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

Gabor Bunkoczi gb360 at cam.ac.uk
Thu Nov 20 09:40:40 PST 2014


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




More information about the phenixbb mailing list