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| | [[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. | | | [[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. |
| |- | | |- |
| ! New Script | | ! Older News |
| | [[PluginDirectory]]: How to set up a personal plugin directory
| | | See [[Older_News]]. |
| |-
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| ! New Script
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| | Add focal blur to images [[FocalBlur]].
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| |-
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| ! New Script
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| | Visualize VDW clashes with [[show bumps]]
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| |-
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| ! New Plugin
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| | Color by [[DSSP]] or [[Stride]] secondary structure assignment
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| |-
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| ! New Script
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| | There is a new script to calculate the [[Radius of gyration]]
| |
| |-
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| ! New Command
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| | [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example.
| |
| |-
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| ! New Script
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| | [[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.
| |
| |-
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| ! New Script
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| | [[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.
| |
| |-
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| ! New Script
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| | Two new scripts: [[AAindex]] and [[Sidechaincenters]]
| |
| |-
| |
| ! New Plugin
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| | [[CAVER_2.0]] update to the CAVER plugin.
| |
| |-
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| ! New Script
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| | [[AngleBetweenHelices]] calculates the angle between two helices.
| |
| |-
| |
| ! Search
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| | [[GoogleSearch]] widget fixed.
| |
| |-
| |
| ! New Script
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| | [[Spectrumany]] creates color gradients with arbitrary color sequences.
| |
| |-
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| ! New Script
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| | [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
| |
| |-
| |
| ! New Script
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| | [[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).
| |
| |-
| |
| ! New Script
| |
| | [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
| |
| |-
| |
| ! New Scripts
| |
| | [[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.
| |
| |-
| |
| ! New Script
| |
| | See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL. | |
| |-
| |
| ! New Script
| |
| | See [[Supercell]], the new script for making XxYxZ supercells.
| |
| |-
| |
| ! New Script
| |
| | 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.
| |
| |-
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| ! New Script
| |
| | See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
| |
| |-
| |
| ! Server updates
| |
| | 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 setting
| |
| | [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
| |
| |-
| |
| ! Fetch
| |
| | [[Fetch]] has been updated to also load electron density maps.
| |
| |-
| |
| ! Schrodinger Buys PyMOL
| |
| | Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale].
| |
| |-
| |
| ! User Movie
| |
| | One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL.
| |
| |-
| |
| ! New setting
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| | [[surface_cavity_mode]] to change how PyMOL displays cavities.
| |
| |-
| |
| ! Search fixed.
| |
| | Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems.
| |
| |-
| |
| ! New Command
| |
| | [[Cache]]—stores information on structures, so we don't have to recompute them.
| |
| |-
| |
| ! Warren
| |
| | News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
| |
| |-
| |
| ! Setting
| |
| | [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
| |
| |-
| |
| ! New Script
| |
| | [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
| |
| |} | | |} |
| |style="vertical-align: top; width: 40%"| | | |style="vertical-align: top; width: 40%"| |
