[phenixbb] mmCIF for deposition

Sat Jan 5 13:51:36 PST 2019

Hi Bernhard,

It’s something I’ll be working more the first half of this year and will be
related to a general reorganization of how the validation tools, table one,
and file deposition tools work. Currently, each tool sort of operates
independently and so the information is not handled consistently.

The plan is to do the final statistics calculation once with the validation
tool and then export the statistics as a table one and eventually as a CIF
file for deposition (the sequence would be added if a sequence file is
available). The cryo-em comprehensive validation tool does this currently
with exporting statistics in a table. The X-ray/neutron comprehensive
validation tool will be changed to follow the same approach.

The additional wrinkle with non-standard residues is that there are many of
those residues. Nigel has a way for combing through our monomer library to
build the relationships (e.g. MSE is based on M). I’m working on a tool to
use those relationships so that the user just provides the canonical
sequence (M) and we will fill in the appropriate non-standard residue (MSE)
in the CIF file. This way, users do not have to manually build the PDB
specific format of putting non-standard residues in parentheses.

The next Phenix is planned for the end of February/early March, and that
will have at least a beta version of this tool.

On Fri, Jan 4, 2019 at 7:44 PM Bernhard Lechtenberg <
blechtenberg at sbpdiscovery.org> wrote:

> Hi Billy,
>
> Do you have any updates on this? I just used tried to use
> mmtbx.prepare_pdb_deposition with the .cif file from phenix.refine and
> fasta sequences as input, followed by pdb_extract to deposit several
> structures to the PDB. The .cif files were accepted by PDB, but the
> refinement statistics were lost and something with the structure factors
> also seemed wrong, as the validation reports did not contain metrics for
> R-free and RSRZ outliers. I don’t quite understand how the second problem
> happens, since mmtbx.prepare_pdb_deposition does not see the structure
> factors. However, when I skipped the mmtbx.prepare_pdb_deposition and
> directly used the output cif from phenix.refine in pdb_extract and then
> uploaded this file to the PDB, both those issues were fixed.
>
> I first used an older phenix version (1.14rc2-3139) on a Mac, then
> upgraded to the latest nightly-built version (dev-3374), but the issue
> persisted.
>
> Additionally, for one my five structures, I had the same issue as Patrick
> described in October (see below), also with both versions of phenix.
>
> Bernhard
>
>
> *Bernhard C. Lechtenberg, PhD  *Postdoctoral Associate
> Riedl Lab
> Cancer Metabolism and Signaling Networks Program
> NCI-Designated Cancer Center
>
>
> 10901 N. Torrey Pines Road, La Jolla, CA 92037
> <https://maps.google.com/?q=10901+N.+Torrey+Pines+Road,+La+Jolla,+CA+92037&entry=gmail&source=g>
>
> *T  *858.646.3100 ext. 4216  *E* blechtenberg at SBPdiscovery.org
>
> *Science Benefiting Patients®*
>
> On Oct 2, 2018, at 4:01 PM, Billy Poon <BKPoon at lbl.gov> wrote:
>
> Hi Pat,
>
> I'm in the process of reworking that tool since it is dropping some
> information from phenix.refine in the process of adding the sequence.
> Something should be available by the end of the week in a new build.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road
> <https://maps.google.com/?q=1+Cyclotron+Road&entry=gmail&source=g>, M/S
> 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fphenix-online.org&data=02%7C01%7Cblechtenberg%40sbpdiscovery.org%7C1f02e727a9a24dbf989308d628bb1cc9%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C636741181463446660&sdata=quN%2BNM5dHlBOs0xk0T53tu3ZN92oLc7v3h6tyZ%2BViXM%3D&reserved=0>
>
>
> On Mon, Oct 1, 2018 at 8:41 AM Patrick Loll <pjloll at gmail.com> wrote:
>
>> Hi all,
>>
>> Following the instructions given here:
>>
>>
>> https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.phenix-online.org%2Fdocumentation%2Foverviews%2Fxray-structure-deposition.html&data=02%7C01%7Cblechtenberg%40sbpdiscovery.org%7C1f02e727a9a24dbf989308d628bb1cc9%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C636741181463456667&sdata=Q6TEdFOFt3wCQqJ4tA1tHWypnlY8Qb9%2BgOR1a6tErO8%3D&reserved=0>
>>
>> I’m attempting to use mmtbx.prepare_pdb_deposition to insert sequence
>> information into the mmCIF that contains the model coordinates.
>> Unfortunately, the program fails with an error (shown below).
>>
>> The sequence file is FASTA format, and contains an entry for each of the
>> (4) chains in the AU, i.e.
>>
>> >A
>> MSEQNCE…
>> >B
>> MSEQNCE…
>> etc.
>>
>> Any bright ideas?
>>
>>
>> ============this is what happens (vide
>> infra)====================================
>>
>>
>> [PJL-iMac:blahblah/PJL_final] loll% mmtbx.prepare_pdb_deposition
>>  filename.cif   seq_name.fasta
>> Starting mmtbx.prepare_pdb_deposition
>> on Mon Oct  1 11:16:23 2018 by loll
>>
>> ===============================================================================
>> Processing files:
>>
>> -------------------------------------------------------------------------------
>>
>>   Found model, filename.cif
>>   Found sequence, seq_name.fasta
>>
>> Processing PHIL parameters:
>>
>> -------------------------------------------------------------------------------
>>   No PHIL parameters found
>> Final processed PHIL parameters:
>>
>> -------------------------------------------------------------------------------
>>   data_manager {
>>     model {
>>       file = “filename.cif"
>>     }
>>     default_model = “filename.cif"
>>     sequence_files = "seq_name.fasta"
>>     default_sequence = "seq_name.fasta"
>>   }
>>
>> Starting job
>>
>> ===============================================================================
>> Validating inputs
>> Using model: filename.cif
>> Using sequence: seq_name.fasta
>> Creating mmCIF block for sequence
>> Traceback (most recent call last):
>>   File
>> "/Applications/phenix-1.14-3260/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py",
>> line 9, in <module>
>>     run_program(program_class=prepare_pdb_deposition.Program)
>>   File
>> "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/cli_parser.py",
>> line 71, in run_program
>>     task.run()
>>   File
>> "/Applications/phenix-1.14-3260/modules/cctbx_project/mmtbx/programs/prepare_pdb_deposition.py",
>> line 98, in run
>>
>> alignment_params=self.params.mmtbx.validation.sequence.sequence_alignment)
>>   File
>> "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/pdb/hierarchy.py",
>> line 1190, in as_cif_block_with_sequence
>>     assert len(chain.residue_groups) + chain.n_missing_start +
>> chain.n_missing_end == len(sequence)
>> AssertionError
>> (gouts of smoke, terrified squealing)
>>
>>
>> The ‘No PHIL parameters found’ message is concerning, but the program
>> clearly seems to be finding the input file names.
>>
>> Suggestions welcome.
>>
>> Thanks,
>>
>> Pat
>>
>>
>> ---------------------------------------------------------------------------------------
>> Patrick J. Loll, Ph. D.
>> Professor of Biochemistry & Molecular Biology
>> Drexel University College of Medicine
>> Room 10-102 New College Building
>> 245 N. 15th St
>> <https://maps.google.com/?q=245+N.+15th+St&entry=gmail&source=g>.,
>> Mailstop 497
>> Philadelphia, PA  19102-1192  USA
>>
>> (215) 762-7706
>> pjloll at gmail.com
>> pjl28 at drexel.edu
>>
>>
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> --
--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
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