Zero residues

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Contents

OVERVIEW

This script will renumber all the residues such that the first one is numbered 0. This is often helpful when dealing with alignments.

Ordering from Sequence End

If you want to change numbering based off the last residue's number in the sequence, just replace first in the code with last.

EXAMPLE

zero_residues 1AFK
zero_residues *
 
# make the first residue's number, 30.
zero_residues 1AFK, 30

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

from pymol import cmd, stored
 
def zero_residues(sel1,offset=0,chains=0):
        """
DESCRIPTION
 
    Renumbers the residues so that the first one is zero, or offset
 
USAGE
 
    zero_residues selection [, offset [, chains ]]
 
EXAMPLES
 
    zero_residues protName            # first residue is 0
    zero_residues protName, 5         # first residue is 5
    zero_residues protName, chains=1  # each chain starts at 0
    zero_residues *
        """
        offset = int(offset)
 
        # variable to store the offset
        stored.first = None
        # get the names of the proteins in the selection
 
        names = ['(model %s and (%s))' % (p, sel1)
                        for p in cmd.get_object_list('(' + sel1 + ')')]
 
        if int (chains):
                names = ['(%s and chain %s)' % (p, chain)
                                for p in names
                                for chain in cmd.get_chains(p)]
 
        # for each name shown
        for p in names:
                # get this offset
                ok = cmd.iterate("first %s and polymer and n. CA" % p,"stored.first=resv")
                # don't waste time if we don't have to
                if not ok or stored.first == offset:
                        continue;
                # reassign the residue numbers
                cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % str(int(stored.first)-offset))
                # update pymol
 
        cmd.rebuild()
 
# let pymol know about the function
cmd.extend("zero_residues", zero_residues)
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