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Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
If you want to contribute new content to this wiki, request an account by emailing accounts (@) sbgrid dot org from your institutional email address.

News & Updates
New Setup	PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install.
New Plugin	PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024.
Official Release	PyMOL v3.0 has been released on March 12, 2024.
New Plugin	CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
Official Release	PyMOL v2.5 has been released on May 10, 2021.
Python 3	New Python 3 compatibility guide for scripts and plugins
POSF	New PyMOL fellowship announced for 2022-2023
Tutorial	Plugins Tutorial updated for PyQt5
New Plugin	PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords	New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update	MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script	dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News	See Older News.

Did you know...
Smooth Smooth performs a window average of coordinate states. Usage smooth [ selection [, passes [, window [, first [, last [, ends]]]]]] # for example, smooth and object with 30 passes and # a window size of 100. smooth myObj, 30, 100 ends = 0 or 1: controls whether or not the end states are also smoothed using a weighted asymmetric window To see smooth in context see this example NOTES This type of averaging is often used to suppress high-frequency vibrations in a molecular dynamics trajectory. This function is not memory efficient. For reasons of flexibility, it uses two additional copies of every atomic coordinate for the calculation. If you are memory-constrained in visualizing MD trajectories, then you may want to use an external tool such as ptraj to perform smoothing before loading coordinates into PyMOL. See Also Load_Traj, protect.

Usage