Thanks to all. Pymol does it readily, as Bob Immormino and Laurie Betts suggested. Other suggestions probably would also work.
Charlie On Aug 20, 2010, at 9:20 PM, James Stroud wrote: > You seem to have two different criteria listed, one more general than the > other: > > 1. You need two or more PDB files to have the side chain atoms in the same > order. > 2. You need a specific ordering of side chain atoms applied to all PDB files. > > The former is easier because it doesn't require some committee to waste their > time agreeing on an ordering. > > If the latter suffices and it is a one-off task, then I can do it for you. I > have an API for this kind of thing, but it is not documented...yet. > > James > > > > On Aug 20, 2010, at 9:50 AM, Charles W. Carter, Jr wrote: > >> Is there a program that will read in a pdb coordinate file and re-order the >> side chain atoms in each residue according to a standard order? >> >> I've a program that compares two files for the same structure, but requires >> that the order of the atoms be the same in both cases. I'm using a variety >> of files in which the residue atoms are ordered either main chain first or >> side-chain first. I've not found a suitable program in the CCP4 suite, >> though one might exist. MOLEMAN2 doesn't seem suitable, either. >> >> Thanks, >> >> Charlie
