[Bioperl-l] Structure::IO::pdb update needed to comply with PDB file format specification change
Fields, Christopher J
cjfields at illinois.edu
Sat Nov 3 02:08:52 UTC 2012
On Nov 2, 2012, at 7:13 PM, Scott Markel <Scott.Markel at accelrys.com> wrote:
> In tracking down a regression test failure we discovered that the Structure::IO::pdb module is out of date relative to the PDB file format specification (http://www.wwpdb.org/docs.html). PDB now writes out to column 79, while pdb.pm is still using the old line length of 71. Our regression failure was caused by a reformatting of 1CRN; journal titles started getting truncated.
> Some of the Perl lines are really simple, e.g.,
> $keywds = $self->_read_PDB_singlecontline("KEYWDS","11-70",\$buffer);
> with others being just a little more detailed, e.g.,
> my ($rec, $subr, $cont, $rol) = unpack "A6 x6 A4 A2 x1 A51", $_;
> It doesn't look like pdb.pm has changed in about 1.5 years. Is there a current module owner? Or someone else working on this?
No one has really taken ownership, so as far as I'm concerned it's open. Any objections?
> If not, we're willing to either compile a list of needed changes (walking through the PDB file format specification and comparing the corresponding column indices in pdb.pm) or provide a new version of the entire file. Please let us know which is preferred.
A new version of the file is fine if you have someone who can work on it. We would also like to change relevant tests and documentation if there is time.
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect email: smarkel at accelrys.com
> Accelrys (Pipeline Pilot R&D) mobile: +1 858 205 3653
> 10188 Telesis Court, Suite 100 voice: +1 858 799 5603
> San Diego, CA 92121 fax: +1 858 799 5222
> USA web: http://www.accelrys.com
> Secretary, Board of Directors:
> International Society for Computational Biology
> Chair: ISCB Publications and Communications Committee
> Associate Editor: PLoS Computational Biology
> Editorial Board: Briefings in Bioinformatics
More information about the Bioperl-l