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  | 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

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