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

[Kaushik Hatti]

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])
>>>> 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]
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb [2]
>>>>
>>>
>>> --
>>> ##################################################
>>>
>>> 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:
>> ------
>> [1] http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2
>> [2] http://phenix-online.org/mailman/listinfo/phenixbb
>>
>
>
>


-- 
People living deeply have no fear of death - Anais Nin
Caution: I am still the dumbest person I have ever known :-)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20141120/49c72473/attachment.htm>