Difference between revisions of "Main Page"

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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
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! Official Release
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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! New Plugin
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| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
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! Official Release
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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! Python 3
 
! Python 3
 
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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! Official Release
 
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| [https://pymol.org PyMOL v2.3 has been released] on February 11, 2019.
 
 
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! POSF
 
! POSF
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
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! Tutorial
 
! Tutorial
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! New Plugin
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| [[ProBiS_H2O|ProBiS H2O]] is a new plugin for identification of conserved waters in protein structures.
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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 
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! Selection keywords
 
! Selection keywords

Latest revision as of 12:54, 12 March 2024

hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
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...

Elbow angle

Type Python Script
Download elbow_angle.py
Author(s) Jared Sampson
License BSD
This code has been put under version control in the project Pymol-script-repo


Introduction

This script allows you to calculate the elbow angle of an antibody Fab fragment object and optionally draw a graphical representation of the vectors used to calculate the elbow angle.



Syntax

elbow_angle object [, light=L [, heavy=H [, limit_l=107 [, limit_h=113 [, draw=0 ]]]]]

The first argument should be a PyMOL object. You can calculate the elbow angles of multiple Fabs from the same object (one at a time) by specifying the chains manually for each Fab.

The `light` and `heavy` arguments are for PDB chain IDs, and `limit_l` and `limit_h` are the last residue of the light and heavy chain variable domains, respectively. (For Kabat-numbered structures, these limits will be 107 and 113, respectively. For structures with different numbering schemes, the limits can be estimated by visual inspection of the PDB file.) ..→

A Random PyMOL-generated Cover. See Covers.


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