Editing Older News (section)

= Older News=
* New Plugin: [[Lisica|LiSiCA]] is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
* New Plugin: [[PyANM|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: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
* 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.
* 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 [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
* [[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
* [[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|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 [[3d_pdf|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 [http://propka.ki.ku.dk/ 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 [http://www.bitgnome.net 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 [http://www.schrodinger.com/news/47/ sale].
* One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 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]]&mdash;stores information on structures, so we don't have to recompute them.
* News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
* [[Fetch_Path]]&mdash;Sets the default path for the [[fetch]] command.
* [[SelInside]]&mdash;Creates a custom selection of all atoms spatially inside some user-defined box.

* [[ContactsNCONT]]&mdash;The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
* [http://www.youtube.com/watch?v=oCRJ4r0RDC4 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 &mdash; 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 [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|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]] &#8212; find the names of all objects in a selection.
* [[CalcArea]] &#8212; find the area of any given object/selection;
* [[ConnectedCloud]] &#8212; find connected clouds of objects in PyMOL.
* [[MakeVinaCommand]] &#8212; Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
* [[DrawBoundingBox]] &#8212; 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]] &#8212; Example using PyMOL and the PDB Web Services.
* [[LigAlign]] &#8212; Ligand-based active site alignment and comparison.
* Added a [[COM|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. &diams; 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 [[:Category:Performance|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
* [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html 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]]

* [[3D_Display_Options|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 [[removeAlt|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 <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!
* [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|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 [http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi#Parameters GeSHI Parameters].
* Adding a special category/section for active PyMOL [[:Category:Development|Development]].
* PyMOL 1.0 has been released!
* [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.


* New PyMol Features: [[Examples_of_cartoon_ring_and_cartoon_ladder_settings|Nucleic Acid Representation Settings]] & Examples.
* Cool new Plug-In: [[Show_NMR_constrains| Show NMR Constrains]].
* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|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_Sequence| peptide sequences]] and [[Nucleic_Acid_Sequence| 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 
# [[Draw]] command and,
# [[Spheres]] Shader Spheres represenation
* Also, [[Ray]] and [[Draw]] now show oversized images scaled into the viewport.

* [[Cealign|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#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.