On Oct 2, 2018, at 4:01 PM, Billy Poon <[email protected]> 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

On Mon, Oct 1, 2018 at 8:41 AM Patrick Loll <[email protected]> wrote:

Hi all,

Following the instructions given here:

https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html

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
[email protected]
[email protected]


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