[cctbxbb] Question/a possible typo in sampling backrub and side chain conformations in mmtbx

[Nigel Moriarty]

I just did a git blame and saw you committed the line with "selfUTLIER".
This answered one question. Bugs are a different matter.

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909      Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Wed, Apr 21, 2021 at 8:59 AM Winter, Graeme (DLSLtd,RAL,LSCI) <
Graeme.Winter at diamond.ac.uk> wrote:

> OK, I checked the diffs and it really is just a load of fixing
>
> function ( args ) :
>
> type stuff
>
> Are you sure I made the change here?
>
> Thanks Graeme
>
> On 21 Apr 2021, at 16:53, Winter, Graeme (DLSLtd,RAL,LSCI) <
> Graeme.Winter at diamond.ac.uk> wrote:
>
> Hi Nigel,
>
> Search and replace was _probably_ to done as an abstract syntax tree
> replacement - but I would be surprised if “O” was replaced with “self”
> (surprised, but not impossible)
>
> Do you have the commit I could check? Evidently if people did not notice
> for 2 years the code is not well tested… but equally I am surprised.
>
> Oh, found it
>
>
> https://github.com/cctbx/cctbx_project/commit/c0ac70cab55b41b874bdb2ec1a97d516eb722e42
>
> looking...
>
> Thanks Graeme
>
> On 21 Apr 2021, at 16:48, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>
>
>> Hi,
>>
>> Not sure if this message was posted earlier or not, that is why I am
>> reposting it.
>>
>> I had a couple of questions about sampling backrub and sidechains using
>> the building or refinement modules in cctbx_project/mmtbx.
>>
>> 1) In the file:
>> mmtbx.building.alternate_conformations.conformer_generation.py
>>
>> In the function def __call__: the if statements for checking whether the
>> sampled side chain conformation is a rotamer outlier or not, the check in
>> the if statement is for "selfUTLIER".
>>
>> Also in the function *set_up_backrub*(self): the atom "O" for the
>> previous residue is not included in the backrun motion, as a result this
>> atom is not moved when the backrub is implemented.
>>
>> I was just wondering if this is a mistake (possibly all instances of "O"
>> being replaced by "self" which would explain both these things, and some
>> other instances throughout the file), or is this code old and not used
>> anymore?
>>
>
> This is exactly the case. It appears that Graeme Winter did a search and
> replace two years ago. I did a git blame and it shows that the original
> code was written by Nat Echols 5 years ago. The fact that the code is
> broken would indicate that the code is not used or tested well. Feel free
> to correct it and submit a pull request.
>
>
>> 2) When trying to run fit_residues.py and tst_fit_residues* scripts in
>> mmtbx.refinement.real_space, I encountered errors mainly related to
>> chem_data/rotamer_chi_angles/ not being present. Looks like this data is
>> not distributed with cctbx. Is this correct, or maybe there is some other
>> known issue ?
>>
>
> You may need the chem_data directory from a Phenix installation.
>
> Nigel
>
>
>> I look forward to hearing from you.
>>
>> Thanks,
>> Swati
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>>
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