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 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- ##################################################

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 :-)

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 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 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 [email protected] 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 :-)

Not directly, I am afraid. However, this is something you can definitely do by using a local copy of the PDB that you have modified appropriately. This will even have the added benefit that results are reproducible (i.e. the shake is not re-done randomly at every access). BW, Gabor On 2014-11-20 18:44, Kaushik Hatti wrote:

Sorry, one more doubt! If I decide to use PDB database, is there a way I can run some routines on the template structure(e.g. Shake coordinates by 1A) before it is considered for MRage pipeline after it is downloaded from PDB server?

Thanks, Kaushik On Nov 20, 2014 11:39 PM, "Kaushik Hatti" wrote:

...

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 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 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] [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] [1]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb [2] [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 [1] [2] http://phenix-online.org/mailman/listinfo/phenixbb [2]

--

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