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Coot

1,072 bytes added, 10:58, 29 March 2015
NCS Rotamer differences
(let ((imol (read-pdb "test.pdb")))
(compare-ncs-rotamer imol "A" "B"))
 
== make RSR in coot 0.8.1 behave like in earlier versions ==
 
Q: We've noticed a new behavior in real space refinement in coot 0.8.1 whereby dragged atoms are more tightly restrained to their initial positions than in earlier versions. This seems to be described in the release notes by:
 
o BUG-FIX: The amount that the other atoms ove with moving the picked atom has been reduced (but is configurable)
 
A: Add e.g. this to your ~/.coot.py file:
 
set_refinement_drag_elasticity(0.8)
 
Q: I'm wondering why this was changed. Does the optimum elasticity change with resolution, map quality, or another experimental limitation? Or does it more of a user preference?
 
A: Because of cis-peptides. My worry was that in the previous regime, it was
too easy to introduce cis-peptides when fitting to low resolution maps.
I believe the current default setting is much less likely to do that.
 
Q: I've tried various settings of refinement_drag_elasticity and I need to lower it to 0.5 or so before any semblance of earlier behavior appears.
 
A: It used to be 0.167, I think.
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