Yes you are absolutely right. I believe the problem is the difficulty of
fitting valine, leucine and isoleucine rotomers and sidechains to what are
essentially "blobs" of map density. Refinement has a hard time with this.
I guess we have to stick with the experimental density.
Best
Ray
--------------------------------------------
On Sun, 3/10/19, Eleanor Dodson <[log in to unmask]> wrote:
Subject: Re: [ccp4bb] Protein modeling issue
To: [log in to unmask]
Date: Sunday, March 10, 2019, 3:40 PM
Both
REFMAC and COOT have an option to regularise (coot) or
idealise (refmac) a structure. These options will correct
bad gemetry if possible, but pay no attention to the fit to
density.
In general i think
it is sensible to inspect the map for regions where there
are serious errors high lighted. However if the resolution
is low, or the region of the protein is poorly ordered, it
may be difficult to see what needs fixing.
Eleanor
On Sat, 9 Mar 2019
at 21:23, Raymond Brown <[log in to unmask]>
wrote:
Hi
folks,
The WHATIF server found the following issue in evaluating a
protein structure.
Structure Z-scores, positive is better than average:
chi-1 / chi-2 rotamer normality : -7.278
(bad ( -3.8, 1.6) )
RMS Z-scores, should be close to 1.0:
Improper dihedral distribution : 2.025
(loose)
Does anyone have a suggestion of what can be done for
example
in Coot or Refmac5 to improve or fix these results?
Many thanks
Ray Brown
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