[phenixbb] mmCIF for deposition

[Billy Poon]

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 <pjloll at gmail.com> 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
> pjloll at gmail.com
> pjl28 at drexel.edu
>
>
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