Knowledge (XXG)

:WikiProject Molecular Biology/PyMol tutorial - Knowledge (XXG)

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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
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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
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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,
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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.
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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
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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
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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
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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.
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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
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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
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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
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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
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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.
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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
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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
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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
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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
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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
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There are also a number of selection operators used for creating local selections according to defined criteria. The most useful ones are summarized below.
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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
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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.
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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
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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
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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:
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in the window labeled Tcl/Tk GUI and navigating to the location where you saved the file. Alternatively, you can type
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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
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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: 1060: 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
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generates copies of the 1G4A structure that pass within 5 angstroms of the original and names them
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Finally, in line with the visual style of wikipedia, it is best to set the background to white.
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is preferably white rather than the default black, for readability and transferability purposes.
183: 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.
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Manipulating cartoon representations in PyMol is a bit idiosyncratic; in particular,
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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
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menu: display common representations such as cartoons, ribbons, sticks, spheres.
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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
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As illustrated by the examples, numerical ranges are indicated by a dash, e.g.
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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.
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for residues 20, 21, and 22. Concatenation is indicated with the + sign, e.g.
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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
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object menu is to use selections. For example, to turn all helices blue, use
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menu: allows text labeling of atoms, residues, or chains. This can get messy.
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The usual place to download a molecular structure file is the PDB website,
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in the Tcl/Tk window, where "filename" is the complete path to the file.
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Knowledge (XXG):WikiProject Molecular and Cellular Biology/PyMol tutorial
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usually contain only one set of coordinates, while structures solved by
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Biomolecular structures are deposited in a public database called the
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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.
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do not try to rotate the molecule or otherwise alter the display
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replaces all other displays with a cartoon representation.
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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:
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to what is already displayed for that selection, while
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at the bottom which functions as a simple command line.
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The PyMOL user interface consists of three components:
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The official PyMol website is located at Sourceforge:
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chains automatically by toggling the selection mode.
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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 483: 482: 403:Common selections 397:count_atoms alpha 381:color blue, alpha 284: 283: 184:Protein Data Bank 76:PyMol user manual 64:DeLano Scientific 22:(Redirected from 1164: 1157: 1153: 1149: 1141: 1126: 1122: 1115: 1104: 1099:asymmetric units 1035: 1034:color blue, ss h 1018: 1014: 1010: 1006: 1000: 994: 986: 979: 975: 957: 835: 824: 819: 815: 676: 672: 619: 613: 607: 601: 595: 594:sele alpha gap 5 585: 581: 580:sele helix, ss h 577: 573: 569: 565: 564:sele not name ca 545: 541: 525: 519: 513: 503: 497: 491: 418: 414: 410: 398: 394: 390: 382: 376: 370: 364: 358: 344:section below.) 339: 327: 319: 315: 310: 303: 226: 206: 165: 27: 1172: 1171: 1167: 1166: 1165: 1163: 1162: 1161: 1155: 1151: 1146: 1139: 1124: 1117: 1113: 1102: 1092: 1083:Show all states 1057: 1033: 1016: 1012: 1008: 1004: 998: 992: 984: 977: 973: 955: 947: 901:as well as its 895: 851: 833: 822: 817: 813: 806: 754: 674: 670: 638: 636:Representations 617: 611: 605: 599: 593: 583: 579: 575: 571: 567: 563: 560: 543: 540:sele resi 20-22 539: 523: 517: 511: 501: 496:sele name ca+cb 495: 489: 449:Select nothing 412: 408: 405: 396: 392: 388: 380: 374: 368: 362: 356: 350: 342:Representations 337: 325: 317: 313: 308: 301: 293: 216: 204: 180: 163: 151: 146: 97:Please see the 94: 56: 54:Obtaining PyMol 29: 28: 21: 20: 12: 11: 5: 1170: 1168: 1160: 1159: 1143: 1136: 1091: 1088: 1087: 1086: 1078: 1056: 1053: 1041:Settings : --> 1025: 1024: 1002: 996: 990: 989: 988: 946: 943: 942: 941: 934: 919:is preferably 917:Representation 914: 894: 891: 850: 847: 805: 802: 801: 800: 796:Settings : --> 793: 789:Settings : --> 786: 782:Settings : --> 779: 772: 765: 753: 750: 749: 748: 732: 726: 710: 704: 637: 634: 622: 621: 618:neighbor alpha 615: 609: 603: 597: 559: 556: 536: 535: 521: 515: 512:sele resi 1-10 509: 504:- selects all 499: 493: 481: 480: 473: 470: 466: 465: 458: 455: 451: 450: 447: 444: 440: 439: 436: 433: 429: 428: 425: 422: 404: 401: 385: 384: 378: 372: 366: 360: 349: 346: 292: 289: 282: 281: 278: 275: 272: 271:Control+Shift 268: 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553: 549: 533: 529: 522: 516: 510: 507: 502:sele resn gly 500: 494: 490:sele symbol c 488: 487: 486: 478: 474: 471: 468: 467: 463: 459: 456: 453: 452: 448: 445: 442: 441: 437: 434: 431: 430: 426: 424:Abbreviation 423: 420: 419: 416: 402: 400: 379: 373: 367: 361: 355: 354: 353: 347: 345: 343: 335: 331: 323: 322:alpha carbons 305: 297: 290: 288: 279: 276: 273: 270: 269: 265: 262: 259: 256: 255: 251: 248: 246:Rotate in 3D 245: 242: 241: 237: 234: 231: 228: 227: 224: 222: 213: 211: 208: 202: 197: 192: 189: 185: 177: 172: 168: 160: 156: 155: 154: 148: 143: 141: 139: 134: 132: 128: 124: 120: 116: 112: 107: 103: 102: 100: 91: 87: 84: 82: 79: 77: 74: 72: 69: 68: 67: 65: 61: 53: 51: 49: 44: 40: 36: 25: 19: 1132: 1128: 1098: 1093: 1081: 1073: 1058: 1050: 1045: 1040: 1038: 1028: 1026: 1020: 1017:cartoon tube 1013:cartoon rect 1005:cartoon oval 999:cartoon loop 965: 959: 950: 948: 936: 924: 920: 916: 910: 896: 887:Reinitialize 885: 883: 877: 872: 867: 864:Save Session 862: 860: 855: 852: 841: 829: 827: 807: 795: 790:Transparency 788: 781: 774: 767: 760: 755: 743: 738: 734: 728: 721: 716: 712: 706: 699: 690: 686: 681: 679: 666: 662: 658: 654: 650: 646: 642: 639: 623: 588: 561: 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: 135: 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:)

Index

Knowledge (XXG):WikiProject Molecular Biology
Knowledge (XXG):WikiProject Molecular and Cellular Biology/PyMol tutorial
WikiProject: Molecular and Cellular Biology
PyMOL
open-source
our help requests subpage
http://pymol.sourceforge.net/
DeLano Scientific
PyMol download resource
PyMol user manual
PyMol reference manual
PyMol wiki
PyMOL download site
Windows
OS X
Linux
IRIX
Solaris
PyMOL download site
PyMol Wiki
OpenGL
Protein Data Bank
pdb file
www.pdb.org
alpha carbons
Representations
hydrogen
heteroatoms
glycine
alpha helix

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