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

[Michael Hothorn]

-------- Original Message --------
Subject: 	Re: [buster-discuss] defining solvent content - missing part 
of structure
Date: 	Tue, 07 May 2013 11:19:35 +0200
From: 	Michael Hothorn <michael at hothorn.de>
To: 	Miguel Ortiz Lombardía <miguel.ortiz-lombardia at afmb.univ-mrs.fr>



No. I downloaded it from globalphasing directly. The sw just stands for
software and holds all my xtal stuff. I managed to get a script to run
that is called seq2seq and that generates a TNT file from plain ASCII
sequence. I used the ASCII sequence of my entire protein making up the
crystal, although I am only providing pdb coordinates for about half of
it. That turned out not to be a smart idea:

  ERROR : [pdb2tnt-0020] unable to get coordinates for
          residue/linkage "END" - please check your sequence
          file!

I guess the TNT file and the pdb file need to match, or am I missing
something?

Is there a way to tell buster that the supplied pdb file make up only
about 50% of the scattering mass. As it is the solvent content seems to
be calculated based on the supplied pdb file, it is much to high.

best wishes,
Michael


On 05/07/2013 11:01 AM, Miguel Ortiz Lombardía wrote:
> 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
>> _______________________________________________
>> buster-discuss mailing list
>> buster-discuss at globalphasing.com
>> https://www.globalphasing.com/mailman/listinfo/buster-discuss
>>



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