[BioPython] parsing pdb files

[Peter]

>>
>> Also, if you wanted to try the latest Biopython code from CVS it
>> should ignore these missing fields in permissive mode (but will print
>> warning messages - see Bug 2751 for details).
>
> Peter,
> Thank you very much. I installed the latest biopython only. Anyways give me
> the link to download it so that i would try it out
>
> Bala

Biopython 1.49 (and earlier) won't parse PDB files missing the
B-factor or occupancy information.

Using the short example script in my earlier email, you should be able
to fix individual PDB files so Biopython 1.49 is happy.  I would
recommend this option first.

Alternatively, using the code in our source code repository (CVS),
which will one day become Biopython 1.50, you can now parse these
"naughty" PDB files - although you'll get a warning message for every
missing B-factor or occupancy (see Bug 2751).  If you want to try this
new unreleased Biopython code, you have to get our latest code from
CVS and install it.  See http://biopython.org/wiki/CVS

In this case, assuming you already have Biopython 1.49, you only
really need to update one file, which you could download from our CVS
webpage, instead
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/PDB/PDBParser.py?cvsroot=biopython

Don't try this unless you are confident you can put things back if
something goes wrong... I would just suggest "fixing" the individual
PDB files instead.

Peter