I have found a small problem with O 6.2.1 that may cause some havoc later
on if one is not vigilant.
There is a change in the output when you tell O to write out a PDB
formatted file in version 6.2.1 from that of version 5.10.3. O 6.2.1
apparently changes a character in the 21st column to a blank. The
following illustrates this:
REMARK Written by O version 6.2.1
REMARK Wed Oct 21 16:07:01 1998
ATOM
3978 MN+2 MN+ A 532 -6.492 30.193 26.532 1.00 25.70 25
1PKA
END
REMARK Written by O version 5.10.3
REMARK Fri Jun 5 15:06:52
1998
REMARK DATE:09-Jul-98 09:51:26 created by user: cz
ATOM 4888
MN+2 MN+2 532 -6.505 30.092 26.791 1.00 27.43 1PKA
END
When you use these ATOM records in a file to generate a psf structure file
using XPLOR 3.8.5.1, the O 5.10.3 version record is properly incorporated.
However, the ATOM record written by version 6.2.1 is not and the record is
omitted from the psf and the pdb files written by XPLOR. Usually the
generate function of XPLOR is very particular and any error stops the
program. In this case XPLOR writes a short error message buried in the log
file and merrily goes on and creates a psf structure file and a pdb file
without the ion. If you have a large list of atoms in your pdb file, it is
easy to not notice that your structure is missing one atom out of several
thousand.
Cheers
************************************************************************
* Edmund W. Czerwinski, Ph.D *
S Associate Professor U
* Sealy Center for Structural Biology *
C Dept. of Human Biological Chemistry & Genetics T
* The University of Texas Medical Branch *
S Galveston, TX 77555-0647 M
* *
B Voice:(409)772-3287 Fax:(409)747-4745 B
* edcz at hbcg.utmb.eduhttp://www.hbcg.utmb.edu/faculty/ *
************************************************************************
