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
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
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|-
 
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! Selection keywords
 
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
 
|-
 
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! Official Release
 
! Official Release
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| [https://pymol.org PyMOL v2.0 has been released] on September 20, 2017.
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
 
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|-
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! Plugin Update
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! New Plugin
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
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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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| [http://pymol.org PyMOL v1.8.6 has been released] on March 9, 2017.
 
 
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! Official Release
 
! Official Release
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| [http://pymol.org PyMOL v1.8.4 has been released] on October 4, 2016.
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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|-
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! New Script
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! Python 3
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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! New Plugin
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! POSF
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| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
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! Official Release
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! Tutorial
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| [http://pymol.org PyMOL v1.8.0 has been released] on Nov 18, 2015.
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| [[Plugins Tutorial]] updated for PyQt5
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|-
 
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! PyMOL Open-Source Fellowship
 
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| Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on http://pymol.org/fellowship
 
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! Official Release
 
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| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released] on May 4, 2015.
 
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
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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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! New Plugin
+
! Selection keywords
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 
|-
 
|-
−
! New Plugin
+
! Plugin Update
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
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! 3D using Geforce
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! New Script
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| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-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 Vision, this was previously only possible with Quadro video cards.
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 
|-
 
|-
 
! Older News
 
! Older News

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...

Propka

Type Python Script
Download propka.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Acknowledgement

propka.py contact and relies on the result from the propka server

The PROPKA method is developed by the Jensen Research Group , Department of Chemistry, University of Copenhagen.

Introduction

This script can fetch the pka values for a protein from the propka server. The "propka" function downloads the results and processes them.
It also automatically writes a pymol command file and let pymol execute it. This command file make pka atoms, rename them, label them and color them according to the pka value.

If you put the mechanize folder and the propka.py script somewhere in your pymol search path, then getting the pka values is made super easy. By the way, did you know, that you don't have to prepare the .pdb file by adding/removing hydrogens? The ..→

A Random PyMOL-generated Cover. See Covers.


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