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-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski
Sent: 16 September 2011 18:25
To: COOT@JISCMAIL.AC.UK
Subject: [COOT] refine/improve Rama
Is there some way to do the Refine/Improve Ramachandran plot not on the
whole molecule? The underlying command stepped-refine-protein-for-rama
doesn't seem to have any other options but the imol, so obviously no
luck.
I also tried set-refine-ramachandran-angles 1 which, afaiu, should
turn Ramachandran restraints on, but I don't see any difference (in
fact, when I refine a zone the residues move away from allowed angles).
I thought that this could be combined with stepped-refine-protein, but
that one would also tackle the whole thing, and one cannot narrow its
action to a zone.
I could, of course, delete the elements I don't want refined and later
reinsert them. Another workaround (maybe) is to fix the atoms I don't
want to move (in which case it'd be totally awesome if one could fix
all
the atoms in a zone at once - is this possible?).
So, perhaps a future version may allow for all of these operations (e.g
fit-protein, stepped-refine-protein, stepped-refine-protein-for-rama)
tp
be applied to a zone? Please?
Having to refine a couple of large low resolution beasts right now, I
sympathise with your distress. I am not sure if this is of any help, but a
naive solution could be:
---
(define (stepped-rama-refine-zone imol chain-id res-start res-end)
(make-backup imol)
(let ((current-backup-state (backup-state imol))
(current-replacement-state (refinement-immediate-replacement-state))
(current-rama-state (refine-ramachandran-angles-state))
(imol-map (imol-refinement-map)))
(turn-off-backup imol)
(set-refine-ramachandran-angles 1)
(set-refinement-immediate-replacement 1)
(set-go-to-atom-molecule imol)
(if (valid-map-molecule? imol-map)
(map (lambda (residue)
(set-go-to-atom-chain-residue-atom-name chain-id residue CA)
(refine-auto-range imol chain-id residue )
(rotate-y-scene 25 0.3)
(accept-regularizement))
(number-list res-start res-end))
(format #t No valid refinement map.~%))
(if (= current-replacement-state 0)
(set-refinement-immediate-replacement 0))
(if (= current-backup-state 1)
(turn-on-backup imol))
(if (= current-rama-state 0)
(set-refine-ramachandran-angles 0
---
What might also help is to turn on the secondary structure restraints and set
the refinement matrix to low -- they seem more powerful than rama restraints to
me.
And if I am allowed a couple of feature requests along similar lines:
1. automatic detection of secondary structure restraints to be used -- coot
knows about secondary structure elements (it can e.g. colour the chain
according to those), it might as well use that knowledge to automatically
restrain the main chain torsions. (I admit I quite often forget to change helix
to strand or vice versa as I walk along the chain.)
2. stepped refine to work on nucleic acids
3. nucleic acid main chain torsion and ring pucker restraints
PS. Well, I was told long time ago that restraining Ramachandran
angles is a BAD idea because they should only be used for validation.
But this is 3A data.
Well, more recently, we were asked what we would pick if we had the choice:
better models or perfect validation tools...
