More YASARA plugins from our group
Contents
ConSurf plugin
This plugin colors the residues in the selected molecules by conservation scores assigned by the ConSurf webserver at consurf.tau.ac.il. If the object name is a valid PDB ID, the plugin will download the preassigned conservation scores, caching them for quick reuse later. If the object name is not a valid PDB ID, the plugin assumes that this is a private structure which you submitted manually to the server before, so that the B-factors already represent the conservation scores and coloring can start immediately.
Coloring can be done in two ways. First by conservation gradient only: cyan is variable, gray is average and purple is conserved. Second by amino acid property and conservation blended together: polars are green, hydrophobics are yellow, negatives are red and positives are blue. Darker colors mean higher conservation, lighter colours mean lower conservation. With the second color option, two thresholds can be given for assigning high and low conservation. Defaults are 80% for upper and 60% for lower threshold. E.g. with an upper threshold of 80%, this means that all residues with a conservation score higher than 80% of the maximum conservation score are considered highly conserved. If the lower threshold is 60%, residues with a score between 60% of max and 80% of max are considered no so conserved. All other residues below the lower threshold are coloured in gray (means variable).
The ConSurf plugin is now a standard YASARA plugin and comes automatically with YASARA.
The plugin is called from:
View > Color > Molecule by ConSurf
Show residue neighbourhood
This plugin shows residues in a sphere around a set of selected residues and makes use of the with distance < X from Yanaconda statement.
If called from the main menu, a residue selection menu is presented to select the residues to be in the center of the sphere. In the second menu it is possible to set the radius of the sphere, i.e. the size of the neighbourhood to show. In the last menu it is possible to hide all other residues but the residues in the sphere.
The plugin is called from the main menu as:
View > Show atoms in > Residue neighbourhood
The plugin can also be called from the Atom- and ResidueContextMenu by right-clicking on an atom or residue. Then the plugin is called as:
Show atoms > Residue neighbourhood
This plugin is now kind of obsolete since Elmar created those spacey selection commands in YASARA (10.11.8 or higher).
Color all residues by physico-chemical property
This plugin does pretty much the same as when you click:
View > Color > Residue > All > ResType
But since I have not found how to change the YASARA color scheme for residue types, I made this plugin. Colors scheme can be modified in the plugin file.
The plugin can be accessed via:
View > Color > Residue by property
Renumber residues per object
This plugin renumbers the residues per object from 1. When run, the first residue in every object will get number 1. Useful for very specific problems.
The plugin can be accessed via:
Edit > Renumber > Residue per object
