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

Kaushik Hatti hskaushik at gmail.com
Thu Nov 20 04:26:56 PST 2014


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]) 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
>>
>> _______________________________________________
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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 :-)
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