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

[Gabor Bunkoczi]

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

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