretty darn close Note that all of the images in this section were colored using the rainbow feature Color pop up menu and ray traced with antialising enabled Pretty and Correct One of the advantages of PyYMOL s cartoon ribbon facility is that it is easy to switch between smoothed versions of protein secondary structure and correct renditions which portray actual main chain coordinates Although cartoons are often used solely to represent protein structures in a schematic sense sometimes it is desirable to combine a schematic overall picture with atomic resolution in one particular location However unless the cartoon track properly with alpha carbon positions the resulting figures will look a little silly Cartoon Representations 38 In the above image the side chains are floating off into space Disabling flat sheets from the Cartoons Menu or issuing the command set cartoon_flat_sheets 0 will make the beta strands follow the true path of the backbone through space and give a more accurate rendition of the structure The appearance of a cartoon over the entire molecule will be substantially
18. on which operation is performed first They have an order of precedence To ensure that the operations are performed in the order you have in mind use parentheses byres chain a or chain b and not resi 125 around 5 PyMOL will expand its logical selection out from the innermost parentheses Atom Selection Macros Macros make it possible to represent a long atom selection phrase such as PyMOL gt select pept and segi lig and chain b and resi 142 and name ca in amore compact form PyMOL gt select pept lig b 142 ca An atom selection macro uses slashes to define fields corresponding to identifiers The macro is used to select atoms using the boolean and that is the selected atoms must have all the matching identifiers object name segi identifier chain identifier resi identifier name identifier Atom Selection Macros 35 These identifiers form a hierarchy from the object name at the top down to the name identifier at the bottom PyMOL has to be able to recognize the macro as one word so no spaces are allowed within it Macros come in two flavors those that begin with a slash and those that don t The presence or absence of a slash at the beginning of the macro determines how it is interpreted If the macro begins with a slash PyMOL expects to find the fields starting from the top of the hierarchy the first field to the right of the slash is interpreted as an object name the second field as an identifier to segi
19. software package cannot be easily surmounted and the same is still true for free programs which aren t available in source form Only open source software allows you to surmount problems by directly changing and enhancing the way software operates and it places virtually no restrictions on your power and opportunity to innovate For these reasons we believe that open source software is an intrinsically superior research product and will provide greatest benefit to computer assisted scientific research over the long term Launched over Christmas break in December 1999 PyMOL was originally designed to 1 visualize multiple conformations of a single structure trajectories or docked ligand ensembles 2 interface with external programs 3 provide professional strength graphics under both Windows and Unix 4 prepare publication quality images and 5 fit into a tight budget All of these goals have since been realized Although PyMOL is far from perfect and lacks such desirable features such as a general undo capacity it now has many useful capabilities for the practicing research scientist We hope that you will find PyMOL to be a valuable tool for your work and we encourage you to let us know what ideas you have for making it even better Words of Caution About the Manual This version of the manual has been updated for PYMOL version 0 86 January 2003 but is still quite rough Prepare yourself for omissions errors and potentially ob
20. the orientation of a molecule into a log file you need to give the command get_view type it or use the GUI button You may find it convenient to get_view several times in a PyMOL session and then edit the log file to select the most useful views Scripts can be executed in several ways Under Windows scripts can be run in a new PyMOL session by double clicking on the script s icon Alternatively you can run a script using the File menu s Run option PyMOL also understands as the typed command that loads a script SYNTAX Gscript file name EXAMP LE PyMOL gt my_script pml You can also include the script file name when launching PyMOL from a command line SYNTAX pymol script file name EXAMPLE Windows C gt pymol exe my_script pml EXAMPLE Unix unix gt pymol com my_script pml png Files Once you are satisfied with the representation and orientation of your molecule you may want to save the image in a graphics file Before you do that you can improve the quality of the graphics by switching from PyMOL s fast default graphics engine OpenGL to its ray tracer The ray tracer is slower but produces higher Scripts and Log Files 24 quality renderings for display and publication Ray tracing shows how light is reflected and how shadows fall in a three dimensional world Ray tracing may take some minutes for a large complex object The keyword ray calls PYMOL s raytr
21. updated June 2004 by Warren L DeLano Ph D Introduction 5 Installation Windows Recommendations e Windows 2000 or XP e A late model 3D OpenGL compatible graphics accelerator card from nVidia ATI 3Dlabs or similar e 512 MB RAM 768 MB or 1 GB preferred e 3 Ghz Pentium 4 processor or similar Minimal System Requirements e Windows 98 and ME or later PYMOL will not run on Windows 95 and NT e 3D OpenGL compatible graphics accelerator card e 256 MB RAM e 500 Mhz Pentium 3 processor Unless you have prior experience with Python we recommend installing a version of PyMOL which does not require an external Python interpreter Avoid versions of which contain py21 py22 py23 or similar in the filename Python Free Installation 1 Download the zip format archive For example pymol 0_90 bin win32 zip 2 Extract the zip file using WinZip Windows XP can open zip files directly 3 Double click on the Setup or Setup exe icon in the folder 4 Answer the questions which follow You can now launch PyMOL from the Start menu Python Dependent Installation If you already have Python installed and wish to use PyMOL with that interpreter the process is virtually identical The only difference is that you need to download a version of PyMOL which matches your desired Python version in the filename For example pymol 0_90 bin win32 py22 zip would work with available from Python 2 2 2 exe gt
22. when you want a fresh start in viewing the molecule It aligns the object or selection so its largest dimension is shown horizontally and its second largest dimension is shown vertically SYNTAX orient selection expression The selection is aligned for maximum visibility in the viewer You can store orientations and recall them later in your PYMOL session using the command view Storing a view only saves the viewpoint on the objects in the viewer It does not save their representation To store a view for later in the session you need to key it that is to give a name or number as an argument to the command view A second argument tells PyMOL whether you want it to store the view or recall it SYNTAX view key action The possible actions are store and recall EXAMPLES PyMOL gt view vl store The current view is named v1 and stored PyMOL gt view vl recall The view keyed v1 is restored PyMOL gt view vl recall is the default argument to view so this also recalls v1 The keyword view only stores an orientation for the duration of the current PyMOL session The next section gives the recipe for saving and restoring views in different PyMOL sessions Saving Your Work PyMOL saves your work in f kinds of processes 1 Before you give a series of commands you can initiate the process of logging your commands into plain text log files that can later be used as scripts 2 At any point ina PyMOL
23. 01 load_callback Callback objects are loaded into PyMOL using the load_callback function cmd load_callback object name state load_callback 62
24. 6 ca PyMOL gt show cartoon a PyMOL gt color pink pept b Atom Selection Macros identifier Residue 142 fills the viewer The alpha carbon of residue 156 is shown as a sphere Chain A is shown as a cartoon Chain B in object is colored pink pept 36 Selection macros must contain at least one forward slash in order to distinguish them from other words in the selection language Being words they must not contain any spaces When using macros it is also important to understand that they are converted into long form before being submitted to the selection engine This can help in the interpretation of error messages Calling Python from within PyMOL Single line Python statements can be issued directly within PyMOL For example PyMOL gt print 1 2 3 Full access is available to standard Python library functions and you can assign results to symbols PyMOL gt import time PyMOL gt now time time PyMOL gt print now 1052982734 94 Multi line blocks of Python can be included within PY MOL command scripts provided that a backslash NV is used for continuation on all but the final line PyMOL gt for a in range 1 6 PyMOL gt b 6 a PyMOL gt print a b 5 OB WN EF PN WSs Calling Python from within PyMOL 37 Cartoon Representations Background Accessibility Cartoon ribbons in PyMOL rival those of the popular Molscript Raster3D packages but PyMOL makes creating high quality images
25. L will pass the command on to the Python interpreter PyMOL will return a Python error message if neither a PyMOL nor a Python keyword is recognized Other Typed Commands and Help 27 Command Syntax and Atom Selections Syntax A typed PyMOL command always starts with a keyword that calls PYMOL to execute an action It ends with a carriage return enter on your keyboard The simplest commands consist of a keyword alone For example typing quit will end your PyMOL session The quit command never takes an argument Many commands have default arguments so you can type the keyword alone and PyMOL will supply the rest For example the default argument to zoom is the selection expression all EXAMP LE PyMOL gt zoom All visible representations are included in the view For some keywords certain arguments are required and others are supplied by default For example the keyword color requires one argument the color name As for zoom the default selection expression is all SYNTAX color color name color color name selection expression EXAMPLES PyMOL gt color red All the representations are colored red PyMOL gt color red name ca Only the representations of atoms named c alpha are colored red When you type a command that has more than one argument color color name selection expression in this case a comma must separate the arguments Selection expressions are an e
26. Makefiles with preinstalled system dependencies Because the installation process is often subject to change please see the INSTALL file from the current distribution for detailed instructions In summary 1 Download and extract the current PyMOL source distribution 2 Configure PyMOL by copying and modifying a Rules make from the setup directory to reflect your system 3 Run make to build pymol 4 Create a pymol com specific to your installation location You should be able to launch PyMOL by running pymol com and it may be convenient to add a symbolic link from this file into your bin directory as pymol This chapter last updated June 2004 by Warren L DeLano Ph D Dependency Based Approaches Getting Started with Mouse Controls Launching Using the Mouse On Windows Click on the Start menu follow it to Programs or All Programs on Windows XP and then release the mouse on PyMOL On Mac OSX native version Double click on the PyMOL icon in the Applications folder on your main hard drive Using a Command Line Various command line options can be included under both Windows and Unix to automatically open files and launch scripts See launching in the reference manual for more information on these options On Windows At the command prompt issue c program files delano scientific pymol pymolwin exe If PyMOL in installed somewhere nonstandard then use the correct drive letter and path On Unix L
27. PyMOL User s Guide written by Warren L DeLano Ph D with assistance from Sarina Bromberg Ph D Copyright 2004 DeLano Scientific LLC All Rights Reserved Table of Contents Copyright Notice and Usage Teri c sscsscsssssssssscsscsssssccsssscsssssssssscssccsseccsssscsssassssescssccssscsssessssssssssssssssssees 1 Copyright NOCE aeriene E E EE E ENE A age eae inte 1 Terms of Usage for the PYMOL User s Manual ecccceecccesececeeeeeseceesaeceaaeceeneeceeeeeaeceeaaeneaaeeeeeeeeaes 1 SETAE O A NN 1 O 2 Why Py MOT a E la Ar e ab atada 2 RASIKA RASI A ALDIRO tdt TT A a EI AEREO AE N AA 2 EOS A aa 3 Wed E ta RT vie e a 3 A NN 4 Welcome to Py MOL iia ii dais lid 4 Is PYMOL Free Sol Walla tii eee 4 MESS DUCA Tt oa RA A E A A NA A ds Loa 4 The DeL ano Scient eM aO A a Ea pabevabovansvee 4 Installation E E T E E T E E E A E A N E E E E E E ET 6 WI WS irritabilidad eie aae ea eE 6 RRECOMMEN ELRO SEAR E E E E TEE EEE AE EE A 6 Minimal System Requirements ecccceccecesecesseceeseeceeeceseececeseeesaeceesaecseaeceeceecsaeecaeeeeaaeceaaeceeaeeeneees 6 Python Fr Installation ici in eae ee ede ae da 6 Python Dependent Installation iiine one nari ii o EE a aE ea ieee aea 6 ETEO E E TN 6 REGCOMIMENG AL ONS cdi eoa 7 Minimal REQUIEM ii ida 7 TEO USE Fink enesis a ne ena ee E tia hiesiiiade 7 TE VOU domotuse EDk radeon a oaee ei araa A aaa Eiaa R E aaa tiee Er 7 trv Kia TH i TD AEE A E AS EA 8 SystemREquire
28. acer to redraw and display the image in the view window See the section titled Ray Tracing for more details To save an image to a file raytraced or not use the Save Image option in the File menu or type the png command SYNTAX png file name EXAMP LE PyMOL gt png SPYMOL_PATH pep The file nam xtension jpeg is added The image file pep jpeg is stored in a path below the PyMOL installation The PNG file format is directly readable by PowerPoint It can be converted into other formats using a package like ImageMagick Session Files If you want to be able to return to the current state of PYMOL then you can create a session file Choose Save Session in the File menu and respond to the dialog box by naming the file with a pse file name extension This utility works like the Save utility in a word processing program A PyMOL session file is a symbolic record of the state of PyMOL s memory including the the objects that have been loaded or created the named selections that have been created and the display in the viewer When you open the saved session file PyMOL s memory returns to the state that was saved Because a session file represents a PyMOL memory state opening one means that you are eliminating everything that you currently have in PyMOL s memory and replacing it with the memory state from the session file A session file differs from a log file or a script in a n
29. aded from Protein Data Bank HETATM records visible ov All atoms in enabled objects with at least one visible representation All atoms with defined coordinates in the current state used in creating movies present pr The selector none won t come up much when you are typing commands directly into PYMOL but it is useful in programming scripts As the table shows many single word selectors have short forms to save on typing Some short forms must be followed by a period and a space in order to delimit the word Short forms and long forms have the same effect so choose the form that suits you EXAMPLES PyMOL gt color blue all It all turns blue PyMOL gt color blue PyMOL gt hide hydro Representations of all PyMOL gt hide h hydrogen atoms are hidden PyMOL gt show spheres hetatom All the atoms defined as HETATOMS PyMOL gt show spheres het in the PDB input file are represented as spheres Property Selectors PyMOL reads data files written in PDB MOL SDF Macromodel ChemPy Model and Tinker XYZ formats Some of the data fields in these formats allow PyMOL to assign properties to atoms You can group and select atoms according to these properties using property selectors and identifiers the selectors correspond to the fields in the data files and the identifiers correspond to the target words to match or the target numbers to compare The items in a list of identifiers are separat
30. al view using a two dimensional sheet of paper To achieve a satisfying 3D effect care must be taken to insure that the stereo pairs are generated with the proper transformation and printed with the correct separation between images A key challenge in preparation of stereo figures is the fact that journals usually shrink images before they are printed In preparing your figure it is essential that your drafts correspond to the final printed size You may need to obtain this information from the journal ahead of time Stereo 48 Movies Concepts States and Frames PyMOL has a powerful and unique molecular movie making capability In order to use it you first need to understand a few key concepts e States States most directly correspond to particular arrangements of atoms at a point in time For example they could consist of steps in a molecular dynamics simulation or individual points of a coordinate interpolation If you are making a movie of a static coordinate set such as a single crystal structure then you have only one state All objects in PyMOL can potentially consist of multiple states e Frames Frames are like the individual images you d find on a movie reel except that in PyMOL frames are composed of states instead of images and frames can have additional actions associated with them such as rotation of the camera The user can fully interact with models while movies are playing NOTE State and frame indexes be
31. and if called without any arguments will attempt to create a distance object between the lb and rb selections if they exist define lb by CTRL SHIFT left clicking one atom define rb by CTRL SHIFT right clicking another dist will create a distance object between the two atoms Conformational Editing Sorry no documentation yet these features won t be too useful until PYMOL is coupled up with an energy minimiation engine Conformational Editing 54 Crystallography Applications Crystal Symmetry Ralf Grosse Kunstleve has provided his SgLite module to enable PYMOL to deduce symmetry relationships from standard space group and unit cell information Currently that information can only be provided to PyMOL as a CRYSTI record in the PDB file which includes the correct space group identifier However it would be only a minor development task to add a means of assigning unit cell and symmetry to any molecule object directly from the API The format of the CRYST1 record is as follows Ll 6 Record name CRYSTI Po 15 Real 9 3 a a Angstroms 16 24 Real 9 3 b b Angstroms 25 33 Real 9 3 c Angstroms 34 40 Real 7 2 alpha alpha degrees 41 47 Real 7 2 beta beta degrees 48 54 Real 7 2 gamma gamma degrees 56 66 LString sGroup Space group 67 70 Integer Z Z value ignored by PyMOL load When you use the load command to read in a PDB file with symmetry informat
32. command name gt for information on a specific command s zoom Rey Rock Hit ESC anytime to toggle between text and graphics noi Hite Sale Get viw zilie efa rr gt gt 1 cios a The default Tcl Tk External GUI included with PyMOL By default PyMOL comes with a single external GUI window which provides a standard menu bar an output region a command input field and a series of buttons One important advantage of the external GUI window is that standard cut and paste functions for text will only work within the External GUI and not within in the PyMOL Viewer Furthermore you must use Ctrl X Ctrl C and Ctrl V to cut copy and paste because a standard Edit menu has not yet been implemented Notes For Developers External GUIs are the foundation for modularity and customizability in the PPMOL system These windows constitute independent processes or threads which can control the behavior of PyMOL and potentially interact with other programs They are completely customizable at the Python scripting level and mutiple external GUIs can exist at once within the restrictions of Tkinter and wxPython External GUIs communicate with PyMOL through the Python API Application Programming Interface Those of you who want to link up you own programs with PyMOL should generally use a separate external GUI window to control the interaction rather than changing internal PYMOL code That way the programs will continue to wor
33. d its backbone atoms are yellow You can also use the disable command to get rid of the pink dots that identify the last named selection in the viewer SYNTAX nable selection nam EXAMPLE PyMOL gt select bb name c o n ca Atoms included in the named selection are indicated with pink dots in the viewer PyMOL gt disable bb The pink dots disappear but the named selection bb is still visible PyMOL gt color red bb You can still manipulate bb You can still operate on the representations of objects that are disabled even with the commands show and hide The results will be apparent when you subsequently enable the object Turning Objects and Selections On and Off 22 Changing Your Point of View Dragging on a molecule with the mouse is often the easiest way to manouver but typed commands such as zoom and orient give you a different form of control allowing computations to direct the view zoom as the name suggests brings an object or selection close up in the center of the field of view If the object or selection doesn t fit in the current view the view opens out to include it If it is just a small part of the current view the view closes in to fill more of the screen with it SYNTAX The camera moves close to the selection so it fills the viewer or moves further away to include all of the selection in the viewer zoom selection expression He de Se HE orient is a useful command
34. eating Compiled Graphics Objects Compiled graphics objects contain equivalents to the normal line and triangle primitives found in OpenGL but also include primitives for spheres and cylinders At the Python level compiled graphics objects are constructed as a simple linear list of Python floating point numbers which is conceptually equivalent to an OpenGL stream from pymol cgo import get constants from pymol import cmd obj BEGIN LINES COLOR 22070 LB L Oy VERTEX 0 0 0 0 0 0 VERTEX 1 0 0 0 0 0 END cmd load_cgo obj cgo01 CGOs support the standard OpenGL BEGIN END formalism as well as a few stand alone primitives SPHERE CYLINDER and TRIANGLE which should NOT appear within a BEGIN END block Creating Compiled Graphics Objects 58 CGO Reference A CGO is simply a Python list of floating point numbers which are compiled by PyMOL into a CGO object and associated with a given state Lowercase names below are should be replaced with floating point numbers Generally the TRIANGLE primitive should only be used only as a last restore since it is much less effective to render than using a series of vertices with a BEGIN END group BEGIN POINTS LINES LINE_LOOP LINE _STRIP TRIANGLES TRIANGLE_STRIP TRIANGLE_FAN VERTEX xX Y Zy COLOR red green blue ORMAL normal x normal y n
35. ed and launched The advantage of using this version is that it is fully compatible with Open Source PyMOL and does not require Fink However unlike MacPyMOL this version does not support direct export of QuickTime movies This binary build is free but not Open Source 1 Download the pymol O_XX bin osx x11 hybrid dmg gz compressed disk image 2 Extract the archive and mount the disk image 3 Copy the PyMOLX11Hybrid folder to the main Applications folder on your hard disk You can then launch PPMOLX11Hybrid by double clicking on the PYMOLX11Hybrid icon Recommendations 7 Linux and Unix System Requirements e 3D OpenGL graphics acceleration There are a several different ways to install PYMOL on Linux Please consult the PYMOL Web Site for additional information Dependency Free Approaches These do not require installing any other packages in a privileged location on your system All you need to do is download a tar ball appropriate for your system such as the following e pymol 0_93 bin linux libc6 i386 tgz for Linux e pymol 0_93 bin 1rix65 r10k tgz for SGI e pymol 0_93 bin solaris8 sun4u tgz for Solaris issue the following commands gunzip lt pymol bin tgz tar xvf setup sh which will install the program and then pymol com will launch PyMOL You may then want to make a symbol link for this file to bin pymol for easy launching ln s PWD pymol c
36. ed by plus signs only Do not add spaces within a list of identifiers The selector resi takes separated lists of identifiers as in EXAMP LE PyMOL gt select nterm resi 1 2 3 or alternatively 1t may take a range given with a dash EXAMP LE Single word Selectors 31 PyMOL gt select nterm resi 1 3 However you will get an error message if you try to combine a list and a range in an identifier to a resi as in select mistake resi 1 3 6 The identifier for a blank field in an input file is and empty pair of quotes EXAMP LE PyMOL gt select unstruct ss A named selection is created to contain all atoms that are not assigned a secondary structure Most property selectors select matches to their identifiers Matching Property Selector Short Form Identifier Selector and Example chemical symbol list list of 1 or 2 letter chemical symbols from the periodic table PyMOL gt select polar symbol o n atom name list list of up to 4 letter codes for atoms in proteins or nucleic acids PyMOL gt select carbons name ca cb cg cd residue name list list of 3 letter codes for amino acids PyMOL gt select aas resn asp glutasn gln or list of up to 2 letter codes for nucleic acids PyMOL gt select bases resn atg residue identifier list list of up to 4 digit residue numbers PyMOL gt select mults10 resi 1 10 100 1000
37. election names from object names selection names are shown inside parentheses in the control panel Manipulating Objects 20 When you delete a selection name the data are still found under the object name but the data are no longer organized as the selection In contrast after you delete an object you must reload the data to have access to it again SYNTAX delete selection nam delete object nam EXAMPLES PyMOL gt delete akeeper akeeper is gone but the object remains PyMOL gt delete pept The atoms and bonds in pept are gone Coloring Objects and Selections You can apply various colors to selections and objects using typed commands Predefined color names are listed under the settings colors pull down menu Many of them can be chosen from the control panel See the section titled Settings to find out how to define more colors SYNTAX color color name All the representations of loaded objects are colored color color name selection expression The representation of the selection is colored EXAMPLES PyMOL gt color white Everything turns white This looks fine on the default black background but causes disappearance if you ve changed the background to white PyMOL gt color orange pept Remember that pept is our object name so the entire object is colored orange PyMOL gt color green resi 50 54 58 The representation of residues numbered
38. gin with 1 and not 0 as most C and Python programmers would expect If you load states into an object with a state index of 0 you are indicating that you want the state to be appended after the last existing state in the object Important Commands To Know load The load command is used to populate states of an object By default each new file loaded will be appended onto the object s states However the optional third argument to the load command is the frame index into which the file should be loaded See help load or consult the reference section for more information load fool pdb mov loads fool pdb into state 1 of mov load foo2 pdb mov loads foo2 pdb into state 2 of mov load foo3 pdb mov 3 loads foo3 pdb into state 3 of mov load foo4 pdb mov 4 loads foo4 pdb into state 4 of mov mset The mset command is used to specify which states get included as frames of a movie If the mset command is not used PYMOL will by default play through all states in sequential order However if you wish to use the other movie commands such as mdo it is necessary to explicity use the mset command to create a movie definition inside of PyMOL The mset command is followed by an arbitrarily list of statements which defines the entire movie Each statement takes on one of three forms 1 A number simply indicates a state is to be played next Movies 49 Wow 2 x A lowercase x immediately followed by a number no
39. gt molauto nocentr nice 3all pdb molscript r gt test2 r3d You can load both PDB and ribbon files directly into PyMOL as separate objects load 3all pdb loads the coordinates load test1l r3d loads molscript ribbon Molscript Input Files Unfortunately PYMOL does not have the ability to write molscript input files which reflect the current atom Compiled Graphics Objects CGOs and Molscript Ribbons 57 colorings and visibilities Therefore you will need to get in the habit of manually editing Molscript input files in order color and customize ribbons appropriately Here are some tips 1 Remove any line starting with transform atom from existing Molscript input files in order to preserve the frame of reference For example transform atom by centre position atom 2 For performance reasons you may want to set the segments to a small number while working with Molscript ribbons in real time Later on you can increase this number recreate and reload the r3d files set segments 2 good for real time graphics set segments 8 good for rendering The easiest way to create new ribbons using PyMOL is to use the save command to write out a PDB file containing the atom selection of interest You can then apply the system command to run molauto and molscript and then load the Raster3D file back into PyMOL save tmp pdb chain C system molauto nocentre tmp pdb molscript r gt tmp r3d load tmp r3d Cr
40. he file pept pdb create and name a corresponding object display a representation of the object in the viewer and add the object s name to the control panel By default PyMOL names the object after the file it read You can assign a different name to the object by typing the name in the command line SYNTAX Getting Started with Commands 18 load data file name object nam EXAMPLES PyMOL gt load SPYMOL_PATH test dat pept pdb The object is named pept PyMOL doesn t use the file nam xtension pdo in the object name He de He Se PyMOL gt load SPYMOL_PATH test dat pept pdb test The object is named test Note that is a comment character so anything you type to the right of in a command line is not interpreted by PyMOL The command for loading a file follows typical PyMOL syntax load is a keyword it calls PyMOL to perform a certain function data file name and object name are arguments to load These arguments tell PPMOL what file to load and what to name it but in general arguments to keywords just supply information that PyMOL needs to carry out commands Manipulating Objects After PyMOL creates an object you can manipulate it in the view window and control panel with your mouse and also by typing commands For example you can change from the default representation called lines to the more hefty sticks First get rid of the lines and then show the sticks SYNTAX hide re
41. included in the selection All of these selections can be used and manipulated as if they were created manually using the select command Note however that these selections are quite fragile and will be automatically deleted in response to a number of common occurences such as loading a new object Example Usage of the pk Atom Selections Assuming that you picked an atom or bond show sticks pkresi show sticks on the residue you picked color read pkchain color the chain you picked remove byres pxkl removes all atoms in the residue you picked The Ib and rb Selections Most of the time the pk1 atom selection will suffice However there are times when you need to specify two or more sets of atom selections This is where Ib and rb come in In addition to the pk atom selection set there are two more atom selections which can be manipulated with the mouse These are 1 the left button or Ib selection and 2 the right button or rb selection Under the Advanced Mouse Controls 53 default mouse configuration e The Ib selection can be redefined using the Ib function which is CTRL SHIFT left click e The Ib selection can be expanded using the 1b function which is CTRL left click e The rb selection can be redefined using the rb function which is CTRL SHIFT right click Certain commands are designed to use lb and rb as default arguments For instance the distance comm
42. inux and MacOS X Fink version If you installed using using a package such as an RPM then there is a good chance that pymol is already in your path If not then edit pymol com in the PyMOL distribution and make sure PYMOL_PATH points to the actual location of the distribution Enter pymol com to start pymol You will probably want to create a link pymol from this file in to a bin directory in your path so that you can launch the program anywhere by simply entering pymol Getting Started with Mouse Controls 10 PyMOL s Windows PyMOL normally starts with two windows The Viewer Window and the External Tcl Tk GUI Window aini x De Qi Pregeres eote Me Reie Qiy Setting Mase Corton werd Som Cer OC Gym ra 0 0000 7 ee Vo a Symmetry to de 00 E nd E a n A ma Sym rs y uvu0O i eE E mm E 5 mtrs di otoso oo YA 000 Sa L ose Sm e symmetry o WA S 00 Executive abject ize createn 5 23712 Ae Oe Internal GUI HARE ee N PyMOL s two windows GUL is an abbreviation for Graphical User Interface which usually consists of menus buttons text boxes and other familiar gadgets By default PyMOL actually has two GUI s 1 an Internal GUI which appears inside the Viewer Window and 2 an External GUI which appears inside of its own window The reasons for this are boring and technical but know that both GUI s will eventually be unified into a single interface in the future The
43. ion matrix information should be output Verify that this information is produced before attempting to display symmetry related molecules symexp The symexp command is used to display symmetry related molecules in the crystal lattice about an atom selection This commands creates a set of new objects with a common prefix Each object in the series corresponds to one symmetry related object which can be treated independently See help symexp or the reference section for usage information In order to visualize only symmetry related atoms within a given distance you need to break the process down into two steps First you use the symexp command to create complete symmetry related objects Then you use hide commands to restrict what is visible to only those areas which you are interested load foo pdb load PDB file with CRYST record symexp sym foo foo 5 0 Create symmetry related foo objects which pass within 5 angstroms of foo using the prefix sym hide not foo expand 5 hide atoms greater than 5 A from foo NOTE The symexp command can potentially create large numbers of objects You will want to use the delete command with a wildcard to remove all objects that share a common prefix delete sym deletes objects starting with sym Crystallography Applications 55 Electron Density Maps The only map file format currently supported is the CNS and XPLOR ASCII format map file PYMOL can read
44. is 41 A O OaE EET 41 Fancy Heladio idilio liarla cis 44 Secondary Structure AssSignMm nt cavovonoconedinc oe sovdecescvastaacsdande ccdesetecdedehe avenedecteustesssdcdeesteeasas 45 A O O E 46 NAS IN O 46 SAVIN SIMA GES it Aa AA A A A A E 47 A RO NN 47 A O ERE E O A S T 48 THEO Ni LenS E AATE EEA E E E EA EEEE EEA A EE AEREE 48 Supported Stered Modes raa ae a a a a TEERDE DE EEEE ADNE EDO EEAS ENEE AE EEAS N ESSEN EEN 48 CTOSSEVE Stered ton ai e Gels de teins li 48 Walleye Stereo us lt de Le e Ate E cela e canteen a 48 Hardware OO a E A A MIS A N E E 48 Table of Contents Stereo Generating Stereo UE A Add 48 I EA AEN IIA NRE EOE I I IOE ON OOT N EE IIO NOE EO E O A NE ONE T 49 Concepts A a 49 States and FAME a Ba EA LO ARE BAO ES 49 Important Commands To Kn0w c cccccccesscessececeeecesaeceesaeceececeeeeecaeeesaecseaaeceaeeceeeeeeeeeeaaeceeaaeneaeeeeeeeees 49 A RAN 49 O 49 M A A A A A A A 50 MO erie eein e ieee nals ieveaceddisasieaesesessaged a E N AEE EEE EE EEE ETEA 50 SIMple Example Sai a e e ce 50 Complex Example Si inna aaea e aO EO ae 51 Previewing Ray traced Movie Images eececccessseeesseceesceceececseeeeeeceeaaeceeaceseeeeceaeeeaeeseaaeceeaeceeaeeeaees 51 cache TAME io e e a LA E AAA SNA A E a Eea is 51 MCARTE NEA 51 SAVING MOVIES an id isla sates 51 atrial Ten URLS ES AE A A A IA E AI ES 52 Advanced Mouse Control seceisssceccissctecesceinedsctacsiesveecessvcevesscncccesscsdecesceccessuceesstecsesssucses
45. jects see previous section Callback objects are trivial Python objects which have a __call__ method for rendering and a get_extent method which tells PyMOL where in space the object is located Once a callback object has been loaded into PyMOL Python will automatically call this object when needed to update the screen PyMOL includes a copy of PyOpenGL under the pymol module hierarchy pymol opengl but usage of this copy is of course optional You can instead bind to the latest version without problems provided that you install it yourself into the Python library that PyMOL is using by default NOTE The current Window s version of PyMOL does not include Numeric which makes heavy usage of PyOpenGL from within PyMOL impractical under Windows at present Example The following Python program shows how you can use a Callback object within PyMOL to perform rendering using OpenGL For more examples see the directory PYMOL_PATH examples devel from pymol opengl gl import from pymol callback import Callback from pymol import cmd class myCallback Callback def __call_ self glBegin GL_LINES glColor3f 1 0 1 0 1 0 glVertex3f 0 0 0 0 0 0 glVertex3f 1 0 0 0 0 0 glVertex3f 0 0 0 0 0 0 glVertex3f 0 0 2 0 0 0 glVertex3f 0 0 0 0 0 0 glVertex3f 0 0 0 0 3 0 glEna def get_extent self Callback Objects and PyOpenGL 61 return 0 0 0 0 0 0 1 0 2 0 3 0 cmd load_callback myCallback gl
46. k together even while development on each program proceeds independently The internal GUI and all external GUI windows can be enabled and disabled using simple command line options see reference for launching The External GUI Window 12 Loading PDB Files Using the External GUI Menu The default external GUI provides a standard Open item in the File menu which you can use to select the file you wish to open Using Commands SYNTAX load lt filename gt EXAMP LE load test dat pept pdb zina De Cit Pregreri Pape Mme Petcare Qiy Seg Mase Cartoon Merd Sabiny Dero te TIEL WIT ESC atytire to teggle benseen text and grapiics Executive abject pept created PyMOL after loading a PDB file Manipulating the View In PyMOL the mouse is the primary control device and keyboard modifier keys SHIFT CTRL SHIFT CTRL are used in order to modulate button behavior A three button mouse is required for effective use of PYMOL but common mice such as the Microsoft Intellimouse and Microsoft Wheel Mouse will work just fine under Windows Basic Mouse Control On mice with a scroll wheel you can push down on the wheel in order to use it as a middle button Loading PDB Files 13 i Here is a table of the basic mouse button keyboard combinations for view manipulation Keyboard Modifier Virtual Trackball In Plane of Screen Scale hift Key ontrol Keys ontrol and Shift Keys
47. lag util mroll start finish loop flag mmatrix The mmatrix command allows you to store and recall a particular viewing matrix to be used to set up frame 1 of the movie This can be particularly helpful when you re trying to preserve a movie s orientation while performing other actions within PyMOL during the same session See help mmatrix or the reference section for more information Simple Examples Here a static structure is subject to a gentle rock The following statements create a sixty frame movie which simply rocks the protein by 10 degrees load test dat pept pdb load a structure mset 1 x60 define the movi util mrock 1 60 10 1 1 issues mdo commands to create 10 deg rock over 60 frames In this next example the protein is rotated through a full 360 sweep about the Y axis over 120 frames load test dat pept pdb load a structure mset 1 x120 define the movi mdo 50 util mroll 1 120 1 issues mdo commands to create full rotation over 120 frames Complex Examples The following is a Python program with a py or pym extension which uses a Python loop to load a large number of numbered PDB files and then configures PyMOL to show them both forwards and backwards from glob import glob from pymol import cmd file_list glob mov pdb for file in file_list cmd load file mov cmd mset 1 d 2 Slen file_list Previewing Ray traced Movie Images PyMOL has the ability to cache
48. ligeatn dian ada aine ei Gae 61 load call back a a NG 62 Copyright Notice and Usage Terms Copyright Notice The PyMOL User s Manual is Copyright O 1998 2004 DeLano Scientific LLC San Carlos California U S A All Rights Reserved Terms of Usage for the PyMOL User s Manual This manual is NOT free It is a PyMOL Incentive Product created to help you use the program while also generating recurring sponsorship for the project This manual is made available for evaluation via the honor system You may evaluate this manual for a continuous period of up to one year without obligation If you wish to continue using this document beyond the end of the evaluation period then you must become a sponsor of the project by purchasing a PYMOL license and a subscription to maintenance and support from DeLano Scientific LLC http www delanoscientific com Of course if you are willing to sponsor the project today then please don t wait a full year to start The sooner your sponsorship comes in the sooner we can apply it to improve the software and documentation Existing PyMOL subscribers may use this manual for no additional cost However subscribers who do not renew their subscription upon expiration must discountinue use of this and all other PyMOL Incentive Products Though we have no direct means of enforcing this we ask in recognition of our_declared scientific mission that you honor the trust placed in you PyMOL users who are unable t
49. m However we just hope to appropriately calibrate your expectations with respect to the code you will find if you with to dive under to hood Though the Preface 2 program is Open Source it is best thought of as a dense semi opaque tool best extended through Python rather than as a C coding environment in which to embed new technologies Strengths e Cross Platform A single code base supports both Unix Macintosh and Windows using OpenGL and Python and a small set of Open source external dependencies e Command Line and GUI Control Real world applications require both e Atom Selections Arbitrary logical expressions facilitate focused visualization and editing e Molecular Splits Joins Structures can be sliced diced and reassembled on the fly and written out to standard files i e PDB e Movies Creating movies is as simple as loading multiple PDB files and hitting play e Surfaces As good if not better than Grasp and mesh surfaces are supported too e Cartoon Ribbons PyMOL s cartoons are almost as nice as Molscript but are much easier to create and render e Scripting The best way to control PyMOL is through reusable scripts which can be written in the command language or in Python e Rendering A built in ray tracer gives you shadows and depth on any scene You also render externally e Output PNG files output from PyMOL can be directly imported into PowerPoint e Conformational Editing Click and drag interface
50. ments ienne a egies eae a a a E esas 8 Dependency Eree Approaches cocida aladdin cid dsd 8 Dependency Based Approaches si oi oeii a e E EE E a EE 9 Getting Started with Mouse Controls 10 Daun Ching RAR 10 Using the MOUSE rr Matec shedeteu canta A eaa iEn a aan 10 Using a Command ime tii sidan Geass ins Gea eu aw Sema nai 10 PYMOL s WindoWS ina is 11 The Viewer WINGO Wis nccsses core tale tc Ed ANA edi 11 The External GUI Window ides cess ciccciessscssvuscvoscocdevtu vets voohutetvenudaesnediavebonevehencveredvesssacsenedvartentangeicanes 12 Loading PDB Fleitas sao 13 Manipulating the Vie Wii di aos 13 BasicyM Ouse Controlan bla it le rside 13 Virtual Trackball Rota A io a e A a A Erais 14 Moving Clipping Planes niinen ereot lea EREDE EEE eraka es aun mien eae 16 Changing the Origin Of Rotation sissien cinere iinn dnd ioa eanes r reisas E iEn eS ens 16 Gettine Comfortabler iine da a N a at ads de 17 Table of Contents Getting Started with Commannd ccssccsssscsssscsssscssssssssssssescssessssscssesssssesssssessssesssssssssssssssssssasssssaccssaes 18 Recording Your Work Optional aeei ea ia Ea ia ore pe EEE EER N TE A ETEK SEa 18 Loading DETE RET EE E E T EE 18 Manipulating Obra Ac 19 Atom ECONO SA A A LONER 19 Coloring Objects and Selections nsii inene i i aa E n r i aao 21 Turning Objects and Selections On and Off ceccceesccecssecesseceeeecseneceeeeecsaeessaecseaaeceaaeceeeeeeses 22 Changing You
51. mplex combinations of selectors using macros and short forms Named Atom Selections Atom selections can be named for repeated use by using the select command SYNTAX select selection name selection expression Th selection name and th selection expression are both arguments to select so they are separated by a comma EXAMPLE Create an atom selection named bb including all atoms named MEMO NA Or CAN color the selection red hide the line representation show it using the stick representation and zoom in on it PyMOL gt select bb name c o n ca PyMOL gt color red bb PyMOL gt hide lines bb PyMOL gt show sticks bb PyMOL gt zoom bb Se od de e de e In this case the selection expression is the property selector name which takes the list of identifiers ca c n o to complete the specification Property selectors and their identifiers are discussed below Named atom selections appear in the PyMOL names list in the control panel They are distinguished from objects by a surrounding set of parentheses The control panel options available under the diamond menu differ between objects and atom selections because objects and named selections play slightly different roles in PyMOL Named selections are pointers to subsets of data that are found under an object name After an object is deleted the data are no longer available unless you reload the object Any named selections that
52. ng paths and filenames PyMOL makes it easier to load such files by automatically completing unambiguous paths and filenames when you hit the TAB key For instance EXAMP LE PyMOL gt load cry If crystal pdb exists in the current directory hitting TAB will generate PyMOL gt load cystal pdb If there is some ambiguity in the filename PyMOL will complete the name up to the point of ambiguity and then print out the matching files in the directory Automatic Inferences There are a small number of fixed string arguments to PPMOL commands For example in PyMOL gt show sticks sticks 1s a fixed string argument to show Because there is only a small set of such arguments to show PyMOL will infer your meaning even if you only provide it with a few letters For example PyMOL gt show st works just as well Keywords are also inferred in this manner so PyMOL gt sh st works too as long as show is the PYMOL only command starting with sh Command Completion using TAB 26 NOTE PyMOL s command language continues to grow and develop so it is important to use full length commands and string arguments in scripts Otherwise you could not be sure that a later command or argument would not cause your abbreviation to become ambiguous For example sh st would no longer work if a shutoff command were added to the PyMOL language Other Typed Commands and Help This Getting Started section used the most frequent
53. o sponsor the project by purchasing a PyMOL license and maintenance subscription are welcome to use Open Source versions of PyMOL and any free documentation that can be found on the internet Trademarks PyMOL DeLano Scientific and the DeLano Scientific Logo are trademarks of DeLano Scientific LLC Macintosh is a registered trademark of Apple Computer Inc registered in the U S and other countries Windows is a registered trademark of Microsoft Corporation in the U S and other countries Linux is a trademark of Linus Torvalds Unix is a trademark of The Open Group in the U S and other countries MolScript is a trademark of Avatar Software AB All other trademarks are the property of their respective owners This chapter last updated June 2004 by Warren L DeLano Ph D Copyright 2004 DeLano Scientific LLC All rights reserved Copyright Notice and Usage Terms 1 Preface Why PyMOL PyMOL is one lone scientist s answer to the frustration he encountered with existing visualization and modeling software as a practicing computational scientist Anyone who has studied the remarkable complexity of a macromolecular structure will likely agree that visualization is essential to understanding structural biology Nevertheless most researchers who use visualization packages ultimately run up against limitations inherent in them which make it difficult or impossible to get exactly what you need Such limitations in a closed source commercial
54. om bin pymol Install a minimal dependency binary build Compile PyMOL from source along with the ext dependencies distribution Because the installation process is often subject to change please see the INSTALL file from the current distribution for detailed instructions In summary 1 Download extract configure and compile the external dependencies 2 Download and extract the current PyMOL source distribution 3 Create a symbolic link from the external dependencies to ext in the PyMOL directory 4 Configure compilation by copying and modifying a Rules make from the setup directory to reflect your system 5 Run make to build pymol 6 Create a pymol com specific to your installation location You should be able to launch PyMOL by running pymol com I usually symbolic link this file into my bin directory as pymol Linux and Unix 8 Dependency Based Approaches You must install the following packages on your system python 2 x tcl 8 x tk 8 x libpng 1 x zlib 1 x glut 3 x glut devel 3 x pmw and numeric numpy not required for RPM packages You then have several choices Using RedHat binary packages RPMs rpm i pymol 0 90 1 rh73 py22 i386 rpm Using Python s distutils to compile and install PyMOL as a standard Python module python setup py build as a user python setup py install as root python setup2 py install as root You can now run PyMOL with pymol com Using
55. onds to them The details of command syntax are in the section titled PyMOL Command Language The PyMOL language is case sensitive but upper case is not used in the current package So just remember to type all your commands in lower case Recording Your Work Optional While you are learning PyMOL or doing complex projects you may want to keep a record of all the commands you give in a plain text log file that you can read and edit To open a log file type the command log_open followed by a file name SYNTAX log_open log file nam EXAMP LE PyMOL gt log_open logl pml All your commands typed or clicked will be recorded in the log file You should give your log file name the extension pml so you can load the file as a script to repeat your commands in a new session see the subsection titled Sessions and Scripts below To stop recording your commands type log_close If you don t type log_close before you exit PyMOL your log file will still be saved to disk If you just want to save the current state of your PyMOL work without concern for the steps you took and the commands you gave you can create a session file see Sessions and Scripts Loading Data Next you need to input your data from a file say atomic coordinates in PDB format SYNTAX load data file name EXAMP LE PyMOL gt load SPYMOL_PATH test dat pept pdb Given this command PyMOL will open and read t
56. ormal z END LINEWIDTH line width WIDTHSCALE width scale for ray tracing SPHERE X y Zz radius uses the current color CYLINDER xl yl zl x2 y2 z2 radius redl greenl bluel red2 green2 blue2 TRIANGLE xb yl Zl 27 NN Zig 22 x3 V3 23 normal x1 normal yl normal z1 normal x2 normal y2 normal z2 normal x3 normal y3 normal z3 redl greenl bluel red2 green2 blue2 red3 green3 blue3 load_cgo CGO lists are loaded into PYMOL using the load_cgo function cmd load_cgo list name state Arbitrary 3D animations can be created by loading CGOs into consecutive states of a given object The example below is a static image from the examples devel cgo03 py cgo animation demonstration program CGO Reference 59 CGO Reference 60 Callback Objects and PyOpenGL This is mainly a developer s function so most users can skip this section You will need some Python knowledge to understand the example Introduction Athough all OpenGL rendering in PyMOL is perfomed at the C level PyOpenGL provides an alternative binding of the OpenGL API from Python Unfortunately it is impossible for PYMOL to produces ray traced images of objects rendered using PyOpenGL Nevertheless PyOpenGL can be used within PyMOL via Callback objects for pure OpenGL based rendering pursposes If you need your graphics to ray tracable then you should use Compiled Graphics Ob
57. p 100 oval 150 rect 200 Customization 99 149 199 250 43 All cartoon ribbons have associated parameters accessible from the set command which allow you to change their appearance See the chapter on Settings for more information Fancy Helices set cartoon_fancy_helices 0 Molscript addicts who simply must have those ribbon helices with tubular edges will not be disappointed with fancy helices set cartoon_fancy_helices 1 Fancy Helices 44 Secondary Structure Assignment It is recommended that you read in PDB files which already have correct secondary structure assignments from a program like DSSP However PyMOL does have a reasonably fast secondary structure alignment algorithm called dss Please be aware that due to the subjective nature of secondary structure assignment in borderline cases dss results will differ somewhat from DSSP SYNTAX dss selection EXAMPLE dss ldfr If you are visualizing an animation you may wish derive secondary structure assignment from a specific state of the animation This can be done with SYNTAX dss selection state EXAMP LE dss mov 1 To change assignments manually the best way is to use the alter command as follows show cartoon alter 11 40 ss H alter 40 52 ss L alter 52 65 ss S alter 65 72 ss H rebuild assign residues 11 40 as helix assign residues 40 52 as loop assign residues 52 65 as
58. png mov0002 png etc If you are compressing movies using Adobe Premiere recommended for best quality you will probably want to convert the files using ImageMagick or a similar package into a format that Premiere is capable of reading such as tga targa format mpng 52 Advanced Mouse Controls Picking Atoms and Bonds The current mouse confiruation is visible on the lower right hand corner of the screen as a matrix Under the default mouse configuration e In Viewing Mode A single atom can be picked using the Pk1 function which is CTRL right click Multiple atoms up to 4 can be picked in series using the PkAt function which is CTRL right middle e In Editing Mode A single bond can be picked using the PkTB function which is CTRL right click 4 Multiple atoms up to 4 can be picked in series using the PkAt function which is CTRL right middle Whenever an atom or bond has been picked a number of atom selections are automatically defined as described in the following table e pk1 The selected atom or the first selected atom in a bond selection e pk2 The second selected atom in a bond selection e pkfrag A fragment of the molecule with its base adjacent to the selected bond or atom e pkchain The contiguous chain of atoms which contains the selected atom or bond e pkresi All atoms in the residue you picked You can click on a selection name to see visually which atoms are
59. presentation show representation EXAMPLES PyMOL gt hide lines The object shown in lines disappears from view PyMOL gt show sticks The object is represented as sticks in the viewer Other representations are cartoons ribbons dots spheres surfaces and meshes See the Section titled Representations Atom Selections If you want to manipulate a subset of the atoms and bonds in a molecule you can use atom selections PyMOL is pretty sophisticated when 1t comes to selecting grouping and naming groups of atoms For example you can select particular residues or atoms in a binding pocket or a hydrophobic patch or all the alanines in a helix and so on The Section titled PyMOL Command Language gives the details for selecting interesting groups of atoms You can use a selection just once or you can name it to make it easier to use again later For example you can zoom in on a selection on the fly SYNTAX zoom selection expression Select the atoms just for zooming Manipulating Objects 19 EXAMP LE PyMOL gt zoom resi 1 10 The selector resi chooses amino acid residues given by the PDB sequence number identifier 1 10 He de He HE Selection expressions range from single words to long complicated expressions An object name may be a selection expression The default selection expression is all which refers to all the atoms that are currently loaded If a selection
60. r POmMtiOl VIEW scccveccrcchecsecessncsceescend edie ia E TE e A EEE REEE E dle 23 Saving YOU Work rro toros 23 Scripts and LOg Files ii ad nie 24 PIS Piles seis iii 24 SESSIONS ccc O hein 25 Command Hne ONO C Er e iaa 25 Command Completion using TAB cecccecccessecesseceeseeeeneecsecesaeceesaeceececeeeeecaeeeaeeseaaeceaaeceeeeeeses 26 Filename Completion using TAB ceccecsccessecesseceeaceeeneeceaeeeaeceeaaecseaeceeeeeceaeesaecseaaeceaaeceeeeeeses 26 Automatic Intern men ico ad dud vaksuce iis at HL E hihi tables 26 Other Typed Commands and Help cra eei esne or a eE ESES E E EE 27 Command Syntax and Atom SelectionS eessesssessccesccesocecoesooesooesocssocesoessesssecesecescesocescossosssosssosesosssesesesesees 28 MM A A E OTE AE EE EEN 28 SELECHON SXPTESSIONS ir ni r eene ia 28 Named Atom Selectos iii ds 29 Singles word Selector rial a ee aea e e E EA EES 31 Property Selector oyee eean E EE E EE AT a EA EE ENEE E EA RAN a 31 Selection Aldana TAE ESE E 34 At m Selection Macros ta a edn eT E E R bats 35 Calling Python from within PYMOL cocooooccconcccnonononnnnoonocnnnnoconncnnnoncnnnonnonccnnn nono ENEE AEREE 37 Cartoon Representations ss cisiivcisscicconsesonsscestssesesdosncshoeseueseesestesocnsssececssteceanedencecssevssensenseccsodestensdedesssssecseesessbiess 38 Joret 424 R11 iii eS a aR i ea anes 38 ACCES dl de eae dee dera da ca a 38 Pretty and COTE a utete ene a taaan duces AE NE IA E E AAA E 38 CUStTOMIZA MOL ii di
61. rated from the van der sl gap X sl gap X Waals radii of s1 by a minimum of X Angstroms PyMOL gt select farfrm_ten resi 10 gap 5 Selects atoms with centers within X Angstroms of the center of any atom in s1 sl around X sl a X PyMOL gt select near_ten resi 10 around 5 Expands s1 by all atoms within X Angstroms of the center of any atom in s1 sl expand X sl e X PyMOL gt select near_ten_x nearl0 expand 3 Selection Algebra 34 s1 within X of Selects atoms in s1 that are within X Angstroms of the s2 s2 PyMOL gt select bbnearten bb w 4 of resi 10 Expands selection to complete residues byres s1 PyMOL gt select complete_res br bbnearl0 Expands selection to complete objects byobject s1 PyMOL gt select near_obj bo near_res Selects atoms directly bonded to s1 neighbor s1 nbr s1 PyMOL gt select vicinos neighbor resi 10 Logical selections can be combined For example you might select atoms that are part of chain a but not residue number 125 EXAMPLE PyMOL gt select chain a and not resi 125 selects atoms that are part of chain a but not residue number 125 PyMOL gt select name cb or name cgl or name cg2 and chain A These two selections are PyMOL gt select name cb cgl cg2 and chain A equivalent select c beta s c gamma 1 s and c gamma 2 s that are in chain A Like the results of groups of arithmetic operations the results of groups of logical operations depend
62. reate highly effective tools for scientific research and to distribute them as broadly as possible while still succeeding as a healthy business As a boot strapped company DeLano Scientific is not beholden to any outside investors who would insist upon maximum returns on investment Thus we have the rare privilege of being able to place Scientific and Medical Progress ahead of Profit in our hierarchy of values We have chosen a free and open source approach for PyMOL because we believe this strategy will have the greatest positive impact on humanity Visualization is key part of understanding the nature of life at the molecular level and powerful visualization tools need to be universally available to all students and scientists if we are to make rapid progress in biomedical research If PyMOL is successful then we hope to expand the scope of our endeavors to meet other critical research needs in related areas Introduction 4 Growth of the DeLano Scientific will depend entirely on the willingness of PyMOL users to adopt nuture and advocate for our volitional approach to software funding Eventually we hope to evolve into a major provider of scientific software for biomedical research and be distinguished by the quality openness and accessibility of our products the trusting and nonexploitive relationships we form with our customers and our willingness to work with all parties in advancing scientific software technologies This chapter last
63. sectavesestdesessdussesveucceesds 53 Picking Atoms and Bonds isir eia i a e oaea e aaa sia un Geist da icons dad llei tii 53 Example Usage of the pk Atom Selections ccccceessecesseceeeceeeseeeaeceeaaeceaeeceeeeeeeeeesaecseaaeneaeeeeeeeees 53 Th 1b and FOr Select iii aid ri da oe ia e in a abi 53 Conformationa Baiting elo oa sane E AAA AA atada 54 Crystallography Applications iiecc cceccssccssoessssscossnsvssossossnessnstsesonss docessesocesncsducdessSessossssetecesveeideseseesesvsueseooseesasts 55 Crystal Symetre ae ni E cost ERN E EEEO Ee N NOO EELEE EE RERS 55 O EES AAIE AS NAAR TE E E A TEA SN ATIA IEE EEE EE SET 55 DA AAEE E E E AT E A a A E 55 Electron Densty Maps naian a ae a GUND BRA an an EEE a 56 J LOFT tE TA RN AA AA AAA A N E EAA 56 Somesbrandus Oder EAE E E Ei EEE O A N etnies 56 Compiled Graphics Objects CGOs and Molscript Ribbons comoommsss 57 NS RR RON 57 MOoISCripUiRabbOms Ai A oobaceducdeaitasesoedavieeuethiakeea odes 57 NO ACS itech A eee ee AMM SIP de Mo O Rr DR Nt tells OR 57 Using MOSCA Pt in aii 57 Creating Compiled Graphics Objects eee eccceceseceseecessaeceeeeceeeeeceaeeeaeceeaaeceaeeceeeeeceeeeaecseaaeneaeeceeeeees 58 CGOERELELEN CES duration dea ues peta O ES EDAD vb db At NEA 59 l ad O dos 59 Callback Objects and PyOpen Gisicccsssssicscscscsscsessscesesessssnsessosnssssosssessousessencsseescsesessncdesncseseaesesevessedesenncsssess 61 TKO AUCTION A A A ecb aa EE EEEREN 61 Example ii adaia
64. session you can save the memory state of the program by creating a session file that can later be loaded to restore that memory state 3 You can write a graphics file to store the image you have created in the viewer for sharing or publication Changing Your Point of View 23 Scripts and Log Files A PyMOL script is just a text file such as a log file containing typed PY MOL commands separated by carriage returns When a script is loaded into PYMOL the commands it contains are executed PyMOL expects scripts to have pml file name extensions this is not strictly required but it is good practice You can use log files as scripts and you can create scripts in a text editor such as emacs jot or notepad It s often useful to keep a text editor open in a separate window while using PY MOL Commands can then be cut and pasted between the two programs You can open a new log file by typing log_open log file name or by clicking on log under the File menu and naming the log file in the dialog box You can also append commands to an existing log file by choosing append or resume in the File menu When you resume rather than append the existing log file is first loaded as a script and then subsequent commands are written to it Once you have opened a log file in any of these ways PyMOL will write and save all your commands whether they are typed or given by clicking on the buttons in the GUI However to store
65. sheet assign residues 65 72 as helix regenerate the cartoon Se SF OSE e Secondary Structure Assignment 45 Ray Tracing Ray tracing produces the highest quality molecular graphics images PyMOL is the first full featured molecular graphics program to include a high speed ray tracer which works with its native internal geometries except text OpenGL Rendering real time manipulation Ray traced Rendering seconds or minutes per frame You can ray trace any Scene in PyMOL by clicking the Ray Trace button in the external GUI or using the ray command The built in raytracer also makes it possible to easily assemble very high quality movies in a snap Important Settings These can be changed using the set command Unless otherwise specified the settings apply only to the ray tracing engine and not the OpenGL renderer Some reconciliation between the two renderers is much needed so be warned that these settings may change in the future Normally the only settings you will need to change are orthoscopic antialias and gamma If you are down in an enzyme active site which is heavily shadowed you may want to increase direct to 0 5 0 7 in order to improve brightness and contrast e orthoscopic 0 or 1 controls whether the OpenGL renderer uses the same orthoscopic transformation as the renderer You ll want to set this to 1 when preparing figures so that OpenGL and raytracing match pixel for pixel e ambient 0 0
66. solete information Make an informed decision to use the PyMOL manual at your own risk Understand that thiss same caution applies to the program as a whole you shouldn t be using PyMOL if you aren t willing to troubleshoot problems and take the initiative on the mailing list in order to discover solutions About the program PyMOL was created in an efficient but highly pragmatic manner with heavy emphasis on delivering powerful features to end users Expediency has almost always taken precedence over elegance and adherence to established software development practices is inconsistent PyMOL is about getting the job done now as fast as possible by whatever means were available PyMOL succeeds in meeting important needs today but we view it as merely an initial step in a promising direction In time we hope that we and others will follow by creating PyMOL like software platforms which meet the needs of users but also provides the design rigor and code quality necessary to enable broad participation of outside developers Though PyMOL will undoubtably continue to expand and improve over the next decade we expectd that its long term impact will primarily be to inspire other development efforts having more time and resources and which will undoubtable achieve greater heights That isn t to say that you can t find good things about PyMOL s internal design Indeed we believe that there are many successful and instructive aspects to the progra
67. space indicates that the previous state should be repeated that many times total 3 HA hyphen immediately followed by a number no space indicates that a numeric sequence of states are to be appended onto the movie starting with the previously played state going to indicated state Once a movie has been defined the red VCR controls in the lower right hand corner of the viewer can be used to step or play through the movie Examples mset 1 x30 creates a 30 frame movie consisting of state 1 played 30 times mset 1 30 creates a 30 frame movie states 1 2 up through 30 mset 1 30 2 58 frames states 1 2 29 30 then 29 28 4 3 down to 2 mset 16523 5 frames states 1 6 5 2 3 in that order See help mset or the reference section for more information mdo The mdo command allows you to bind a particular series of PyYMOL commands to a frame in the movie For instance you can perform a rotation about the axis at each frame of the movie in order to sweep the camera about the object See help mdo or the reference section for more information NOTE The util module includes two python commands for generating mdo commands util mrock and util mdo These functions have not been documented but the source code can be found in the file modules pymol util py Since they are actual python functions explicit parenthesis are required to invoke them util mrock start finish angle phase loop f
68. ssential type of keyword argument They can be simple or complex with several different kinds of syntax Selection expressions Selection expressions stand for lists of atoms in arguments that are subject to PyMOL commands You can name the selections to facilitate their re use or you can specify them anonymously without names Object and selection names may include the upper or lower case characters A a to Z z numerals 0 to 9 and the underscore character _ Characters to avoid include Bae ES ee eT ET ITA E ei Pe ange of Selection expressions describe the class of atoms you are referencing Most of them require identifiers to complete the specification For example the selector resi references biopolymer residues by sequence Command Syntax and Atom Selections 28 number and the identifier gives the number The selector name references atoms according to the names described in the PDB and the identifier gives the name ca for alpha carbons cb for beta carbons etc A handful of selection expressions don t require identifiers but most do PyMOL uses several logical operators to increase the generality or specificity of selection expressions Logical combinations of selectors can get complex so PyMOL accepts short forms and macros that express them with a minimum of keystrokes This section describes named selections and then gives the syntax for making selections in a progression from simple one word selectors to co
69. the back far clipping plane Clipping Planes Front Back Control of clipping planes The advantage of the PyMOL clipping plane control is that tedious tandem manipulations of the clipping planes now becomes easy through the diagonal motions shown below Expand Move Wedge Wedge Inward Shift Right Click Move Wedge Shrink Outward Wedge Changing the visible wedge by moving clipping planes in tandem You can also use the clip command to control the clipping planes Changing the Origin of Rotation When visualizing molecules it is frequently necessary to change the origin of rotation so that you can inspect a particular region of the molecule The fastest way to do this in PyMOL is to Control Shift Middle Click on a visible atom in the scene Moving Clipping Planes 16 Set Origin of Rotation Getting Comfortable At this point we recommend that you spend five or ten minutes getting comfortable with the controls described in this chapter Specifically you should be able to accomplish the following tasks 1 Load a PDB file into PyMOL 2 Rotate translate and zoom the camera 3 Adjust the front and back clipping planes to clearly view a slice of the molecule 4 Change the origin of rotation about any particular atom of interest Getting Comfortable 17 Getting Started with Commands This section steps through a typical PyMOL session introducing typed commands and describing how PyMOL resp
70. uality images with ideal geometries lighting and shadows Compiled graphics objects are a PYMOL specific format which enables any Python programmer to create three dimensional geometries and animations which can be displayed at high speed via OpenGL and also rendered into maximum quality images via the raytracer without any additional work Molscript Ribbons NOTE Molscript is a commercial software free to academics available at http www avatar se molscript and must be obtained separately It is our intention to eventually implement our own Molscript quality ribbons directly from within PyMOL but that day has not yet come PyMOL can automatically translate Raster3D format input files output by Molscript with r option into Compiled Graphics Objects for display and rendering inside of PyMOL PyMOL expects these files to have the file extension r3d NOTE the Raster3D to CGO interpreter is a bare minimum Python implementation and doesn t include anything beyond what is required to read what is output by Molscript load load test dat pept r3d loads one of th xample raster3d files Using Molscript molauto When using molauto to preparing input files for PYMOL it is important to use the nocentre option to prevent any transformation of the protein That way the PDB file and the Molscript ribbons will be in the same frame of reference Unix gt molauto nocentre 3all pdb molscript r gt testl r3d Unix
71. umber of ways You have to open a log file before you give the commands you want to save but a session file can be created at any point A session file is invoked by choosing open under the file menu while a log file is run as a script Also you can t write or edit session files as you can log files and scripts It s a good idea to create session files at strategic points in PyMOL sessions for example when you decide to explore one of several options In this way session files can be used to replace an undo utility which PyMOL lacks You can store any number of PyMOL states in successive session files and revert to them effectively undo ing the work you did since creating the session file Command Line Shortcuts Since almost nobody likes to type PYMOL s command line interface includes several shortcut features designed to reduce typing If you are a unix user you will recognize the similarity with features found in tesh or bash Session Files 25 Command Completion using TAB If you type the first few characters of a command and then hit TAB PyMOL will either complete the command or print out a list of which commands match the command EXAMP LE PyMOL gt sel hitting TAB will produce PyMOL gt select If you hit the TAB key on a blank command line PYMOL will output a list of its commands Filename Completion using TAB Some of the files you need to load into PyYMOL may have lo
72. you You will never be required to pay software license fees in order to use Open Source PyMOL or to share it with others who might find it useful Nevertheless PyMOL is not free to develop document maintain and support If you decide to adopt the package then you are asked and expected to contribute to the project in some manner Although such contributions may take a variety of forms most PyMOL supporters choose to sponsor the project by purchasing usually through their school or employer a license and a renewable subscription to maintenance and support All such contributions are entirely volutary since we have intentionally abandoned the usual means of compelling compliance Instead we depend on your free will to provide vital funding for development and to cover other necessary expenses In return we provide specific incentives called Incentive Products as a reward for helping to fund the project Example incentive products include this manual extra features enhanced platform specific binary versions and various other conveniences Please take this request seriously If you value PyYMOL then it is clearly in your interest to sponsor it To find out how to donate or to purchase a license visit the PYMOL web site at_http www pymol org The DeLano Scientific Mission DeLano Scientific LLC is a private vision centered software company which owns develops and supports the PyMOL package Our mission as a commercial entity is to c

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