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

[Oleg Sobolev]

Hi Swati,


> I had a couple of questions about sampling backrub
>
To the best of my knowledge Phenix does not use backrub motion in
production anywhere. So there are not many chances to find a
production-quality code to work with 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?
>
The whole mmtbx.building.alternate_conformation was written back in 2015 by
Nat Echols and if I remember correctly was an unfinished project. The
observations you made (like "selfUTLIER") only increase the suspicion that
the code is not working anymore.


> 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 ?
>
Correct, chem_data is not part of cctbx and many tests/functionality won't
run without it. Naturally, you need info on rotamers to sample them which
is in chem_data along with many other necessary for macromolecules data.

You can take a look at "def backrub_move" in
cctbx_project/mmtbx/refinement/real_space/fit_residue.py which I wrote.
Take a note of disclaimer though: "These functions are not used anywhere.
And not tested anymore. ...". They can still be in a working condition, but
no warranty is provided.

Best regards,
Oleg Sobolev.


>
> I look forward to hearing from you.
>
>
> Thanks,
>
> Swati
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