Home
Reading
Searching
Subscribe
Sponsors
Statistics
Posting
Contact
Spam
Lists
Links
About
Hosting
Filtering
Features Download
Marketing
Archives
FAQ
Blog
 
Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: Structure::IO::pdb update needed to comply with PDB file format specification change
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Saturday 3rd November 2012 02:08:52 UTC (over 4 years ago)
On Nov 2, 2012, at 7:13 PM, Scott Markel  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Structure::IO::pdb module is out of date relative to the PDB file format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:  [email protected]
> 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
> 
> http://www.linkedin.com/in/smarkel
> 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

Thanks Scott!

chris
 
CD: 3ms