[phenixbb] MRage against local "select" PDB database on commandline

[Gabor Bunkoczi]

Not directly, I am afraid. However, this is something you can definitely 
do by using a local copy of the PDB that you have modified 
appropriately. This will even have the added benefit that results are 
reproducible (i.e. the shake is not re-done randomly at every access).

BW, Gabor

On 2014-11-20 18:44, Kaushik Hatti wrote:
> Sorry, one more doubt!
>  If I decide to use PDB database, is there a way I can run some
> routines on the template structure(e.g. Shake coordinates by 1A)
> before it is considered for MRage pipeline after it is downloaded from
> PDB server?
> 
> Thanks,
>  Kaushik
> On Nov 20, 2014 11:39 PM, "Kaushik Hatti" <hskaushik at gmail.com> wrote:
> 
>> Hi Gabor,
>> 
>> Actually the database is not split at chain alone but domain level
>> too. Many multi-domain proteins are split into each structure file
>> containing a single domain eg, 1xxxB_1, 1xxxB_2,... I specifically
>> want to pick homologous structure from this custom database and not
>> the entire PDB. I will try to hack this at my end and will share it
>> here if I succeed.
>> 
>> Thanks,
>> Kaushik
>> 
>> On Thu, Nov 20, 2014 at 11:10 PM, Gabor Bunkoczi <gb360 at cam.ac.uk>
>> wrote:
>> Dear Kashik,
>> 
>> hmm, I am not sure I can help you here. MRage uses some general
>> purpose code to fetch PDB entries (from the iotbx.fetch module), and
>> this code is also utilised elsewhere. People would probably frown at
>> me if I modified this without consulting them first, but
>> fortunately, they are also on this mailing list, and will hopefully
>> chime in at some point.
>> 
>> However, I am wondering whether you could not solve this problem in
>> a different way. In case 1vjhA.pdb happens to be chain A from
>> 1vjh.pdb, you could just change the accession number (blast XML
>> Hit_accession record) to 1vjh_A, and MRage will automatically fetch
>> entry 1vjh and extract chain A. Can you not recompile the database
>> to use these accession numbers? The domain information you can
>> encode with the alignment, i.e. simply omit the residues that do not
>> belong to the domain.
>> 
>> Best wishes, Gabor
>> 
>> On 2014-11-20 12:26, Kaushik Hatti wrote:
>> 
>> Dear Gabor,
>> 
>> Thanks so much for the suggestions. I built custom sequence
>> database,
>> did all-vs-all blast and stored output as XML files. Also
>> understood
>> how blast output.xml could be used for MRage "homology" scope.
>> 
>> However, some of my PDBIDs are not 4 but 6 characters long. The
>> filename includes chainID and domain information as well. Hence,
>> when
>> I run MRage I get this error:
>> 
>> XXXXXXXX
>> Error: Invalid PDB ID '1vjhA.pdb'. IDs must be exactly four
>> alphanumeric characters, starting with a number from 1-9.
>> This entry cannot be used: Invalid PDB ID '1vjhA.pdb'. IDs must be
>> exactly four alphanumeric characters, starting with a number from
>> 1-9.
>> XXXXXXXX
>> 
>> I have also placed 1vjhA.pdb under "vj" dir, 2i9yA.pdb under "i9"
>> etc...
>> 
>> Am I missing something? How can I overcome this?
>> 
>> Thanks,
>> Kaushik
>> 
>> On Mon, Nov 17, 2014 at 5:34 PM, Gabor Bunkoczi <gb360 at cam.ac.uk>
>> wrote:
>> 
>> Hi Kaushik,
>> 
>> yes, this is possible, although with some restrictions.
>> 
>> If you have a local copy of the PDB, you can set the PDB_MIRROR_PDB
>> environment variable to point to the root directory. This does not
>> have to contain the whole PDB, as long as the entries you need to
>> access are present. Entries in the root folder should be divided up
>> to subfolders that are given by the second and third character of
>> the accession ID. Only the actual structure files can be fetched in
>> this way, but this is sufficient for MRage to work.
>> 
>> As for your query about customising blast, you can build a blast
>> database against whatever subset you like, and make sure this is
>> the
>> default. If there are multiple blast executables in the path, the
>> first one will be picked up. However, it may actually be easier for
>> you to run the blast search separately, request XML output, and
>> feed
>> this to MRage's "homology" scope.
>> 
>> Let me know if you need more details!
>> 
>> Best wishes, Gabor
>> 
>> On 2014-11-17 07:47, Kaushik Hatti wrote:
>> 
>> Hi,
>> 
>> I am new to Phenix. Sorry if my question is naive.
>> 
>> For a given mtz file, I want to pick templates from a local PDB
>> database (its actually iTasser template library) and perform
>> Molecular
>> Replacement using MRage. I have already installed Blast,
>> downloaded
>> iTasser PDB library
>> (http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2 [1] [1]
>> [1])
>> and
>> extracted sequences from both the downloaded PDB template library
>> set
>> and target protein for which mtz is available.
>> 
>> How should I go about building pipeline to perform MR using
>> templates
>> from locally downloaded select PDB database?
>> 
>> Are there any more parameters available for parameter name:
>> services
>> under scop: search other than "local" and "ncbi"?
>> 
>> Thanks in advance,
>> Kaushik--
>> 
>> People living deeply have no fear of death - Anais Nin
>> Caution: I am still the dumbest person I have ever known :-)
>> 
>> Links:
>> ------
>> [1] http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2 [1] [1]
>> 
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>> 
>> --
>> ##################################################
>> 
>> Dr Gabor Bunkoczi
>> 
>> Cambridge Institute for Medical Research
>> Wellcome Trust/MRC Building
>> Addenbrooke's Hospital
>> Hills Road
>> Cambridge CB2 0XY
>> ##################################################
> 
>  --
> 
>  People living deeply have no fear of death - Anais Nin
>  Caution: I am still the dumbest person I have ever known :-)
> 
>  Links:
>  ------
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>  [2] http://phenix-online.org/mailman/listinfo/phenixbb [2]
> 
> --
> 
> People living deeply have no fear of death - Anais Nin
> Caution: I am still the dumbest person I have ever known :-)
> 
> 
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