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

[Swati Jain]

Hi everyone,

Thanks a lot for the information. Seems like you all agree that this code
is old and not tested.

Regarding the chem_data question, I don't have a phenix license. I was able
to get some chem_data information (geostd from sourceforge and mon_lib and
rama and rota evaluation information from the Richardson lab), but not the
directory that is needed for the fit_residue* functions.

However, the individual_sites real space refinement seems to be working
fine, both the test script as well as when I try it myself. Am I correct is
assuming that it does not require any additional data (apart from the
openly available data I was able to get) or the code is not throwing any
errors and just skipping steps?

Thanks a lot,
Swati

On Wed, Apr 21, 2021 at 9:18 PM 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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