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  • PyMOL mailing list
    ...and share news related to PyMOL. And is also a place to interact with the PyMOL community, a community that spans the whole world. ...igh that your questions has already been asked and answered in the mailing list, hence always is a good idea to check that before asking a question. If you
    798 bytes (131 words) - 01:04, 19 October 2015

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  • Identify
    '''identify''' returns a list of atom IDs corresponding to the ID code of atoms in the selection. == PYMOL API ==
    429 bytes (61 words) - 01:04, 19 October 2015
  • Order
    order names-list, sort, location # puts 1frg at the top of the list
    679 bytes (98 words) - 02:16, 28 March 2014
  • Set state order
    ''New in PyMOL 1.7.4'' == PyMOL API ==
    521 bytes (71 words) - 22:50, 21 April 2015
  • Get object list
    '''cmd.get_object_list''' is an API only command which returns the list of all molecular objects in selection. It will not return selection names o == PyMOL API ==
    1 KB (176 words) - 02:46, 3 April 2017
  • Set raw alignment
    ''New in PyMOL 2.3'' * '''raw''' = list: list of lists (columns) with <code>(model, index)</code> tuples
    691 bytes (94 words) - 03:14, 7 January 2019
  • Ls
    ...tool if you have many directories full of files --- you don't have to quit PyMOL, you can just '''cd''' to the directory and '''ls''' to find the contents. # list all files in the current directory
    644 bytes (101 words) - 02:16, 28 March 2014
  • PyMOL mailing list
    ...and share news related to PyMOL. And is also a place to interact with the PyMOL community, a community that spans the whole world. ...igh that your questions has already been asked and answered in the mailing list, hence always is a good idea to check that before asking a question. If you
    798 bytes (131 words) - 01:04, 19 October 2015
  • List Secondary Structures
    import pymol pymol.stored_ss = []
    249 bytes (35 words) - 02:16, 28 March 2014
  • Set Color
    ...een 0 an 255 can be used as well. (If at least one value is larger than 1, pymol will interpret all 3 values as between 0 and 255). If an existing color nam ===PYMOL API===
    1,016 bytes (138 words) - 18:49, 14 October 2019
  • Id Atom
    ===PYMOL API=== list = cmd.id_atom(string selection)
    284 bytes (45 words) - 03:06, 28 March 2014
  • Get Color Indices
    ...trieve the Pymol color names and corresponding internal color indices. The Pymol names can be used to designate color for objects, see [[Color]]. To retrie ...to convert that to RGB color values if you need to use the colors outside Pymol.
    2 KB (273 words) - 19:27, 29 May 2018
  • List Colors
    # This is how to do it from the PyMOL command line or .pml script: import pymol
    384 bytes (59 words) - 02:16, 28 March 2014
  • TransformSelectionByCameraView
    This little script was posted to the PyMol list. It will orient the molucule like cmd.orient() does, but does so by the ca https://sourceforge.net/p/pymol/mailman/message/10097639/
    862 bytes (127 words) - 04:40, 14 December 2015
  • Iterate State
    ...he current atom. One common usage is to extract the positions as a python list to alter then write back to the molecule using alter_state. * space = dict: namespace dictionary (API only) {default: pymol namespace}
    2 KB (253 words) - 07:02, 3 January 2016
  • Get names of type
    '''get_names_of_type''' returns a list of object and/or selection names. ===PYMOL API===
    640 bytes (94 words) - 18:49, 14 October 2019
  • Intra fit
    ===PYMOL API=== Warren provided a great example on the PyMOL list. If the NMR ensemble has all the structures loaded as multiple states (whi
    2 KB (222 words) - 04:31, 26 June 2017
  • Disable
    ...tions of an object. It is the equivalent of deselecting the object in the list in the top panel of the [[Internal_gui|Internal GUI]]. ===PYMOL API===
    636 bytes (90 words) - 23:57, 20 May 2014
  • Volume color
    * ramp = str, list or empty: named ramp, space delimited string or list with (x, color, alpha, ...) or (x, r, g, b, alpha, ...) values. If empty, g PyMOL>volume_color vol
    1,020 bytes (123 words) - 03:15, 5 March 2018
  • FindObjectsNearby
    finds all PyMOL object names within [radius] Angstroms of [target]. fileName, string, if not blank the list called [fileName] is written to disk
    2 KB (325 words) - 02:16, 28 March 2014
  • Get raw alignment
    '''get_raw_alignment''' is an API only function that returns a list of lists of (object,index) tuples containing the raw per-atom alignment rel * ''Reimplemented in PyMOL 2.3, order of returned atom tuples can differ to previous versions''
    2 KB (255 words) - 03:14, 7 January 2019
  • Load coords
    == PyMOL API == * '''coords''' = list: Nx3 float array
    814 bytes (101 words) - 22:50, 21 April 2015
  • Centerofmass
    ''New in PyMOL 1.7.2. See the [[center_of_mass]] script for older PyMOL versions.'' PyMOL> fetch 1ubq, async=0
    757 bytes (92 words) - 00:06, 17 October 2016
  • ListSelection2
    * list multiple residues once * '''output''' controls if the list is hidden (default), printed on screen (S) or saved in a file (P)
    3 KB (399 words) - 23:33, 26 May 2014
  • PyMOLWiki:About
    Reading the [[PyMol list]] for years, we users noticed a trend: person A would ask a question, perso ...created by Jason Vertrees for the purpose of founding a knowledgebase for PyMOL users. The site also espouses the open-source mode: to post any code on th
    986 bytes (164 words) - 00:49, 28 March 2014
  • Transform selection
    ...ection. The matrix should actually be passed in as a single list -- not a list of lists. === PYMOL API ===
    2 KB (349 words) - 20:24, 9 July 2015
  • Spectrum
    ''New in PyMOL 1.6: Supports any [[iterate]] expression, like [[spectrumany]]'' ''New in PyMOL 1.6: Supports space separated color list as palette, like [[spectrumany]]''
    4 KB (522 words) - 02:11, 24 November 2019
  • Property Selectors
    ...el, 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 ...entifiers are separated by plus signs (+) only. Do not add spaces within a list of identifiers. The selector '''resi''' takes (+)-separated lists of identi
    8 KB (1,154 words) - 04:50, 11 December 2017
  • Pymol-script-repo
    The [[Pymol-script-repo]] is the preferred place to host scripts which are published on # A convenient way, to let PyMOL users download all scripts at the PyMOLWiki, with a minimum of effort.
    2 KB (217 words) - 03:24, 10 December 2018
  • Git intro
    ...up of PyMOL users initiated together with Jason Vertrees, a project to let PyMOL scripts be We hope that script authors and PyMOL users would be interested in this option.
    2 KB (250 words) - 02:16, 28 March 2014
  • Enable
    ...tations of an object. It is the equivalent of selecting the object in the list at the top of the [[Internal_gui|Internal GUI]]. ===PYMOL API===
    886 bytes (130 words) - 23:57, 20 May 2014
  • Get object matrix
    ...'s initial position when loaded in. '''get_object_matrix''' will return a list of floats with that matrix for a named object. According the pymol source code, this is an "unsupported command".
    959 bytes (137 words) - 02:16, 28 March 2014
  • Pdb conect nodup
    The '''pdb_conect_nodup''' setting in pymol controls if duplicated connectivity record ([http://www.wwpdb.org/documenta ...t may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records (<tt>pdb_conect_nodup=0</tt>) and t
    1 KB (201 words) - 01:04, 19 October 2015
  • Supercell
    ...99ab%40mail.gmail.com&forum_name=pymol-users thread on pymol-users mailing list]. run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/xtal.py
    900 bytes (121 words) - 16:19, 20 July 2020
  • Psico
    |download = https://github.com/speleo3/pymol-psico ...eloped as an in-house script collection, but grew to a quite comprehensive PyMOL extension. Some of the provided commands are already in the PyMOLWiki [[:Ca
    5 KB (689 words) - 03:58, 4 March 2019
  • Fetch Host
    * mirror URL with "divided" layout ''(new in PyMOL 1.6)'' ''New in PyMOL 1.3''
    1 KB (204 words) - 04:50, 11 December 2017
  • Aa codes
    ...code below and drop it into your .pymolrc file. Then, each time you load PyMOL, "one_letter" and "three_letter" will be defined. # kind of hash by just adding a matching list, and zipping.
    2 KB (380 words) - 02:46, 18 September 2017
  • Get Names
    '''get_names''' returns a list of object and/or selection names. ===PYMOL API===
    1 KB (169 words) - 03:47, 7 March 2016
  • Jump
    ...ut not necessarily in any order. This script allows the user to specify a list of frames and flipping through the set of frames is controlled by a user-de ===PyMOL API===
    3 KB (421 words) - 03:06, 28 March 2014
  • Ccp4 pisa
    The script selects atoms from the list of the contacts found by PISA. ...our pdb file to find the interfaces. Then by using the ccp4_pisa script in PyMOL we separately select atoms for all interface types and individual interface
    1 KB (194 words) - 01:42, 28 March 2014
  • Unset deep
    ''New in PyMOL 1.8.4'' * '''settings''' = str: space separated list of setting names or empty string for all settings {default: }
    719 bytes (95 words) - 00:07, 17 October 2016
  • Molecular Sculpting
    ...n "molecular sculpting" in PyMOL mailing list.[http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00359.html ]: ...o the configuration the molecules possess when they were first loaded into PyMOL.
    2 KB (225 words) - 04:22, 12 November 2018
  • Get View
    ===PYMOL API=== *3 = return formatted string instead of a list
    1 KB (225 words) - 02:13, 14 September 2020
  • Load
    ...ust end in ".ccp4", Raster3D input (Molscript output) must end in ".r3d", PyMOL session files must end in ".pse", and pickled ChemPy models with a ".pkl" c ===PYMOL API===
    5 KB (824 words) - 04:03, 8 January 2018
  • BiologicalUnit
    '''Note:''' PyMOL 1.8 can load biological units from mmCIF files with the '''[[assembly]]''' ...reate biological units for proteins. (This was created as a workaround of PyMOL's semi-functioning [[Symexp]] command.) It's also a fun script to play wit
    4 KB (500 words) - 02:19, 19 September 2016
  • Iterate
    ...ymol''' module namespace, and thus exposes objects like '''cmd''' and '''[[pymol.stored|stored]]'''. The order of iteration is that of the internal atom ord ...modification of '''x, y, z''' (and atom-state level settings in Incentive PyMOL 1.7+).
    7 KB (1,031 words) - 04:03, 8 January 2018
  • ObjectByArrows
    ...he left and right arrows on your keyboard to moving up and down the object list. Note that this script supports objects, but is untested for groups. from pymol import cmd
    2 KB (191 words) - 02:16, 28 March 2014
  • Radius of gyration
    ...ourceforge.net/mailarchive/message.php?msg_id=27288491 pymol-users mailing list]! from pymol import cmd
    2 KB (277 words) - 02:27, 28 May 2019
  • Advanced Coloring
    ...OL can be assigned a color using the small rightmost buttons in the object list (in the upper right part of the main GUI window. The [[Color]] command will PyMOL has a predefined set of colors that can be edited in the ''Settings->Colors
    6 KB (849 words) - 03:47, 7 March 2016
  • Quickdisplays
    !colspan="3;"|List of functions | style="text-align:center;"| prints a list of functions
    5 KB (728 words) - 05:46, 18 January 2015
  • Leap Motion
    ...to get the [https://www.leapmotion.com Leap Motion Controller] working in PyMOL, using the Leap Python API. ...yMOL 2.0 on all platforms, with MacPyMOL "syspython", and with Open-Source PyMOL on Gentoo Linux and MacOS.
    3 KB (433 words) - 04:50, 11 December 2017

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