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• Plugins Tutorial
  See the [[plugins]] page for how to install and use exisiting plugins. ...utorial shows how to write a PyMOL plugin with PyQt. '''The full source of the demo plugin is [https://github.com/Pymol-Scripts/pymol2-demo-plugin availab
  4 KB (636 words) - 03:42, 24 June 2019
• PyShifts
  Determining the structure of biomolecules is an important step in understanding how they ...biomolecule. Accordingly, chemical shifts are now routinely used to model the secondary and tertiary structure of proteins.
  5 KB (668 words) - 03:40, 3 February 2020
• Colorblindfriendly
  Certain colors are indistinguishable to people with the various forms of color blindness, and therefore are better not used in figu ...reference to consult when making all kinds of figures, not just those made using PyMOL.
  4 KB (585 words) - 04:50, 11 December 2017
• Views
  ...terface for store and recall the camera view. This plugin is an wrapper to the [[view]] command. ...option on the "Scene" menu (the last one). Double-click an entry to rename the view. Erase it's name to delete it.
  898 bytes (125 words) - 02:11, 24 November 2019
• Enable
  ...selecting the object in the list at the top of the [[Internal_gui|Internal GUI]]. : the name of an object or a named selection (default="all")
  886 bytes (130 words) - 23:57, 20 May 2014
• Jupyter
  * Directly using the PyMOL API ** Running PyMOL and Jupyter in the same interpreter
  3 KB (392 words) - 03:43, 6 December 2021
• Launching From a Script
  ...as the interpreter. This is supported by all versions of PyMOL, including the pre-compiled bundles provided by Schrödinger. For advanced users, the following PyMOL versions also allow to run PyMOL from an existing Python pr
  4 KB (675 words) - 05:13, 26 May 2020
• Command Line Options
  ...controlling it immediately from startup. Run ''''help launching'''' from the command line for detailed listings of options for your current version of P -A3 internal GUI only, no splash (-qx -X 68 -Y 100)
  5 KB (729 words) - 04:31, 26 June 2017
• Azahar
  [[Image:Azahar_GUI.png|480px|thumb|Azahar GUI.]] Azahar (pronounced /ɑːsɑːˈɑːr/) is a plugin that extends the PyMOL's capabilities to visualize, analyze and model glycans and glycoconju
  6 KB (985 words) - 05:01, 22 June 2020
• Surface quality
  ...n quality photos, and truer representations of the biological surface, set the value higher--to something like 2, 3 or 4. In practice typical values are ...puter about 2 minutes just to prepare the surface for showing in the PyMOL GUI (this does not include any ray-tracing or rendering). Lastly, ray tracing
  1 KB (182 words) - 03:27, 14 November 2016
• MovieSchool 1
  ...d through movies, than static images alone. This little page will provide the necessary ideas, links, code and examples for making movies in PyMOL. # to stop the movie when you're ready
  3 KB (425 words) - 02:16, 28 March 2014
• Morph
  ...bject, '''morph''' can create an interpolated trajectory from the first to the second conformation. ...N morphings between all consecutive states and back from state N to 1 (so the morph will have N*steps states). If state2=0, create N-1 morphings and stop
  4 KB (614 words) - 03:24, 10 December 2018
• MOLE 2.0: advanced approach for analysis of biomacromolecular channels
  ...f the functionality and instructions on working with MOLE 2 please consult the [http://dx.doi.org/10.1186/1758-2946-5-39 paper] or our [http://webchem.ncb ...as been released. The binaries and plugins are available for download from the [https://webchem.ncbr.muni.cz/Platform/App/Mole | main page].
  3 KB (468 words) - 02:39, 24 July 2017
• Dssp
  ...ift.cmbi.ru.nl/gv/dssp/ DSSP] program, which computes secondary structure. The command updates PyMOL's '''ss''' atom property. The [[dssp]] command is available from the [[psico]] package and requires the [http://swift.cmbi.ru.nl/gv/dssp/ dssp] binary (or mkdssp, dsspcmbi, dssp-2
  1 KB (210 words) - 03:27, 13 November 2017
• Undo
  ...by unchecking `Edit -> Undo Enabled`, and can be re-enabled by rechecking the same menu item. Currently, the undo stack supports the previous 25 actions or up to 1GB memory used. These will later be configura
  2 KB (272 words) - 03:21, 22 June 2021
• MtsslDock
  ...directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. Alternatively install the plugin via the Plugin Manager.
  5 KB (840 words) - 05:13, 26 May 2020
• Category:Uncategorized
  It's not GUI, but you could simply bind a function key such as F1 to a command: You have to load the potential data by Delphi or some other program like AMBER version 9:
  0 members (0 subcategories, 0 files) - 01:29, 28 March 2014
• Optimize
  ...[http://openbabel.org openbabel], allowing the user to optimize (minimize) the energy of any molecule uploaded on PyMOL. The plugin can be downloaded through the project [[git_intro | Pymol-script-repo]].
  6 KB (815 words) - 03:23, 29 April 2019
• Pytms
  ...repo/blob/master/plugins/pytms.py downloaded separately], or together with the [https://github.com/Pymol-Scripts/Pymol-script-repo pymol-script-repository The '''pytms.py''' file should be placed in the '''plugins''' folder.
  9 KB (1,151 words) - 04:40, 14 December 2015
• Msms surface
  [[msms_surface]] is available from the [[psico]] package and requires the [http://mgltools.scripps.edu/downloads#msms msms] binary. * [[MSMS]] (plugin with GUI)
  1 KB (173 words) - 03:27, 13 November 2017

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