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• 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
• 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
• MAC Install
  ...hrodinger.com Schrödinger] provides pre-compiled PyMOL to paying sponsors. The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG enco Installation: Drag '''PyMOL.app''' on the '''/Applications''' shortcut. (In principle, you could drag it into any Fin
  5 KB (752 words) - 04:22, 12 November 2018
• Group
  ...neath a '''+''' sign in the object tree (see images) in the Pymol Internal Gui. # put all of objState into the group "ensemble".
  2 KB (312 words) - 19:48, 29 May 2017
• Git install scripts
  If you don't have the option or don't feel like installing git on your system, then go to: Click the "ZIP" button, near the top left corner.
  5 KB (711 words) - 03:24, 10 December 2018
• Cluster mols
  cluster_mols is a PyMOL plugin that allows the user to quickly select compounds from a virtual screen to be purchased or s ...cluster_mols also highlights both good and bad polar interactions between the ligands and a user specified receptor. Additionally there are a number of
  8 KB (1,334 words) - 18:29, 25 May 2022
• GROMACS Plugin
  ...add molecular dynamics simulation feature. It is meant to be easy to use. The plugin uses GROMACS tools as a back-end. Project is developed as an open so * Easy to use GUI, to take advantage of complex software GROMACS.
  6 KB (822 words) - 03:27, 13 November 2017
• Advanced Coloring
  ...the upper right part of the main GUI window. The [[Color]] command will do the same. PyMOL has a predefined set of colors that can be edited in the ''Settings->Colors'' menu.
  6 KB (849 words) - 03:47, 7 March 2016
• Leap Motion
  ...https://www.leapmotion.com Leap Motion Controller] working in PyMOL, using the Leap Python API. The script was tested with PyMOL 2.0 on all platforms, with MacPyMOL "syspython
  3 KB (433 words) - 04:50, 11 December 2017
• Biochemistry student intro
  This is the very first introduction to the powerful molecular visualizer PyMOL.<br> We will only cover the very basic steps to get a image of your enzyme and put in your written stud
  17 KB (2,610 words) - 19:16, 20 May 2014
• Linux Install
  ....com Schrödinger] provides pre-compiled (64 bit) PyMOL to paying sponsors. The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG enco ...de the latest version, but if the provided package fits your needs this is the most convenient way to install PyMOL.
  5 KB (713 words) - 05:01, 22 June 2020
• Color
  '''color''' sets the color of an object or an atom selection to a predefined, named color, an RG For a script that enumerates all the colors see, [[List_Colors]].
  6 KB (1,020 words) - 02:11, 24 November 2019
• Ideas
  ...want to discuss an idea or feature implementation just send and e-mail to the [[PyMOL_mailing_list]]. If you want to request a new feature or report a bu ...work may not be ideal since once mistake could potentially to destabilize the entire platform.
  17 KB (2,322 words) - 01:04, 19 October 2015
• Practical Pymol for Beginners
  ...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
• CMPyMOL
  |license = The MIT License (MIT) ...terface for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.
  8 KB (1,116 words) - 05:42, 31 May 2016
• ProBiS H2O
  The most recent version can be obtained at the [http://insilab.org/probis-h2o/ Insilab web page]. ...erved water sites''', we developed '''ProBiS H2O''' workflow that supports the complete
  7 KB (1,055 words) - 19:27, 29 May 2018
• Bnitools
  [[File:bnitools.png||thumb|right|Screenshot of the BNI Tools plugin menu]] ...n for PyMOL which adds additional functionalities and presets to the PyMOL GUI.
  8 KB (934 words) - 05:42, 31 May 2016
• Show contacts
  ...rnatively, the selections can be chosen using a dialog box accessible from the Plugins menu. == The Code ==
  12 KB (1,422 words) - 03:11, 1 April 2019
• MovieSchool 5
  ...tell. We start simple and build up the complexity. Here's an outline of the ideas: * '''camera motions'''&mdash;just moving the camera around your scene
  15 KB (2,259 words) - 02:16, 28 March 2014
• Older News
  ...sica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm. ...sion-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D
  13 KB (1,965 words) - 03:24, 10 December 2018

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