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Hi Billy,
<div class=""><br class="">
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<div class="">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.</div>
<div class=""><br class="">
</div>
<div class="">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.</div>
<div class=""><br class="">
</div>
<div class="">Additionally, for one my five structures, I had the same issue as Patrick described in October (see below), also with both versions of phenix.</div>
<div class=""><br class="">
</div>
<div class="">Bernhard<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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<b class=""><span style="font-size: 8pt; font-family: Arial; color: rgb(214, 61, 36);" class="">Bernhard C. Lechtenberg, PhD<span class="Apple-converted-space"> </span><br class="">
</span></b><span style="font-size: 8pt; font-family: Arial; color: gray;" class="">Postdoctoral Associate<br class="">
Riedl Lab<br class="">
Cancer Metabolism and Signaling Networks Program<br class="">
NCI-Designated Cancer Center</span></p>
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<span><img apple-inline="yes" id="806CD092-88ED-4961-835B-F7A8F2D7C27C" src="cid:24A04CE0-5418-4257-A8D1-8084CA766BC9@burnham.org" class=""></span>
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<span style="color: gray; font-family: Arial; font-size: 8pt;" class=""><br class="Apple-interchange-newline">
10901 N. Torrey Pines Road, La Jolla, CA 92037</span></p>
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<b class=""><span style="font-size: 8pt; font-family: Arial; color: gray;" class="">T </span></b><span style="font-size: 8pt; font-family: Arial; color: gray;" class="">858.646.3100 ext. 4216 <span class="Apple-tab-span" style="white-space: pre;">
</span></span><b class=""><span style="font-size: 8pt; font-family: Arial; color: gray;" class="">E</span></b><span style="font-size: 8pt; font-family: Arial; color: gray;" class=""> </span><span style="color: gray; font-family: Arial; font-size: 8pt;" class=""><a href="mailto:blechtenberg@SBPdiscovery.org" class="">blechtenberg@SBPdiscovery.org</a></span></p>
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<i class=""><span style="font-size: 8pt; font-family: Arial; color: gray;" class="">Science Benefiting Patients®</span></i></p>
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<blockquote type="cite" class="">
<div class="">On Oct 2, 2018, at 4:01 PM, Billy Poon <<a href="mailto:BKPoon@lbl.gov" class="">BKPoon@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Pat,
<div class=""><br class="">
</div>
<div class="">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.</div>
<div class=""><br clear="all" class="">
<div class="">
<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">
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<div dir="ltr" class="">
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<div class="">
<div class="">--</div>
<div class=""><span style="font-size:12.8000001907349px" class="">Billy K. Poon</span><br class="">
</div>
</div>
<div class="">Research Scientist, Molecular Biophysics and Integrated Bioimaging</div>
<div class="">Lawrence Berkeley National Laboratory</div>
<div class="">1 Cyclotron Road, M/S 33R0345</div>
<div class="">Berkeley, CA 94720</div>
<div class="">Tel: (510) 486-5709</div>
<div class="">Fax: (510) 486-5909</div>
<div class="">Web: <a href="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" originalsrc="https://phenix-online.org" shash="Y/qDQVwzBL3DI7vRvkrsM2KAGZrpf1ZRbH6QcnLkU0LQq0hECRZNz/AKex9dAkQTLLRMVuNWnJpAn4NpUM/YBHUviaMKBb0JOK+8atmq/Cd72RNamH/ydC1ujurXesKml61h42M2ZbL35C334DIIO/WCXmd79gIZnCE/vH0xXEI=" target="_blank" class="">https://phenix-online.org</a></div>
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<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">On Mon, Oct 1, 2018 at 8:41 AM Patrick Loll <<a href="mailto:pjloll@gmail.com" class="">pjloll@gmail.com</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br class="">
<br class="">
Following the instructions given here:<br class="">
<br class="">
<a href="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" originalsrc="https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html" shash="rJh/l2roJTQB/VU1bnGitWd5V5ldKNdJQbxS6enEmf6lCim9Sy8MaoJpvXEGT6hsc83lr38kjHUPT475jCxG7GztfwgU2XL49ESoorp34DnPi1alpx9Wpf6a1uVveFQ/FNusnGPLk0ekOq0dGWnyvpPKmepfZEQuYrQwjkYVsxg=" rel="noreferrer" target="_blank" class="">https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html</a><br class="">
<br class="">
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).<br class="">
<br class="">
The sequence file is FASTA format, and contains an entry for each of the (4) chains in the AU, i.e.<br class="">
<br class="">
>A<br class="">
MSEQNCE…<br class="">
>B<br class="">
MSEQNCE…<br class="">
etc.<br class="">
<br class="">
Any bright ideas?<br class="">
<br class="">
<br class="">
============this is what happens (vide infra)====================================<br class="">
<br class="">
<br class="">
[PJL-iMac:blahblah/PJL_final] loll% mmtbx.prepare_pdb_deposition filename.cif seq_name.fasta<br class="">
Starting mmtbx.prepare_pdb_deposition<br class="">
on Mon Oct 1 11:16:23 2018 by loll<br class="">
===============================================================================<br class="">
Processing files:<br class="">
-------------------------------------------------------------------------------<br class="">
<br class="">
Found model, filename.cif<br class="">
Found sequence, seq_name.fasta<br class="">
<br class="">
Processing PHIL parameters:<br class="">
-------------------------------------------------------------------------------<br class="">
No PHIL parameters found<br class="">
Final processed PHIL parameters:<br class="">
-------------------------------------------------------------------------------<br class="">
data_manager {<br class="">
model {<br class="">
file = “filename.cif"<br class="">
}<br class="">
default_model = “filename.cif"<br class="">
sequence_files = "seq_name.fasta"<br class="">
default_sequence = "seq_name.fasta"<br class="">
}<br class="">
<br class="">
Starting job<br class="">
===============================================================================<br class="">
Validating inputs<br class="">
Using model: filename.cif<br class="">
Using sequence: seq_name.fasta<br class="">
Creating mmCIF block for sequence<br class="">
Traceback (most recent call last):<br class="">
File "/Applications/phenix-1.14-3260/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 9, in <module><br class="">
run_program(program_class=prepare_pdb_deposition.Program)<br class="">
File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program<br class="">
task.run()<br class="">
File "/Applications/phenix-1.14-3260/modules/cctbx_project/mmtbx/programs/prepare_pdb_deposition.py", line 98, in run<br class="">
alignment_params=self.params.mmtbx.validation.sequence.sequence_alignment)<br class="">
File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1190, in as_cif_block_with_sequence<br class="">
assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence)<br class="">
AssertionError<br class="">
(gouts of smoke, terrified squealing)<br class="">
<br class="">
<br class="">
The ‘No PHIL parameters found’ message is concerning, but the program clearly seems to be finding the input file names.<br class="">
<br class="">
Suggestions welcome.<br class="">
<br class="">
Thanks,<br class="">
<br class="">
Pat<br class="">
<br class="">
---------------------------------------------------------------------------------------<br class="">
Patrick J. Loll, Ph. D. <br class="">
Professor of Biochemistry & Molecular Biology<br class="">
Drexel University College of Medicine<br class="">
Room 10-102 New College Building<br class="">
245 N. 15th St., Mailstop 497<br class="">
Philadelphia, PA 19102-1192 USA<br class="">
<br class="">
(215) 762-7706<br class="">
<a href="mailto:pjloll@gmail.com" target="_blank" class="">pjloll@gmail.com</a><br class="">
<a href="mailto:pjl28@drexel.edu" target="_blank" class="">pjl28@drexel.edu</a><br class="">
<br class="">
<br class="">
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