AlphaToAll
From PyMOLWiki
Overview
AlphaToAll will expand the alpha-carbon property that you specify to all atoms in the residues. For example, if you set the b-factor column to some different value for all alpha carbons, this script will propagate those values into all the atoms as well.
In the example below, notice the color of the sticks.
The alpha carbon here has a color property that does not match the rest of the residue.
This script will fix that, expanding the color attribute to the rest of the atoms.
Usage
# expand propertyName in objName on all the alpha carbons # to every atom, for each residue alphaToAll objName, propertyName # Example #1 # For all objects, for each residue, set every atom's b-column value # to match that residue's alpha carbon's b-column value. alphaToAll *, b # Example #2 # For selection 1qox and c. A expand the alpha carbon # colors to all atoms in the selection alphaToAll 1qox and c. A, color
The Code
from pymol import cmd, CmdException def alphaToAll(sel, col="b",forceRebuild=False): """ alphaToAll -- expand any property of the alpha carbons to all atoms in the residue PARAMS sel The selection or object (include "*" for all objects) to operate on. This will read the alpha carbon's "COL" property and expand that down to all atoms in the given residues in sel. col Any valid PyMOL property. For example, 'b' or 'q' or 'color', etc. DEFAULT: b, for B-factor as we most often overwrite that column forceRebuild If a color changes, this will rebuild the objects for us. For speed, we DEFAULT this to False. RETURNS None, just epxands the properties as dicsussed above. NOTES This script is useful for instances where we update the b-factor column for the alpha carbons and then want to expand that color to all atoms for smoother looking images. AUTHOR: Jason Vertrees, 2009. """ col = '(' + ','.join(col.split()) + ')' space = {'props': dict()} cmd.iterate('byca (%s)' % (sel), 'props[model,segi,chain,resi] = ' + col, space=space) cmd.alter(sel, col + ' = props.get((model,segi,chain,resi), ' + col + ')', space=space) if forceRebuild != False: cmd.rebuild(sel) cmd.extend("alphaToAll", alphaToAll)
