[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 In tracking down a regression test failure we discovered that the Structure::IO::pdb module is out of date relative to the PDB file format specification (http://www.wwpdb.org/docs.html).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
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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Thanks Scott!


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