[Biopython] Bio.PDB question - from PQR to an "extended" PDB

[paul at tonair.de]

Dear all, 

a PQR functionality within biopython would be great!


Regarding the output of extended PDB files I would like to
write:
There is no detailed description on such files:


http://www.sci.ccny.cuny.edu/~mcce/doc/running_mcce2.php [1] 

see
chapter 3.2.4:
step2_out.pdb: input structure file of step 3 in mcce
extended pdb format 

extended means: the conformer is added beyond the
element located somewhere around column 80. 

Is there any workaround
with the currect biopython release to read in PQR and dump out such an
extended PDB file? 

Cheers & thanks,
Paul 

On Thu, 13 Oct 2011
12:48:22 +0200, Mikael Trellet  wrote:  

This PQRParser class would be
a nice add to Bio.PDB indeed, and shouldn't take a very long time to
develop. Could work on it with you Joao, if the need exists obviously.


Regards, 

Mikael 

On Thu, Oct 13, 2011 at 12:43 PM, João Rodrigues 
wrote:
 Hello Paul,

Straight from Pymol :)

Bio.PDB cannot read PQR
files as is, but since the format is quite similar
to the PDB it should
be easy to convert.

The first step is to know if you want to develop a
converter too (you will
need the forcefield atomic charges and radius
for that) or just a "parser".
Parsing is easy, it's a matter of adapting
the current SMCRA objects and
PDBParser. Converting requires much more
and is probably superfluous given
the PDB2PQR software.

Some important
information on the
format:
http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr
[3]

I think the best course of action is to add a PQRParser class that
has
different residue properties than the regular PDB. For example,
occupancy
and bfactor are not used at all..

Let me know what you
think,

Cheers,

João

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 --

Mikael TRELLET,
Computational structural biology group, Utrecht
University
Bijvoet Center,
The Netherlands

 

Links:
------
[1]
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[2]
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[3]
http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr
[4]
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[5]
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