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

Tue May 7 12:22:03 CEST 2013

Yes, the tnt file must be consistent with the pdb file.

In autobuster you can always pass the "solc" parameter with the solvent
content that you consider appropriate for the full sequence.

If running Buster-TNT from the interface, you deal with the missing part
by including its atoms (C,N,O,S,H) in the total structure (I haven't
done that for a long time... it may have changed)

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 11:39, Michael Hothorn a écrit :
> 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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> 
> 

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