That works very well, thanks Judit, and thanks to Paul for the initial
script.
Is there a way to give refine-zone a list of residues rather than a
range? refine-residues doesn't seem to adopt the restraints I set in
refine/regularize control (e.g. ramachandran, secondary structure
restraints), but refine-zone does, and I'd quite like to use the
ramachandran restraints, as I find they come in very handy at low
resolution.
Or alternatively, if there's a way to set ramachandran restraints for
refine-residues via the scripting interface, that would also work.
Cheers,
Oli
From: COOT automatic digest system lists...@jiscmail.ac.uk
Date: 27 January 2009 11:06:15 AM
To: COOT@JISCMAIL.AC.UK
Subject: COOT Digest - 21 Jan 2009 to 26 Jan 2009 (#2009-15)
Reply-To: Mailing list for users of COOT Crystallographic Software COOT@JISCMAIL.AC.UK
There is 1 message totalling 99 lines in this issue.
Topics of the day:
1. Stepped version of sphere refine?
From: Debreczeni, Judit judit.debrecz...@astrazeneca.com
Date: 27 January 2009 3:54:34 AM
Subject: Re: Stepped version of sphere refine?
Recently, someone (I'm sorry, I can't recall who, and I couldn't find
the post in question) posted a extremely useful scheme script
to refine
residues in a sphere centered around the active residue.
That was Paul. (Who else? ;-) )
I was wondering if
anyone knows of a way to alter the script (reproduced below)
from a key
binding to a scheme function, such that it can then be called with
'stepped-refine-protein-with-refine-func'?
If no one got back to you on this one in the meantime, you might try
something like the following quick-and-dirty approach:
---
(define (stepped-sphere-refine imol)
(let ((imol-map (imol-refinement-map)))
(if (not (valid-map-molecule? imol-map))
(info-dialog Oops, must set map to refine to)
(let ((current-steps/frame (dragged-refinement-steps-per-
frame))
(refine-func
(lambda (chain-id res-no)
(set-go-to-atom-chain-residue-atom-name chain-id
res-no CA)
(let ((active-atom (active-residue)))
(if (not (list? active-atom))
(format #t No active atom~%)
(let* ((centred-residue (list-head (cdr
active-atom) 3))
(other-residues (residues-near-residue
imol centred-residue 4))
(all-residues (if (list? other-residues)
(cons centred-
residue other-residues)
(list centred-
residue
(format #t imol: ~s residues: ~s~% imol
all-residues)
(refine-residues imol all-residues)
(accept-regularizement)
(rotate-y-scene 30 0.6)))
(set-dragged-refinement-steps-per-frame 100)
(stepped-refine-protein-with-refine-func imol refine-func
1)
(set-dragged-refinement-steps-per-frame current-steps/
frame)
---
JED
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