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.
zero_residues 1AFK zero_residues *
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.
import pymol def zero_residues(sel1,offset=0): """ PURPOSE: renumbers the residues so that the first one is zero, or offset . USAGE: zero_residues protName # first residue is 0 USAGE: zero_residues protName, 5 # first residue is 5 EXAMPLE: zero_residues * """ offset = int(offset) # 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 == offset ): continue; # reassign the residue numbers cmd.alter("%s" % p, "resi=str(int(resi)-%s)" % str(int(stored.first)-offset)) # update pymol cmd.sort() # let pymol know about the function cmd.extend("zero_residues", zero_residues)