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

[Pavel Afonine]

Hi Swati,

a possible (and perhaps the best!) way to know that your installation 
works as intended is to run tests (tst*.py files) located in

cctbx_project/mmtbx/refinement/real_space

If they pass then all is good (for the code these tests are exercising, 
of course)!

Good Luck,
Pavel

On 4/22/21 02:13, Swati Jain wrote:
> 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 
> <mailto: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
>         <http://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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