On 30/08/2022 22:26, Gong, Zhen wrote:
Dear Coot developers and users,
I would like to change some torsion angles of a ligand in coot but it
did not work as what I expected. I was able to play with the torsion
angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the
figure below).
One implies the other, it seems to me.
The restraint file for the torsion angle (C06 C07 N08 O10) is defined
quite well: LIG CONST_23 O09 N08 C07 C06 -5.58, which is close to
zero. Therefore, O9, O10 N08 should be more or less in the same plane
with the benzene ring.
I agree.
By default Coot does not refine torsion angles.
Also torsions named "CONST" are not refined.
You can turn on torsion angle refinement in the R/RC dialog
If I click on the ligand with “real space refinement”, it should make
the O9, O10 N08 more or less in the same plane with the benzene ring.
However, coot did not do it.
If you don't have plane restraints for the nitro and ring atoms then
coot doesn't know (hasn't been told) to keep them planar. All you've
done is said to Coot "here's a torsion angle, don't use it.|
The corollary of the above is to turn on torsion angle refinement and
rename the torsion var_23.
You could also add O09 to the ring plane restraint with perhaps double
or triple the esd.
Paul.
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