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  • 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
  • Single-word Selectors
    | All atoms currently loaded into PyMOL | All hydrogen atoms currently loaded into PyMOL
    3 KB (400 words) - 04:50, 11 December 2017
  • Get Coordinates I
    There are several ways to extract or load atomic coordinates in PyMOL using the python API. ''New in PyMOL 1.7.4''. This is the fastest method to extract coordinates from a selection
    3 KB (407 words) - 07:02, 3 January 2016
  • Split selection
    import pymol from pymol import cmd
    2 KB (320 words) - 01:44, 28 March 2014
  • Transform odb
    from pymol import cmd import pymol
    2 KB (316 words) - 04:07, 28 March 2014
  • Pml2py
    ...?msg_id=27331786 pymol-users mailing list] (Subject: Convert pml script to Pymol Python script, Fri, 8 Apr 2011). from pymol import cmd, parsing
    4 KB (467 words) - 04:30, 3 March 2020
  • PluginArchitecture
    This page describes PyMOL's plugin architechture since version 1.5.0.6. ...ule which uses PyMOL's API. The following entrypoints add functionality to PyMOL:
    4 KB (547 words) - 03:24, 10 December 2018
  • MtsslDock
    mtsslDock is a PyMOL plugin for distance constrained rigid-body docking. ...in labelling, trilateration and distance-constrained rigid body docking in PyMOL''', Gregor Hagelueken, Dinar Abdullin, Richard Ward and Olav Schiemann, DOI
    5 KB (840 words) - 05:13, 26 May 2020
  • Load Traj
    Since version 1.0, PyMOL uses the [http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ Molfile Plug *PyMOL does not know how to wrap the truncated octahedron used by Amber You will n
    3 KB (369 words) - 03:14, 5 March 2018
  • Polarpairs
    ...pairs with the [[find_pairs|cmd.find_pairs]] function and return them as a list of atom pairs. It finds (more or less) the same contacts like [[distance|cm from pymol import cmd
    2 KB (276 words) - 03:11, 1 April 2019
  • Plugin manager
    28 bytes (3 words) - 15:24, 26 November 2014
  • Pdbsurvey
    ...character. Then you're ready to go. Just hit 'pdbsurvey' from within your PyMol instance, and the program returns the report file. The pdb ftp server is up from pymol import cmd
    10 KB (1,133 words) - 02:16, 28 March 2014
  • Ramp New
    *'''range''' = list: values corresponding to slots in the ramp {default: [-1, 0, 1]} *'''color''' = list or str: colors corresponding to slots in the ramp or a given palette name:
    8 KB (1,198 words) - 17:32, 14 August 2015
  • Azahar
    Azahar (pronounced /ɑːsɑːˈɑːr/) is a plugin that extends the PyMOL's capabilities to visualize, analyze and model glycans and glycoconjugated ...on menus, two of which are used to specify residues to be connected from a list of predefined templates. And the third one, selects the chemical bond to be
    6 KB (985 words) - 05:01, 22 June 2020
  • Multisave
    ...cord, and is terminated with END. Loading such a multi-entry PDB file into PyMOL will load each entry as a separate object. == Changes in PyMOL 1.8.4 ==
    3 KB (311 words) - 06:13, 6 March 2017
  • Color
    ...es and color by the new values. This example is possible because commands PyMOL does not recognize are passed to the Python interpreter --- a very powerfu ...'s PyMOL script repository (http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/)
    6 KB (1,020 words) - 02:11, 24 November 2019
  • Cart to frac
    from pymol import cmd Python list of fractional coordinates
    2 KB (331 words) - 02:19, 19 September 2016
  • Isomesh
    ...hey match, and if they do not, then figuring out why not. ''From the PyMOL list. Author: Warren DeLano.''
    4 KB (555 words) - 04:05, 7 December 2020
  • Load new B-factors
    ...selections. In such cases, [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ data2bfactor.py] is a better choice. PyMOL>loadbfacts 1LVM
    3 KB (462 words) - 15:32, 20 October 2014
  • MtsslTrilaterate
    mtsslTrilaterate is a PyMOL plugin for the trilateration of objects based on distance restraints. ...mtsslTrilaterate program is a python code and it works as a plugin for the PyMOL program. It is a part of the mtsslSuite package and is optimized to work in
    7 KB (1,169 words) - 15:24, 26 November 2014
  • Align
    ...rejection. The RMSD can also be captured with a python script, see the [[#PyMOL API|API paragraph]] below. Note that the output prints "RMS" but it is in f == PyMOL API ==
    4 KB (558 words) - 04:50, 11 December 2017

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