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:[email protected]]
10901 N. Torrey Pines Road, La Jolla, CA 92037
T 858.646.3100 ext. 4216 E [email protected]mailto:[email protected]
Science Benefiting Patients®
On Oct 2, 2018, at 4:01 PM, Billy Poon
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]mailto:[email protected] [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbbhttps://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-online.org%2Fmailman%2Flistinfo%2Fphenixbb&data=02%7C01%7Cblechtenberg%40sbpdiscovery.org%7C1f02e727a9a24dbf989308d628bb1cc9%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C636741181463466669&sdata=S5Y55I0NxgVfkdUevXh3BQFr%2Fy6YJbF6TtYg48B7muA%3D&reserved=0 Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-onlin... Unsubscribe: [email protected]
