Revision as of 02:00, 28 March 2014

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.

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

Draw command and,
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.

@@ Line 1: / Line 1: @@
 = 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
+* [[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
@@ Line 7: / Line 125: @@
 # [[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.

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