Difference between revisions of "Older News"

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= Older News=
= Older News=
* [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
* [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
* [[DistancesRH|Distances RH]]
* PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
* Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ 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
* [[b2transparency]] can set surface transparency based on atom b-factor
* [[psico]] is a python module which extends PyMOL with many commands
* [[psico]] is a python module which extends PyMOL with many commands

Revision as of 12:46, 18 November 2013

Older News

  • 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.

  • 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.