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

[Michael Hothorn]

Removing the END statement in the pdb file does not resolve the issue. I 
guess buster expects the records in the TNT file to be actually 
represented by coordinates in the supplied pdb file.

Michael

On 05/07/2013 11:33 AM, Miguel Ortiz Lombardía wrote:
> Weird, we also got the software from GlobalPhasing directly.
>
> As for seq2seq, I have no clue, I have never used. Have you tried to
> remove the "END" line in your pdb file?
>
> 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 11:20, Michael Hothorn a écrit :
>>
>>
>> -------- 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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