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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

Page text matches

• 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
• 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
• CMPyMOL
  ...on program PyMOL. It combines the protein 3D visualization capabilities of PyMOL and the protein's 2D contact map with an interactive interface for scientif * PyMOL. (It is recommended that the user add the PyMOL installation directory to the $PATH environment variable.)
  8 KB (1,116 words) - 05:42, 31 May 2016
• Cluster mols
  cluster_mols is a PyMOL plugin that allows the user to quickly select compounds from a virtual scre ...lar fingerprints [http://openbabel.org/wiki/FP2] and loading them into the PyMOL window. cluster_mols also highlights both good and bad polar interactions
  8 KB (1,334 words) - 18:29, 25 May 2022
• Settings
  PyMOL is incredibly useful because of its flexibility. Almost any setting can be ==List of settings==
  13 KB (1,729 words) - 14:21, 9 June 2014
• Plane Wizard
  import pymol from pymol import cmd
  20 KB (2,632 words) - 05:54, 9 January 2017
• BiologicalUnit/Quat
  '''Note:''' PyMOL 1.8 can load biological units from mmCIF files with the '''[[assembly]]''' from pymol import cmd, stored
  4 KB (554 words) - 02:19, 19 September 2016
• Kabsch
  '''Note:''' PyMOL has built-in commands to do RMSD fitting. This script is typically not need # Open PyMol
  26 KB (4,053 words) - 03:23, 29 April 2019
• Distancetoatom
  1. a list with coordinates [x,y,z]<br> NB! older PyMOL versions only support b or q and the distance will overwrite this property
  4 KB (603 words) - 15:24, 26 November 2014
• Apbsplugin
  For the new plugin in Incentive PyMOL 2.0, see [[APBS Electrostatics Plugin]]. software package into PyMOL.
  5 KB (781 words) - 02:21, 20 August 2018
• Practical Pymol for Beginners
  ...can appear daunting to new users. This guide is intended to introduce the PyMOL interface and basic tasks without leaving the mouse behind. ==The PyMOL Interface==
  12 KB (1,971 words) - 02:46, 3 April 2017
• Bnitools
  ...plug in for PyMOL which adds additional functionalities and presets to the PyMOL GUI. Install it using the 'Install Plugin' menu within PyMOL:<br>
  8 KB (934 words) - 05:42, 31 May 2016
• Spectrumbar
  from pymol.cgo import * from pymol import cmd
  6 KB (822 words) - 01:44, 28 March 2014
• Fetching scripts
  * A command to list all available scripts? .../ python-wikitools] (this looks good to me!)</s> can never be bundled with PyMOL due to GPL v3.
  6 KB (959 words) - 02:16, 28 March 2014
• ProBiS H2O
  Python 2.7, NumPy (>= 1.6.1), SciPy (>= 0.9), scikit-learn (>= 1.18), PyMOL software, ProBiS (installed during ProBiS H2O setup). ProBiS H2O is installed as a PyMOL plugin:
  7 KB (1,055 words) - 19:27, 29 May 2018
• Scene
  ...ons, so you get the desired smooth transitions. Mix this with [http://www.pymol.org/ax/ AxPyMOL] and you have movies in PowerPoint with very little work. == PyMOL API ==
  6 KB (867 words) - 06:32, 11 January 2016
• Pytms
  '''PyTMs''' is a PyMOL plugin that enables to easily introduce a set of common post-translational ..., or together with the [https://github.com/Pymol-Scripts/Pymol-script-repo pymol-script-repository]<br>
  9 KB (1,151 words) - 04:40, 14 December 2015
• Show contacts
  |download = [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/show_contacts.py] ...ugin for displaying polar contacts. Good hydrogen bonds (as determined by PyMOL) are shown in yellow. Electrostatic clashes (donor-donor or acceptor-accep
  12 KB (1,422 words) - 03:11, 1 April 2019
• Older News
  ...gin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL. * New Plugin: [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
  13 KB (1,965 words) - 03:24, 10 December 2018
• MovieSchool 5
  ...eady been hinted at--that lead to the final goal: allowing you to generate PyMOL movies to tell the stories you want to tell. We start simple and build up Many of the movie scripts below assume that you have readied PyMOL for movie generation. To do that use the following code:
  15 KB (2,259 words) - 02:16, 28 March 2014
• Stereo 3D Display Options
  ...eo 3D display options best suited for molecular graphics applications like PyMOL. Please strive to provide objective factual information based on first-han ...read_name=DED5C399-7534-4D3D-8B19-E3676C4F1867%40weizmann.ac.il&forum_name=pymol-users verified working under FC 12]
  15 KB (2,331 words) - 04:22, 12 November 2018
• PLoS
  ...(i)'' raw, starting data (''e.g.'', PDB files) to ''(ii)'' actual, working PyMOL or Python scripts and ''(iii)'' final output image files. 2) Download [http://www.doe-mbi.ucla.edu/~sawaya/uvla/fold/csos3-left.pml Pymol script for left half of stereo image]. The script can be modified to produc
  41 KB (6,131 words) - 18:10, 31 October 2015