[buster-discuss] [buster-develop] Fwd: refining occupancies of alternate conformations

Miguel Ortiz Lombardia miguel.ortiz-lombardia at afmb.univ-mrs.fr
Fri Sep 18 19:03:38 CEST 2009

Hi again!

Le 18 sept. 09 à 17:05, Miguel Ortiz Lombardia a écrit :

> Le 18 sept. 09 à 15:08, Claus Flensburg a écrit :
>> there is a jiffy named: pdb2occ, which will detect and setup
>> input cards for this situation. See:
>> http://www.globalphasing.com/buster/manual/autobuster/manual/autoBUSTER7.html#pdb2occ
> Excellent!
> Sorry, I had missed that part (additional tools) of the
> documentation... May I suggest to add a link to this tool in the
> manual, there where occupancy refinement is dealt with?
>> There is a problem with the current version if you have residues
>> with alternate
>> conformations that do not have the same number of atoms, so you
>> should check the
>> output file of pdb2occ. See: http://www.globalphasing.com/buster/issues.html
>> This is fixed in the next patch-release.
> No problems in my case, but thanks for letting me know

Unfortunately, there were problems in fact, I failed to notice them.  
Some of the NOTE BUSTER_COMBINE OCC are missing. I haven't found a  
reason for that. In my case, all residues with alternative  
conformation have the same number of atoms. However, that was easy to  
fix by hand.


Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombardia at afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2

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