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The '''internal GUI''' is the GUI that is natively built into PyMOL. Hide the internal gui with,

This sets how PyMOL renders the internal GUI & controls. The default setting, 0. Image:Ig_mode1.png|internal_gui_mode, set to 1. Notice the coloring under the controls.

...sets how large the internal gui controls are. An internal GUI control is the button you click on to enable/disable a protein, select colors, etc. # set the size to some positive integer

...edback]] is the openGL-based command line area. Setting this to 0 removes the area; setting it to 1 makes one line visible (so you can see what you're ty # set the number of lines shown to 'int', where int is

[[File:PyMOLProbity_GUI.png|480px|thumb|right|The PyMOLProbity GUI can be used to inspect and adjust clashes and flip orientations of flippabl ...ps://github.com/jaredsampson/pymolprobity PyMOLProbity] is a plugin allows the user to produce MolProbity-style

...esentation for certain selections, or roll their own hand-made versions of the command (see below). ====GUI====

...e, modify, delete, and reset keyboard shortcuts. This functionality mimics the [[Set_Key]] function. The Keyboard Shortcut Menu is located in the "Setting" menu heading.

...t_color_indices''' in combination with '''get_color_tuple''' will retrieve the RGB values for colors. will retrieve the Pymol color names and corresponding internal color indices. The Pymol names can be used to designate color for objects, see [[Color]]. To

This determines if PyMOL takes up the entire desktop screen or not. ...e the "F" button in the bottom-right corner of the [[Internal_Gui|internal GUI]] to toggle full screen.

The [[Builder]] is a PyMOL GUI menu that allows you to easily build up structures by hand from various ele To access the [[Builder]] simply select the "Builder" option from the PyMOL GUI (see images).

...ernal gui]], the [[internal prompt]], label fonts etc. by a multiple of 1. The setting was introduced to scale by a factor of 2 on high resolution [https: * '''--retina''' [[Command_Line_Options|command line option]] sets the factor to 2

...ing the object in the list in the top panel of the [[Internal_gui|Internal GUI]]. : the name of an object or a named selection (default="all")

...never changes are made. This can be used to mask multiple operations from the user to make it appear as if only one operation occurred. See examples. # remove the waters

...properties and settings. It opens when clicking the "Properties" button in the upper right. Screenshot of PyMOL with the properties panel open, after applying "A > preset > pretty" to PDB 1rx1:

A plugin is a Python module which uses PyMOL's API. The following entrypoints add functionality to PyMOL: ...ugin__(app)</code>]] is called during plugin initialization (if defined by the plugin)

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

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.

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.

...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.

...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")

* Directly using the PyMOL API ** Running PyMOL and Jupyter in the same interpreter

...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

...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)

[[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

...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

...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

...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

...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].

...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

...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

...directory. After PyMOL has been started, the program can be launched from the PLUGINS menu. Alternatively install the plugin via the Plugin Manager.

...[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]].

...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.

[[msms_surface]] is available from the [[psico]] package and requires the [http://mgltools.scripps.edu/downloads#msms msms] binary. * [[MSMS]] (plugin with GUI)

...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

...neath a '''+''' sign in the object tree (see images) in the Pymol Internal Gui. # put all of objState into the group "ensemble".

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.

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

...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.

...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.

...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

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

....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.

'''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]].

...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.

...intended to introduce the PyMOL interface and basic tasks without leaving the mouse behind. ==The PyMOL Interface==

|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.

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

[[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.

...rnatively, the selections can be chosen using a dialog box accessible from the Plugins menu. == The Code ==

...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

...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