How to handle NH3 rotators on NCO?

[russell-taylor]

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]

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]

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

[russell-taylor]

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]

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.