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

[Nigel Moriarty]

> 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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