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Update __init__.py #528
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Update __init__.py #528
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Update ensemble_refinement to 2020 version. Added DEN restraints (now used by default). Fixed refinement flag manager. Added support for importing external TLS parameters from additional PDB.
Tom
Can you tell me why DEN is default?
Do you have any tests for these changes?
Cheers
Nigel
…---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Wed, Sep 16, 2020 at 9:09 AM Tom Burnley ***@***.***> wrote:
@tomburnley <https://github.com/tomburnley> requested your review on: #528
<#528> Update *init*.py.
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Hi Nigel,
DEN -> we found in testing that it makes the simulations more stable
without negatively affecting sampling. W/out DEN on some occasions parts
of the structure can unfold out of density. The attractive terms in Amber
may alleviate this but for now w/ the repel potential it's better. The DEN
pairs are regenerated multiple times during the simulation so sampling does
not seem to be compromised.
Testing -> yes... see separate email.
Cheers,
Tom
On Wed, 16 Sep 2020 at 17:15, Nigel W. Moriarty <[email protected]>
wrote:
… Tom
Can you tell me why DEN is default?
Do you have any tests for these changes?
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : ***@***.***
Fax : 510-486-5909 Web : CCI.LBL.gov
On Wed, Sep 16, 2020 at 9:09 AM Tom Burnley ***@***.***>
wrote:
> @tomburnley <https://github.com/tomburnley> requested your review on:
#528
> <#528> Update *init*.py.
>
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Just a note, there are bunch of functions of the model class that deal with TLS:
get_header_tls_selections()
extract_tls_selections_from_input()
determine_tls_groups(self, selection_strings, generate_tlsos)
I see a lot of code to deal with TLS in this particular file, so maybe something more is going on, so I would not insist on using them in this particular case instead of things like
self.model.tls_groups.tlsos = fit_tlsos
fit_tlsos = [tls_tools.tlso(t=o.t, l=o.l, s=o.s, origin=o.origin) for o in tls_params.tls_params]
make_header("Import External TLS", out = self.log) | ||
print('External TLS model: ' + self.params.import_tls_pdb, file=self.log) | ||
pdb_import_tls = self.params.import_tls_pdb | ||
pdb_tls_inp = iotbx.pdb.hierarchy.input(file_name=pdb_import_tls) |
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please use iotbx.pdb.input() instead, preferably checking if the file exists.
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Still this, with the explanation in the previous message.
Move all import statements to header. Remove duplicate self.assign_solvent_tls_groups() in Import TLS from reference model.
There are unused imports causing the Checks tests to fail.
An update will cause the CI to run again and the error for Full and Base should go away since I checked in some updates to the |
Remove unused imports
Thanks! The Ci branch failures are fine. That pipeline does not run on the final, merged code with the updates to |
This requested change seems to be missed:
|
Can you explain the need for this and point to an example of use I can copy from please. |
@tomburnley , iotbx.pdb.hierarchy.input() seems to be a very thin wrapper that pretty much constructs hierarchy and keep input object: cctbx_project/iotbx/pdb/hierarchy.py Lines 2493 to 2536 in 1be58fd
The original reason to create an extra layer for such a simple task is not clear to me in the first place. I could very well miss something, so clarifications from anyone are welcomed. As of now, I believe this whole layer better be removed, therefore advocate against using it anywhere. In practical terms regarding this pull request I suggest to change this:
to this:
Other examples of iotbx.pdb.input() usage can be found e.g. in iotbx/command_line/pdb_labels_comparison.py and many other files across the repository. |
Updated version of ensemble refinement to include den restraints and echt b-factor model to accompany paper submitted to Acta D. Tested with phenix-1.19.2-4158. Issues with previous pull request (#528 (comment)) fixed.
Updated version of ensemble refinement to include den restraints and echt b-factor model to accompany paper submitted to Acta D. Tested with phenix-1.19.2-4158. Issues with previous pull request (#528 (comment)) fixed.
Updated version of ensemble refinement to include den restraints and echt b-factor model to accompany paper submitted to Acta D. Tested with phenix-1.19.2-4158. Issues with previous pull request (cctbx#528 (comment)) fixed.
Update ensemble_refinement to 2020 version. Added DEN restraints (now used by default). Fixed refinement flag manager. Added support for importing external TLS parameters from additional PDB.