patch for XPLOR PDB files
rull at PANDA.CHEM.RUU.NL
Fri Oct 10 09:28:14 EST 1997
Attached is a script 'patchXPLORpdb' which will slightly alter
the formatting of PDB files as produced by XPLOR.
The patches are intended to circumvent problems which are sometimes
encountered due to nomenclature differences between XPLOR and the
official PDB rules, and problems related to the use of 'segid' where
PDB has 'chainID'.
The script will correct 4-character atom names such as HG11, HD23 etc.
to 1HG1, 3HD2 etc. 3-character names are unchanged, although
2HB would be preferred instead of HB2, etc.
Names such as HG11 are not recognized by PROCHECK (causing annoying
but harmless error messages) and by WHATIF (causing the program to
skip the unrecognized protons, even when using the all-atom topology
By default the script will also copy the first character of the
SEGID (if present) to the position of the CHAINID. Very often SEGID's
will be used to discriminate polypeptide chains in multimers.
Although the extended PDB format allows the SEGID to be defined in the
coordinates file, many programs will not use the SEGID to distinguish
between chains. The current version of AQUA (1.4.1) is an example.
By simply copying the identifier one can ensure that chains will be
recognized when needed. This option can be switched off.
After installing the script as an executable file, typing
will show the (very simple) usage instructions.
The script can also be retrieved from our ftp-server and through the
AQUA home page (http://www-nmr.chem.ruu.nl/users/rull/aqua.html).
Thanks to Weiping Shao, Irene Nooren, Greg Warren and others for
reporting the problems.
J.A.C. Rullmann http://www-nmr.chem.ruu.nl/users/rull/rull.html
Bijvoet Center for Biomolecular Research mailto:rull at nmr.chem.ruu.nl
Utrecht University, Padualaan 8, phone: int+31.30.253 3641
3584 CH Utrecht, the Netherlands fax: int+31.30.253 7623
More information about the X-plor