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@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

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People living deeply have no fear of death - Anais Nin
Caution: I am still the dumbest person I have ever known :-)