Hey Paul, I believe I have figured out the problem - but not the solution.
On closer inspection, it wasn't just the numerically labelled chain IDs that weren't read, a few of the alphabetical chains were also not read. What happens is REFMAC restarts atom numbering once 100000 atoms are reached when outputting the refined coordinates. COOT was reading in the first 99999 atoms, numbered 1-99999 by REFMAC, then the second 99999 atoms, again numbered 1-99999 by REFMAC. At this point, however, REFMAC for some reason made the next atom 100000 and then restarted numbering at 1. This atom, numbered 100000, was not read by COOT and nor where any subsequent atoms. The input coordinates that I used for REFMAC, which again consisted of 60 chains, was created by combining sets of 10mers, thus the atom numbering restarted after each 10 chains. REFMAC had no problem refining these coordinates and COOT had no problem reading these coordinates. To further confirm that COOT is failing once it reads atom 100000, I wrote a little perl script to properly renumber the atoms in the REFMAC refined coordinates. In this file, there are correctly 246960 atoms. Within my perl script, I formatted the output such that the atom numbers eat into the spaces after "ATOM" like so: ATOM 246960 O LEU 7 736 64.294 96.393-111.576 1.00 34.97 I see now that the last atom COOT reads in is atom number 99999. Perhaps, I fear, this is a problem with the PDB format - that the column width for atom numbers can not accommodate more than 99999 atoms. Ed On Tue, Jun 2, 2009 at 9:39 AM, Paul Emsley <paul.ems...@bioch.ox.ac.uk>wrote: > Edward Miller wrote: > >> Hey Folks, >> >> I'm working on refining a full capsid containing 60 chains. >> >> Using the chain ID column, I've numbered my chains A-Z, a-z, and 0-7. I >> was successfully able to refine my capsid in refmac using this chain ID >> naming scheme. >> >> However, coot fails to read in any of the chains labeled 0-7. >> > > I don't know why this is failing - I will try to make a synthetic PDB file > with 60 chains to see if I can reproduce this. > > Relatively recently Eugene has extended mmdb to work with the hybrid_36 > format. So for now you could go that route. > > Paul. >
