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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! POSF
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! Official Release
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| [https://pymol.org/fellowship PyMOL Open-Source Fellowship program] accepting applications for 2018-2019
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
 
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! New Plugin
 
! 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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| [[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
 
! Official Release
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| [https://pymol.org PyMOL v2.1 has been released] on March 13, 2018.
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
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! New Plugin
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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
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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
 
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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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! 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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! New Plugin
 
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| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
 
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! New Plugin
 
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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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! 3D using Geforce
 
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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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! 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...

SelInside

selInside selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples.

Usage

# find all atoms inside the box spanned by (0,0,0) and (10,10,10)
# for the example PDB, 1hpv
fetch 1hpv
pseudoatom b1, pos=[0,0,0]
pseudoatom b2, pos=[10,10,10]
selInside b1 or b2


The Code

<source lang="python"> import pymol from pymol import cmd, stored from random import randint

def selInside(bounding_object, target="*", radius=None): 

   """
   Selects all atoms of a given target type inside some selection that acts like a bounding box.

   PARAMS:
       bounding_object -- [PyMOL object/selection] the object/selection inside of which we want to choose atoms
       target -- [PyMOL selection] that defines the atoms to select.  Use "solvent" to select
                 only solvent atoms inside the selection
       radius -- [float] expand the box by this many angstroms on all sides

   RETURNS:
       (string) name of the selection created

   ..→
A Random PyMOL-generated Cover. See Covers.


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