On 06/12/2024 18:09, Joel Meyerson wrote:
That was also helpful.
OK, good.
1. After running refine_residues_py() the auto_fit_best_rotamer() function did
a very nice job fixing up all the side chains I tested.
Good.
Is there any reason not to run auto_fit_best_rotamer() on every side chain
during the refinement process?
Speed?
Rotamer fitting is a different algorithm to real space refinement, so it
can't be added *during* refinement. You can do one then the other - or
cycles.
Note that there is the function backrub_rotamers_for_chain(imol, chain_id).
I'd like to understand what you would consider best practice.
I'd calculate the correlation coefficient of each residue with and
without sidechains, then calculate the rmsd of the differences and you
can use that to identify outliers (more than 2 rmsd from mean, say). You
can also do molecule_atom_overlaps(imol) to find wrong rotamers (maybe
these will correlate with badly fitting sidechains) - maybe try fitting
rotamers and then add hydrogen atoms and then scoring atom overlaps.
With proficiency with python and the Coot api web page to hand, this
should take an hour or two to whip up.
(I'd try it using chapi).
2. You mentioned doing a local refinement after running
auto_fit_best_rotamer(). Would this be accomplished with refine_residues_py()
over an ~3 residue window centered on the target residue?
Yes, that is what I meant.
3. What does rotamer_auto_fit_do_post_refine_state() do?
Reports the state of the flag that specifies if Coot should do a RSR on
the residue after a rotamer fit (often you do, sometimes not).
4. Do you have any plans to release a Coot 1 binary on the Coot site?
Not much beyond what is already there.
I have been spending my "making binaries" time instead helping those who
package Coot 1 for others so that you can find it in Debian, Ubuntu(?),
Arch, Flatpak and Homebrew.
Paul.
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