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This is removing the option to run phenix.refinement on individual residues within the residue portion of qFit. This code block was always False and there was no ability to turn it on to True wit qFit protein or ligand.
Unless phenix becomes more stable with their variable names, I suggest not re-implementing this with Phenix.
Note from Daniel Keedy on the job of this block of code:
'It is subtly different from just refinement with all anisotropic B’s, b/c the single residue in question is trimmed to Cbeta before refinement. The aniso refinement then moves the Cbeta in subtly different ways than it would if the sc was holding it more in place. This may have the result of exaggerating anisotropy along certain potentially useful directions for bb sampling. I don’t know how big that effect really is/was, tho. We have moved away from that strategy with qFit 3 of course. I don’t see a huge need to keep that code there, if we don’t know how well it works. Tagging / preserving it in some way outside the active code base could be useful, as there is a not-insignificant code block there (tho it seems it is never used as phenix_aniso is always False (?)), and it’s not inconceivable we would want to retry that strategy at some point in the future.'
Pull Request Checklist
devbranch?Exceptions will be made for urgent bugfixes.
dev?If not, please rebase your PR onto the most recent
devtip.Explain to a new user by completing the sentence: 'This PR will: ...'
This is removing the option to run phenix.refinement on individual residues within the residue portion of qFit. This code block was always False and there was no ability to turn it on to True wit qFit protein or ligand.
Unless phenix becomes more stable with their variable names, I suggest not re-implementing this with Phenix.
Note from Daniel Keedy on the job of this block of code: 'It is subtly different from just refinement with all anisotropic B’s, b/c the single residue in question is trimmed to Cbeta before refinement. The aniso refinement then moves the Cbeta in subtly different ways than it would if the sc was holding it more in place. This may have the result of exaggerating anisotropy along certain potentially useful directions for bb sampling. I don’t know how big that effect really is/was, tho. We have moved away from that strategy with qFit 3 of course. I don’t see a huge need to keep that code there, if we don’t know how well it works. Tagging / preserving it in some way outside the active code base could be useful, as there is a not-insignificant code block there (tho it seems it is never used as phenix_aniso is always False (?)), and it’s not inconceivable we would want to retry that strategy at some point in the future.'