Older News

Older News

• New Plugin: LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
• New Plugin: PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
• New Plugin: Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
• New Plugin: MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
• PyMOL can now be 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.
• New Plugin: GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
• New Software: CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
• New Script: cgo_arrow draws an arrow between two picked atoms.
• Tips & Tricks: Instructions for generating movie PDFs using .mpg movies from PyMOL.
• Cluster Count calculates statistics on the B-values for all atoms in the selected object.
• Make Figures aids you in making publication quality figures for the currently displayed scene.
• Distances RH
• PyMOL is now available on the iPad as a free download from the AppStore. See pymol.org/mobile for more info.
• Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here X11 Libraries.
• select_sites can set author/paper selections according to SITE annotation in pdb file
• b2transparency can set surface transparency based on atom b-factor
• psico is a python module which extends PyMOL with many commands
• uniprot_features makes named selections for sequence annotations from uniprot
• Gyration_tensor Calculates chain-wise gyration tensor of a protein.
• set_phipsi can set phi/psi angles for all residues in a selection
• dehydron A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
• pymol2glmol is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
• cyspka is an experimental surface cysteine pKa predictor.
• Contact_Map_Visualizer visualize residues corresponding to the contact map. See CMPyMOL.
• spectrum_states colors states of multi-state object
• TMalign is a wrapper for the TMalign program
• The gallery has been updated to include a few new ideas and scripts for rendering
• save_settings can dump all changed settings to a file
• Instructions for generating 3D PDFs using PyMOL.
• Wiki has been updated. Please report any problems to the sysops.
• Create objects for each molecule or chain in selection with split_object and split_chains
• Rotkit: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function.
• Forster-distance-calculator: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See DisplacementMap.
• propka: Fetches the pka values for your protein from the propka server. propka generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
• PluginDirectory: How to set up a personal plugin directory
• Add focal blur to images FocalBlur.
• Visualize VDW clashes with show bumps
• Color by DSSP or Stride secondary structure assignment
• There is a new script to calculate the Radius of gyration
• New Command
• Map_set Performs a given operation on a map: can create consensus volumes, for example.
• ColorByDisplacement Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.
• DisplacementMap Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
• Two new scripts: AAindex and Sidechaincenters
• CAVER_2.0 update to the CAVER plugin.
• AngleBetweenHelices calculates the angle between two helices.
• GoogleSearch widget fixed.
• Spectrumany creates color gradients with arbitrary color sequences.
• BbPlane will draw CGO planes across the backbone highlighting planarity of arrangement.
• Center Of Mass has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere).
• Jump is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
• ResDe is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
• See BiologicalUnit, for a workaround to the buggy Symexp command or if you just want to learn more about symmetry expansion in PyMOL.
• See Supercell, the new script for making XxYxZ supercells.
• See Split_Object_Along_Axis, for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
• See Consistent_View/_Map_Inspect, which is a toolkit for rapidly inspecting multiple maps and models.
• The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend. We are now fully functional. A deep thanks to BitGnome for donating time and hardware for the PyMOL project.
• Fetch_Host has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
• Fetch has been updated to also load electron density maps.
• Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the sale.
• One of our users has posted another interesting movie, images from which were created with PyMOL.
• surface_cavity_mode to change how PyMOL displays cavities.
• Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
• Cache—stores information on structures, so we don't have to recompute them.
• News about Warren DeLano's passing may be read on Warren's memorial page.
• Fetch_Path—Sets the default path for the fetch command.
• SelInside—Creates a custom selection of all atoms spatially inside some user-defined box.

• ContactsNCONT—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
• PCR Rap video made with PyMOL (YouTube).
• Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
• New — Search the PyMOLWiki via GoogleSearch
• PyMOL is known to work under Mac OS X 10.6+ (Snow Leopard) using the new Fink and incentive builds. See Installing PyMOL under Fink.
• PyMOL now has a Set command for basic settings, and a Set_bond command for bond-only settings.
• PyMOL now comes with some builtin examples: look in the examples directory of your source tree.
• group command has been added.
• The truly awesome grid_mode setting has been added.
• Ellipsoids representation added for drawing thermal ellipsoids.
• GetNamesInSel — find the names of all objects in a selection.
• CalcArea — find the area of any given object/selection;
• ConnectedCloud — find connected clouds of objects in PyMOL.
• MakeVinaCommand — Use PyMOL to create a valid command line for the new Vina docking software.
• DrawBoundingBox — Draw a bounding box around your selection.
• Locate loaded PyMOL objects that are nearby some other object with FindObjectsNearby.
• Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with LoadDir.
• PDB Web Services Script — Example using PyMOL and the PDB Web Services.
• LigAlign — Ligand-based active site alignment and comparison.
• Added a simple script for finding the center or mass, or moving a selection to the origin.
• Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests. ♦ New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).
• New category about PyMOL performance: making the impossible possible, and the difficult easier/faster.

• ImmersiveViz -- Headtracking user interface for PyMOL (watch the video)!
• Colorama --a PyMOL plugin which allows to color objects using adjustable scale bars
• ProMOL plugin added. Catalytic site prediction, other tools. Redirects to website.
• EMovie plugin added. Easy movies in PyMol using a GUI.
• DYNMAP plugin page created. Check it out!
• EZ-Viz

• Stereo 3D Displays.
• Massively restructured the TOPTOC and make the OLD_TOPTOC for the older version. Still need to add more content to the TOPTOC.
• Added a simple script for removing specific alternately located atoms.
• Added a starter gallery of PyMOL-created Journal Covers.
• Added some information on how PyMOL handles Nonstandard_Amino_Acids.
• Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been very fortunate to have hosting from BitGnome.Net; they've done an incredible job!
• Gallery -- Did you make a cool image? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).

• Updated the wiki. Also installed the newer GeSHI extension. Please keep an eye out for source code that is improperly tagged and so improperly formatted. See GeSHI Parameters.
• Adding a special category/section for active PyMOL Development.
• PyMOL 1.0 has been released!
• PyMOL Official Documentation is also available for subscribers.

• New PyMol Features: Nucleic Acid Representation Settings & Examples.
• Cool new Plug-In: Show NMR Constrains.
• Check out PyMol's new Nucleic Acid Rendering
• Added DynoPlot script for plotting data within PyMol; an interactive Ramachandran plot.
• Added Kabsch script for optimal alignment of two sets of vectors.
• Some details have been released about 0.99beta11's release and new features.

• A new map function is in the beta build, Map_Trim.
• Details on how to build peptide sequences and nucleic acid sequences by hand.
• New Transform_odb script to transform coordinates with .odb file from O or LSQMAN

• How to create multiple Distance objects.
• Nuccyl's address changed.

• PyMol gets some new features. PyMol 0.99beta07 added these commands for testing, check out the new

1. Draw command and,
2. Spheres Shader Spheres represenation

• Also, Ray and Draw now show oversized images scaled into the viewport.

• CE Align v0.8-RBS released. Better than before. See test case comparisons.
• Slerpy, a set of pymol command extensions to simplify complex movie making is now available.
• Updated the Kabsch code with a more elegant solution; fixed a small rotation bug.