Update __init__.py

[tomburnley]

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.

[nwmoriarty]

Tom

Can you tell me why DEN is default?

Do you have any tests for these changes? Cheers

Nigel

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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 [email protected] wrote:

@tomburnley https://github.com/tomburnley requested your review on: #528 https://github.com/cctbx/cctbx_project/pull/528 Update init.py.

— You are receiving this because your review was requested. Reply to this email directly, view it on GitHub https://github.com/cctbx/cctbx_project/pull/528#event-3773994548, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHYQPDIXHD5S4EZ74YCT3DSGDPLDANCNFSM4RPB7OWQ .

[tomburnley]

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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Wed, Sep 16, 2020 at 9:09 AM Tom Burnley [email protected] wrote:

@tomburnley https://github.com/tomburnley requested your review on: #528 https://github.com/cctbx/cctbx_project/pull/528 Update init.py.

— You are receiving this because your review was requested. Reply to this email directly, view it on GitHub https://github.com/cctbx/cctbx_project/pull/528#event-3773994548, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAHYQPDIXHD5S4EZ74YCT3DSGDPLDANCNFSM4RPB7OWQ

.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cctbx/cctbx_project/pull/528#issuecomment-693511586, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSF77V6VBGGQ2ZLVTQSFHLSGDQBXANCNFSM4RPB7OWQ .

[bkpoon]

There are unused imports causing the Checks tests to fail.

In file __init__.py:
time imported at line 34
miller imported at line 19
geometry_restraints imported at line 17
cdl_utils imported at line 636
xray imported at line 21

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 master branch.

[bkpoon]

Thanks! The Ci branch failures are fine. That pipeline does not run on the final, merged code with the updates to master.

[olegsobolev]

This requested change seems to be missed:

please use iotbx.pdb.input() instead of iotbx.pdb.hierarchy.input(), preferably checking if the file exists.

[tomburnley]

This requested change seems to be missed:

please use iotbx.pdb.input() instead of iotbx.pdb.hierarchy.input(), preferably checking if the file exists.

Can you explain the need for this and point to an example of use I can copy from please.

[olegsobolev]

@tomburnley , iotbx.pdb.hierarchy.input() seems to be a very thin wrapper that pretty much constructs hierarchy and keep input object: https://github.com/cctbx/cctbx_project/blob/1be58fdfe34797a7126eb9ab22c5805326c4a154/iotbx/pdb/hierarchy.py#L2493-L2536

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:

pdb_tls_inp = iotbx.pdb.hierarchy.input(file_name=pdb_import_tls)
tls_params = pdb_tls_inp.input.extract_tls_params(pdb_tls_inp.hierarchy)

to this:

pdb_tls_inp = iotbx.pdb.input(file_name=pdb_import_tls)
tls_params = pdb_tls_inp.extract_tls_params(pdb_tls_inp.construct_hierarchy())

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.