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

Miguel Ortiz Lombardia miguel.ortiz-lombardia at afmb.univ-mrs.fr
Fri Sep 18 17:05:47 CEST 2009


Le 18 sept. 09 à 15:08, Claus Flensburg a écrit :

> Hi Miguel,
>
> On Fri, Sep 18, 2009 at 12:22:08PM +0200, Miguel Ortiz Lombardia  
> wrote:
>> D\351but du message r\351exp\351di\351 :
>>
>>>
>>> In the meantime, it would be useful if at least BUSTER can output a
>>> list of residues with alternative conformations.
>>
>> I found at least a way of getting this info: running gelly_refine  
>> with:
>>
>> NOTE BUSTER_SET AlterConf = { *|*:*.* }
>> NOTE BUSTER_SET AlterConf LIST
>>
>> But having a way of automatically create a set for each of the
>> residues listed so the altertative occupancies can be restrained to
>> sum 1.0 would be great.
>
> 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

>
> You might also find these two examples interesting:
>
> http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExampleOccupancyRef
> http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample1osgDisulfideAlternateBroken


Yes, I had seen them, thank you!


Best regards,


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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