For dealing wih PDBv3.0 format, our lab has two new facilities to
offer:
MolProbity, our structure validation and improvement webserver
(http://molprobity.biochem.duke.edu/ ), now accepts coordinate files
in
either PDBv2.3 or PDBv3.0 format and uses the latter for computations.
A formal description of this and other new features will be posted
soon.
We have written a fast 2-way PDB format converter (in Perl or
Python)
dubbed the Remediator, which is currently available for download from:
http://kinemage.biochem.duke.edu/software/remediator.php
Details of the Remediator:
Converts PDBv2.3 atom names (including hydrogens) to PDBv3.0 names
using the PDB's components dictionary, parsed into a hash table
for speed. Also converts DNA residue names from A,C,T,G,U,I to
DA,DC,DT,DG,DU,DI These changes affect any PDB record that begins
with ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, or LINK. The program
has the capacity to convert in both directions by using the
appropriate flag, but converts to the new format by default.
----------------------
USAGE: remediator.pl [-options] input_file >output.file
options:
-h outputs this help message
-pdb converts a .pdb coordinate file (default)
-kin converts a .kin kinemage file (under development)
-oldout output file will use the PDBv2.3 naming conventions
-remediated output file will use the remediated naming (default)
----------------------
Dave & Jane Richardson
Richardson Lab
211 Nanaline Duke Bldg.
Duke U Med Ctr
Durham NC 27710-3711 USA
1-919-684-6010; fax 684-8885
