Additionally, since this was asked before, I am running COOT 0.5.2 Ed
On Tue, Jun 2, 2009 at 6:00 PM, Edward Miller <[email protected]> wrote: > 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 <[email protected]>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. >> > >
