Subject: Re: CCL:PDB format with 100000 atoms

From: "Andrew Dalke" <[email-masked]>
Date: Sat, 27 May 2000 11:30:19 -0600

Keith Refson <[email-masked]> asked CCL:
>According to the Brookhaven PDB format website it seems that only a 5
>digit field is allowed for the atom sequence number, so there is no
>way of generating a correct PDB file containing 100000 atoms or more.
>
>Has anyone else come up against this limit and found any workaround?

XPLOR uses a base-36 digit for the first field (that is,
99998
99999
A0000
A0001
  ...
Z9999
).  This takes you up to 36,000 atoms.

This isn't legal, according to the PDB format.  There are some
submitted structures with over 100,000 atoms.  In that case, the PDB
splits the submission into two parts.  For example and 1BGL and 1BGM
are parts of the same structure - 66344 and 66310
  http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1BGL
  http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1BGM

I personally believe software reading a PDB file should ignore the
atom index fields.  The ones from the PDB always have numbers starting
>from 1 and never have gaps.  I've never seen files elsewhere which
encoded information in those numbers.  (There can be different numbering
schemes as when creating the full structure from a monomer, but that
scheme exists only long enough to renumber it in the proper form.)

For output, I've usually extended XPLOR's notation, and let the first
character of the serial number go to 'A' after '9'.  I then continue
the ASCII sequence after 'Z', so '[', '\', ']', ... .  That gives up
to 2 million atoms, though after that it loops back to 0 and starts
generating '\000' (C's end-of-string character) and '\n' (newline)
which would affect parsing.  Something will have to be done when
we start manipulating 2 million atom structures but the most I've done
to date is a million atoms, for a software stress test.

                    Andrew
                    [email-masked]