Difference between revisions of "Zero residues"
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(New page: == OVERVIEW == This script will renumber all the residues such that the first one is numbered 0. This is often helpful when dealing with alignments. == EXAMPLE == <source lang="python"> zero_residues ...) |
(No difference)
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Revision as of 12:44, 2 April 2007
OVERVIEW
This script will renumber all the residues such that the first one is numbered 0. This is often helpful when dealing with alignments.
EXAMPLE
zero_residues 1AFK
zero_residues *
INSTALL
Copy the source code below, to "zero_residues.py" and then simply run the file. The command, "zero_residues" will now be defined and can be used as in the examples above.
CODE
import pymol
def zero_residues(sel1):
"""
PURPOSE: renumbers the residues so that the first one is zero.
USAGE: zero_residues protName
EXAMPLE: zero_residues *
EXAMPLE: zero_residues 1ESR
"""
# variable to store the offset
stored.first = None
# get the names of the proteins in the selection
names = cmd.get_names(sel1)
# for each name shown
for p in names:
# get this offset
cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resi")
# don't waste time if we don't have to
if ( stored.first == 0 ):
continue;
# reassign the residue numbers
cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % stored.first)
# update pymol
cmd.sort()
# let pymol know about the function
cmd.extend("zero_residues", zero_residues)