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

[Swati Jain]

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?


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 ?


I look forward to hearing from you.


Thanks,

Swati
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