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[ccp4bb] remediated pdb and coordinate formates ...
 

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CCP4bb <-- 2007 <-- May 2007 <-- 04 May 2007
Previous message:
Subject: Re: wwPDB Announcement: Release of Remediated PDB Data
From: Alwyn Jones alwyn {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2007-05-04 		Next message:
Subject: Protein structure images
From: Alex Alex {- dot -} Goldsmith {- at -} LUMINORUM {- dot -} COM
Date: 2007-05-04


Subject: remediated pdb and coordinate formates ...
From: "Ingo P {- dot -} Korndoerfer" ipk {- at -} CRYSTAX {- dot -} COM
Date: 2007-05-04
dear all ...

beyond iupac nomenclature ...

the remediated pdb sounds very nice, so i had a short look at the
formats they provide and found this:

mmcif, pdbxml, and pdb

and

http://biomol.dowling.edu/WPDB/

has a very nice discussion of advantages and disadvantages of the
various formats ...

it sounds to me like mmcif would be the best way to go, but i do
understand that is less amenable to quick and dirty processing with
grep, sed and awk etc ..., and therefore users have been reluctant to
use it.

but i think i would be willing to put up with having to add another 10
lines to my scripts to process mmcif, if
that allows me to take home all the other advantages.

the biggest problem at this point is, as far as i know (and this is also
what the above website states), that my favourite refinement program
does not really work with anything but pdb, so i am not really sure
whether it is the users who are reluctant to use mmcif (as above website
states) ...

wouldn't it be nice to try and teach our favourite refinement programs
mmcif ?

ingo
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