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! Official Release
! Official Release
| [https://pymol.org PyMOL v2.1 has been released] on March 13, 2018.
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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! New Plugin
| [[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
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
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! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
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! New Plugin
| [[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
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! New Script
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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! New Plugin
| [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
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! New Plugin
| [[PyANM|PyANM]] is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
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! New Plugin
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
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! New Plugin
| [[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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! 3D using Geforce
| 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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! Older News
! Older News

Latest revision as of 11:54, 12 March 2024

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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...

Map set

Map_set created this consensus volume representation of aligned ligands bound to kinases. See example below.

Map_set provides a number of common operations on and between maps. For example, with Map_set you can add two maps together or create a consensus map from a series of maps or even take a difference map.

Usage

map_set name, operator, operands, target_state, source_state

operator may be,

  • average
  • copy
  • difference
  • maximum
  • minimum
  • sum
  • unique

Examples

# add 3 maps
map_set my_sum, sum, map1 map2 map3

# calculate the average map
map_set my_avg, average, map1 map2 map3

Detailed Example

This example shows you how to create a consensus map of the bound ligand in a conserved pocket.

<source lang="python">

  1. fetch some similar proteins from the PDB

fetch 1oky 1h1w 1okz 1uu3 1uu7 1uu8 1uu9 1uvr, async=0

  1. align them all to 1oky; their ligands
  2. should all now be aligned

alignto ..→

A Random PyMOL-generated Cover. See Covers.


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