1101:. This may include multiple copies of a single molecule, in which case selecting only one of the copies is a simple matter. A more complex procedure is required for multimeric structures where the asymmetric unit PDB coordinates do not correspond to a complete assembled complex. (This is usually because they contain monomers from multiple adjacent multimers.) Reconstructing the biological molecule requires the
198:, which allows you to search based on a four-character PDB ID or based on keyword descriptions of a particular structure. Once you have found the structure you're looking for, click the 'download files' link on the left side of the page, then click the first link labeled "PDB file" and download it to an appropriate location on your computer. You can open the file in PyMOL by clicking
1123:. The prefix is used to name the new representations that will be generated by the command, the molecule name is the name of the loaded PDB, the object name is the name of the selection to be duplicated (usually the same as the molecule name), and the distance is the range in angstroms over which to construct copies. The command
1085:. Because 'thick' representations like sticks and cartoons can look awkward with multiple overlaid structures, the ribbon and line representations are particularly useful for NMR structures. Be sure to look at the raytraced version of ribbon structures, as it is very different from the OpenGL-rendered realtime view.
825:, your computer might appear to "freeze" or become unresponsive; this is normal, because the raytracing calculation will be using most of your CPU for a short amount of time. Except for very complex representations of surfaces, reasonably fast computers should not freeze for more than a few minutes at most.
295:
Single-clicking anywhere on the molecule will make a selection. Below the mouse matrix in the right-hand panel, the word "selecting" is displayed, followed by the selection mode. Clicking this line cycles through selection modes. You can select individual atoms, residues (amino acids), or polypeptide
1067:
usually contain multiple sets of coordinates corresponding to alternative models satisfying the set spatial restraints determined by the NMR experiments. NMR structures are deposited in the PDB as a single file containing multiple sets of coordinates. To view NMR structures, open the PDB file as
105:
The most current version of PyMol freely available as a precompiled build is 0.99r6, which was released in March 2006; later versions are freely distributed only as source code, and require subscription for access to precompiled versions. We do not intend to support compiling your own version,
286:
The editing and viewing modes can be toggled by clicking anywhere in the mouse matrix display. Right- or double-clicking anywhere in the display pane brings up a viewing menu with a simplified set of options, including a zoom function that automatically fits the molecule to the display size.
939:
depends on the size of the molecule being illustrated. For a single polypeptide chain, coloring by secondary structure is usually best. For a multi-protein complex, coloring by individual polypeptide chain or by subunit type offers a clearer illustration of how the structure is
45:
molecular visualization program, for the creation of images of biomolecules such as proteins, DNA, and related complexes. This page provides introduces the software and demonstrates how to create high-quality images of proteins. Specific requests for assistance can be posted at
218:
Manipulating the structure in the Viewer window is easiest with a three-button mouse, as the middle button is assigned unique functions; on some systems clicking the right and left buttons simultaneously will simulate a middle-click. PyMOL calls its manipulation interface the
905:
and any other important structural features. However, if little is known about the protein, or you are only creating a single image, the following parameters are generally recommended. These suggestions apply even if you are using another visualization program.
702:
menu: allows you to delete and rename selections and objects, and zoom and orient the view to emphasize a particular object. The "preset" list contains predefined simple macros for generating a basic display, e.g. a cartoon protein structure colored by residue
223:, which is displayed for reference at the bottom of the right-hand panel in the Viewer window. The mouse matrix has two main modes, viewing and editing; viewing is by far the more useful for our purposes. The important viewing functions are summarized below.
299:
Each separate selection appears as its own entry in the list of displayed representations in the top section of the right-hand panel. Clicking each box once will toggle the display of that selection or object. By default, the most recent selection is called
311:
rather than clicking on the molecule. You can type your commands into the Tcl/Tk window (which contains a scrolling view of the history of past commands) or directly onto the command line in the viewer window (what you type here will appear next to the
677:. The distinctions are subtle and largely irrelevant for simple purposes, but in general, objects are more flexible than selections. Deleting an object will also entirely remove its contents, while deleting a selection retains the selection's content.
190:
and usually has the file extension .pdb. The vast majority of published molecular structures will be distributed in this format, which is a human-readable text-based format that you can open and read in any text editor, such as
Microsoft Notepad.
858:. This is very useful for saving intermediate states of complex manipulations, especially since PyMol does not have a generalized "undo" function. Before you take an action that might damage your previous work, you should save your session.
820:
command and/or sizing the protein manually using the right mouse button so that the area of interest fills the whole window. Your maximum realistic resolution will be slightly smaller than the resolution of your monitor. After you type
640:
Each item in the list in the right-hand panel represents a selection or object. When you load a new PDB file, a new object is automatically created. Each item has five boxes to the left of its name, labeled A, S, H, L, and C for
614:- selects all atoms in all residues that have at least one atom within 5 angstroms of an alpha carbon. That is, if a single atom in a residue meets the selection criteria, the whole residue will be included in the new selection.
853:
PyMol allows you to save its current internal state, including all molecules you have loaded, all selections, objects, and representations, and all display settings in a PyMol session file, which has the file extension
169:
PyMOL Tcl/TK GUI: This window contains the familiar File/Edit/etc. navigation bar, as well as a command line and controls for manipulating multi-frame structures (these will generally not be important for our
173:
PyMOL Console: This window is optional, and not launched by default. It contains diagnostic information, error messages, and status output messages that result from commands entered in the Tcl/Tk window.
161:
window contains a central area in which the molecule is displayed, a right-aligned column containing information about different selections and representations of the molecule, and a single line labeled
968:
menu for a loaded PDB. By default, smoothing is enabled in cartoon representations so that helices and especially sheets are shown as roughly straight, rather than bent to follow the protein backbone.
958:) does not do what you might expect from other programs. Important manipulations of the cartoon representation are summarized here. To use these commands, you will most likely want to first click
47:
756:
Not all color and display options are accessible from the color menu associated with each entry in the object list. Most relevant other options are located under the Tcl/Tk window menus.
377:- reorient the viewer so that the set of alpha carbon fills the viewing window. This is most useful for selections that cover a localized region, for example a small-molecule ligand.
669:; the latter are displayed with parentheses around the name and the former in plain text. You can create your own objects using the same selection syntax as above, with the command
574:
creates a selection containing all glycine residues and all atoms from residues 1-5. The same operators can be used to combine named selections into a new selection; e.g. if
1138:
The chosen cutoff must be large enough to generate at least one complete molecule, which will probably also generate extraneous fragments of related molecules. The command
133:. PyMol is copyrighted free software, so please pay attention to the license terms offered to you upon installation. You will be asked to consider sponsoring the project.
1105:
command to generate symmetry-related copies of the molecule. (Alternatively, one or more biological unit files are usually available directly from the PDB, but come as
680:
The Show menu begins with a submenu called "as", which contains most of the same options available directly under the Show or Hide menus. The distinction is important:
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hides objects more than 5 angstroms away from the original. Setting this size smaller than the size that generated the new copies will remove the extra fragments.
340:, which will produce a new entry in the representations list called "alpha". (The buttons and actions one can perform on each representation are covered in the
897:
There is no single best way to represent and display all proteins. Ideally, we would be able to show several images of each protein, illustrating its overall
816:
in the Tcl/Tk window or at the viewer prompt. Raytracing is always done at the current size of the window, so you can optimize your use of space by using the
589:
There are also a number of selection operators used for creating local selections according to defined criteria. The most useful ones are summarized below.
17:
876:
command, which can open .pse files as well as plain PDB files. You can also save individual components of your session as separate PDB files using the
1039:
Because different proteins are best represented with different depictions, we can't give a thorough overview of all possible knobs to twiddle. See
889:, which restores PyMol to the state in which it was originally launched. This will remove any molecules you've opened or selections you've made.
23:
391:, which also colors alpha carbons blue without creating a separate entry in the representations list. Another useful command to know is
210:
When the file is open, the molecule will be displayed in the Viewer window, although not in a particularly attractive representation.
1072:
To view the structures in succession, as frames of a movie, click "Play" in the Tcl/Tk window. The frame rate can be set in the menu
840:
file as the filename you specify; you can also include a path to a location besides the current directory. Alternatively, use the
129:. Be sure that you download the build appropriate for your operating system, and follow the appropriate instructions from the
792:- alter opacity and transparency for different representations; most useful for rendering a surface in partial transparency
136:
A number of external plugins and scripts have been developed for PyMol; many of these are collected and documented in the
812:
utility for the production of high-quality images. The raytracing utility is very easy to use; simply type the command
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Naming your selections is not required; commands that take a selection-expression argument can also be used like this:
203:
in the window labeled Tcl/Tk GUI and navigating to the location where you saved the file. Alternatively, you can type
1044:
all for a complete listing of parameters (listed alphabetically; all those related to cartoons begin with the word
126:
110:
778:- toggles display of double and triple bonds in line and stick views (default: show all bonds as a single line)
624:
Alpha carbons are used here as a simple example, but most of these commands are most useful in displaying an
407:
PyMOL provides predefined shortcuts for commonly selected items. They are used as single identifiers, e.g.
832:. This will cause you to lose your raytraced image and return to the OpenGL-rendered version. The command
1094:
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715:
menu: hide a particular representation (e.g., if both cartoons and ribbons are on, this looks ugly, so
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olor. Clicking on a box will display a dropdown menu for that selection. Note the distinction between
187:
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generates copies of the 1G4A structure that pass within 5 angstroms of the original and names them
930:
898:
799:- raytracer options; this is the place to look if rendering is very slow or causing memory errors
1051:
Finally, in line with the visual style of wikipedia, it is best to set the background to white.
913:
is preferably white rather than the default black, for readability and transferability purposes.
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1001:- thin ribbons following the backbone, the way loops are shown in the default representation.
785:- various options for the display of cartoon structures, including size of helices and sheets
34:
336:, whose names are shown in plain text. To create a new selection, you can use the command
186:(PDB). The standard file format for storing molecular coordinates in the PDB is called a
925:
485:
Other types of identifiers are used to select by atom, residue, or chain properties.
949:
Manipulating cartoon representations in PyMol is a bit idiosyncratic; in particular,
983:
When displaying local side chains along with a cartoon structure, it is best to set
75:
328:. Note that the list of representations in the viewer window distinguishes between
321:
304:, but you can give new selections a name on the command line when you create them.
80:
520:- selects chain A (note: usually chain designations are single letters or numbers)
1064:
1027:
The best way to choose secondary structure color schemes besides the two in the
902:
709:
menu: display common representations such as cartoons, ribbons, sticks, spheres.
625:
527:
307:
It is usually easier to define selections on the command line using the command
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PyMOL Viewer: the window in which molecules are manipulated and displayed. This
42:
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As illustrated by the examples, numerical ranges are indicated by a dash, e.g.
137:
85:
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usual; all coordinate sets will be loaded, but only one displayed by default.
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to 0 so that the cartoon and sidechain representations appear to be connected.
809:
551:
542:
for residues 20, 21, and 22. Concatenation is indicated with the + sign, e.g.
531:
476:
324:
in a molecule. This will store all of the alpha carbons in the representation
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prompt at the bottom of the window). The simplest selection is something like
1032:
object menu is to use selections. For example, to turn all helices blue, use
731:
menu: allows text labeling of atoms, residues, or chains. This can get messy.
547:
194:
The usual place to download a molecular structure file is the PDB website,
461:
207:
in the Tcl/Tk window, where "filename" is the complete path to the file.
24:
Knowledge (XXG):WikiProject
Molecular and Cellular Biology/PyMol tutorial
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usually contain only one set of coordinates, while structures solved by
505:
1154:. This is useful because choosing an excessively large radius for the
182:
Biomolecular structures are deposited in a public database called the
629:
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menu in the Tcl/Tk window and navigate to your preferred location.
596:- selects everything at least 5 angstroms away from an alpha carbon
534:
secondary structure (other options are l = loop, "" = unstructured)
63:
608:- selects all gamma carbons within 5 angstroms of any alpha carbon
118:
106:
although it is not difficult. The most current version is 0.99r8.
38:
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830:
do not try to rotate the molecule or otherwise alter the display
122:
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62:. It is copyrighted free software written and distributed by
695:
replaces all other displays with a cartoon representation.
399:
will tell you how many alpha carbons are in the selection.
602:- selects everything within 5 angstroms of an alpha carbon
1158:
command can generate a very large number of new objects.
1019:- various shapes for tracing out the backbone, of which
352:
Important tasks you can perform on selections include:
689:
to what is already displayed for that selection, while
166:
at the bottom which functions as a simple command line.
153:
The PyMOL user interface consists of three components:
980:. To turn smoothing back on, set both variables to 1.
58:
296:
chains automatically by toggling the selection mode.
266:
Move clipping plane (cuts off/shadows distant atoms)
195:
1145:All symmetry-related fragments can be deleted with
1097:structures are sometimes represented in the PDB as
747:
for options in rainbow coloration by residue index.
742:for options in coloring by secondary structure, or
1080:To view all the structures simultaneously, click
861:Saving sessions is done in the Tcl/Tk menu under
685:displays a cartoon representation of a selection
109:Precompiled versions of 0.99r6 are available for
1109:files that can be quite large when unzipped.)
764:- changes the background from the default black
479:, as defined by HETATM records in the PDB file
836:on the command line will save your image as a
570:selects all the alpha carbons in helices, and
566:selects everything except the alpha-carbons,
415:to select all of the currently loaded atoms.
18:Knowledge (XXG):WikiProject Molecular Biology
8:
995:- reset cartoon representations to defaults.
332:, whose names are shown in parentheses, and
620:- selects all atoms bonded to alpha carbons
35:WikiProject: Molecular and Cellular Biology
417:
225:
371:- display the alpha carbons as spheres.
771:- toggles depth cuing fog (default on)
586:selects alpha carbons not in a helix.
828:After you have raytraced your image,
725:does exactly what it says on the tin.
720:will leave only cartoons displayed).
584:sele alpha_not_helix, alpha not helix
554:. Parentheses are used for grouping.
546:selects all residues that are either
7:
498:- selects all alpha and beta carbons
341:
1090:Reconstructing biological molecules
178:Downloading and opening a PDB file
31:
871:). Restoring is done through the
562:Standard boolean operators work:
884:A related and useful command is
1116:takes the following arguments:
808:PyMol contains a fast built-in
514:- selects residues 1 through 10
359:- do not display alpha carbons.
606:sele name cg within 5 of alpha
1:
1059:Protein structures solved by
849:Saving and restoring sessions
628:or the region around a bound
526:- selects all atoms assigned
383:- show alpha carbons in blue.
60:http://pymol.sourceforge.net/
956:show ribbon, <object: -->
929:to illustrate the protein's
1055:Representing NMR structures
978:set cartoon_smooth_loops, 0
972:To turn off all smoothing:
893:Recommended representations
320:, which selects all of the
214:Basic molecule manipulation
1173:
1140:hide (not (1G4A expand 5))
1125:symexp dup,1G4A,(1G4A),5.0
974:set cartoon_flat_sheets, 0
582:are already defined, then
492:- selects all carbon atoms
737:menu: color options; see
612:sele byres alpha around 5
572:sele resn gly or resi 1-5
277:Reset origin of rotation
101:for complete information.
48:our help requests subpage
1023:is usually the clearest.
438:Select all loaded atoms
365:- display alpha carbons.
149:PyMOL interface overview
1119:,<molecule name: -->
263:Reduce a selection box
71:PyMol download resource
1147:delete <prefix: -->
1120:,(<object name: -->
1118:symexp <prefix: -->
205:load <filename: -->
81:PyMol reference manual
1095:X-ray crystallography
1061:X-ray crystallography
834:png <filename: -->
568:sele name ca and ss h
260:Grow a selection box
348:Most important tasks
280:Move clipping plane
37:supports the use of
1121:),<distance: -->
985:cartoon_flat_sheets
931:secondary structure
600:sele alpha around 5
576:sele alpha, name ca
558:Selection operators
389:color blue, name ca
338:sele alpha, name ca
131:PyMOL download site
99:PyMOL download site
1048:) and experiment.
869:Save Session As...
369:show sphere, alpha
993:cartoon automatic
945:Cartoons in PyMol
544:sele resn asp+asn
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403:Common selections
397:count_atoms alpha
381:color blue, alpha
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184:Protein Data Bank
76:PyMol user manual
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623:
588:
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537:
518:sele chain a
484:
427:Description
406:
386:
351:
333:
329:
318:sele name ca
306:
298:
294:
285:
221:mouse matrix
220:
217:
209:
199:
193:
181:
152:
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113:2000 or XP,
108:
104:
96:
95:
92:Installation
57:
32:
1152:delete dup*
1133:dup02000000
1129:dup01000000
1082:Movie : -->
1074:Movie : -->
1065:protein NMR
1029:Color : -->
903:active site
744:Color : -->
739:Color : -->
687:in addition
626:active site
528:alpha helix
524:sele ss h+s
477:heteroatoms
475:Select all
460:Select all
393:count_atoms
252:Zoom/scale
196:www.pdb.org
144:Basic usage
43:open-source
960:Show : -->
951:Show : -->
940:assembled.
911:Background
886:File : -->
881:function.
878:File : -->
873:File : -->
868:File : -->
863:File : -->
843:Save Image
842:File : -->
810:raytracing
762:Background
723:Everything
722:Hide : -->
717:Hide : -->
691:Show : -->
682:Show : -->
673:replacing
667:selections
657:abel, and
552:asparagine
532:beta sheet
375:zoom alpha
363:show alpha
357:hide alpha
330:selections
314:PyMOL: -->
249:Translate
200:File : -->
164:PyMOL: -->
138:PyMol Wiki
86:PyMol wiki
804:Rendering
797:Rendering
769:Depth Cue
548:aspartate
421:Shortcut
291:Selecting
229:Keyboard
170:purposes)
1150:, as in
1046:cartoon_
961:as : -->
745:Spectrum
692:as : -->
645:ctions,
508:residues
462:hydrogen
409:sele all
188:pdb file
1107:gzipped
964:in the
962:Cartoon
921:cartoon
783:Cartoon
718:Ribbons
700:Actions
693:Cartoon
683:Cartoon
663:objects
506:glycine
469:hetatm
334:objects
274:Select
243:(none)
235:Middle
127:Solaris
111:Windows
1156:symexp
1135:, etc.
1114:symexp
1103:symexp
952:Ribbon
926:ribbon
703:index.
671:create
630:ligand
464:atoms
454:hydro
413:sele *
326:(sele)
302:(sele)
257:Shift
238:Right
159:OpenGL
125:, and
1075:Speed
1030:By ss
937:Color
740:By ss
735:Color
729:Label
653:ide,
649:how,
446:none
443:none
232:Left
119:Linux
41:, an
39:PyMOL
16:<
1042:Edit
1021:tube
976:and
966:Show
954:(or
899:fold
874:Open
866:(or
856:.pse
818:zoom
713:Hide
707:Show
675:sele
665:and
578:and
472:het
432:all
309:sele
201:Open
123:IRIX
115:OS X
33:The
923:or
838:PNG
823:ray
814:ray
550:or
530:or
457:h.
411:or
66:.
50:.
1131:,
1036:.
1015:,
1011:,
1007:,
632:.
435:*
395:;
140:.
121:,
117:,
1148:*
1077:.
933:.
659:C
655:L
651:H
647:S
643:A
26:)
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