[buster-discuss] defining solvent content - missing part of structure

[Miguel Ortiz Lombardía]

Hi,

At least in our installation the script resides precisely where indicated:

$BDG_home/bin/buster/pirToSeq.pl

Is your installation from some kind of 'fink' package? (I am guessing
from the path that you show, including 'sw') If so, check that the
maintainer of the package included all the files.

Cheers,


Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
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
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Le 07/05/13 09:59, Michael Hothorn a écrit :
> Hi,
> 
> I am trying to refine a partial model: I have a molecular replacement 
> solution that comprises about 50% of the asymmetric unit and I would 
> like to specify the scattering mass that is missing in the initial pdb 
> file to buster. I read in the manual that this can be done by supplying 
> a TNT sequence file
> 
> $BDG_home/bin/buster/pirToSeq.pl <file.pir>
> 		      <file.seq>
> 
> 
> However, I cannot find the recommended script in my buster 2.10 
> installation:
> 
> mhothorn at crunchy:/fml/ag-hothorn/share/sw/buster_2.10$ find -name *.pl
> ./lib/libmap.pl
> ./lib/libxtal.pl
> ./lib/libbdg.pl
> ./lib/libfloat.pl
> ./lib/cryptic.pl
> ./lib/cgi-lib.pl
> ./lib/libhtml.pl
> ./bin/buster/cleanup.pl
> ./buffet/lib/libtnt.pl
> ./buffet/lib/XfitHelper.pl
> ./buffet/lib/libbuster.pl
> ./buffet/lib/jos1dHelper.pl
> ./buffet/lib/xplot84Helper.pl
> ./buffet/lib/jos2dHelper.pl
> ./buffet/cgi-bin/save.pl
> ./buffet/cgi-bin/deltmp.pl
> ./buffet/cgi-bin/delcrd.pl
> ./buffet/cgi-bin/changeprefs.pl
> ./buffet/cgi-bin/changepass.pl
> ./buffet/cgi-bin/index.pl
> ./buffet/cgi-bin/createMap.pl
> ./buffet/cgi-bin/map.pl
> ./buffet/cgi-bin/restart.pl
> ./buffet/cgi-bin/delProject.pl
> ./buffet/cgi-bin/jos.pl
> ./buffet/cgi-bin/dosave.pl
> ./buffet/cgi-bin/resume.pl
> ./tnt/data/protgeo_eh99_omega_torsion.pl
> 
> Could you please provide advice on how to specify the missing atoms to 
> buster (so that it assumes the correct solvent content for example).
> 
> Thanks!
> Michael
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> 

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