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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb