[phenixbb] mmCIF for deposition

Bernhard Lechtenberg blechtenberg at sbpdiscovery.org
Fri Jan 4 17:44:48 PST 2019 

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

[cid:24A04CE0-5418-4257-A8D1-8084CA766BC9 at burnham.org]

10901 N. Torrey Pines Road, La Jolla, CA 92037
T  858.646.3100 ext. 4216  E blechtenberg at SBPdiscovery.org<mailto:blechtenberg at SBPdiscovery.org>
Science Benefiting Patients®

On Oct 2, 2018, at 4:01 PM, Billy Poon <BKPoon at lbl.gov<mailto: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, 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<mailto: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., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjloll at gmail.com<mailto:pjloll at gmail.com>
pjl28 at drexel.edu<mailto:pjl28 at drexel.edu>


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