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Computational Crystallography Toolbox
https://cctbx.github.io
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How to handle NH3 rotators on NCO? #244

Closed russell-taylor closed 1 year ago

russell-taylor commented 1 year ago

We get a lot of messages: "Could not add MoverNH3Rotator to chain B NCO 103: MoverNH3Rotator(): Partner does not have three bonded friends" because the rotator is attached to a Cobalt that has six bonded neighbors.

Should we generalize to allow a larger number of bonded neighbors? If so, how do we ensure that the orientation starts with one that we expect rather than randomly picking the neighbor that is parallel in bonding to ours?

Asked Jane about this.

russell-taylor commented 1 year ago

Yes, we should generalize to the larger number of neighbors. In that case, we can leave the initial orientation the same as they were placed.

russell-taylor commented 1 year ago

These happen when running mmtbx.reduce2 output.description_file_name=4fen_new.txt D:\data\Richardsons\4fen.pdb

russell-taylor commented 1 year ago

Modified to continue placing NH3 with >3 neighbors and not having a preference function in that case. It still tries an initial placement that is 120 degrees away from a dihedral choice, but it will move to any other better location.

russell-taylor commented 1 year ago

The warning is in rotatable_bonds.py:axes_and_atoms_aa_specific(). It returns an empty list in that case. This does not seem to impede optimization.