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 <[email protected]> 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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