On 31/08/2022 01:37, Gong, Zhen wrote:
Hi Paul,
I think it is a bug. I was able to rotation O10 along the C07-N08
bond, but not the O9. Here is what I got:
Color-by-chain seems normal to me.
Hi Zhen,
My guess is that you are using Torsion General. I don't recall ever
using that tool in anger (as it were). For this sort of thing, I would
use Edit Chi Angles, and I suspect that if you edit your restraints
dictionary as suggested then that will "just work."
Regards,
Paul.
p.s. It is a bug though and I've made a note.
Zhen
*From: *Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
*Date: *Tuesday, August 30, 2022 at 20:25
*To: *Gong, Zhen <zg2...@cumc.columbia.edu>, COOT@JISCMAIL.AC.UK
<COOT@JISCMAIL.AC.UK>
*Subject: *Re: [EXTERNAL] Re: Bug in coot to change torsion angles?
On 31/08/2022 01:17, Gong, Zhen wrote:
Hi Paul,
Thank you very much for your timely reply. There are still some
puzzles for me.
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.
I do not agree. One changes the position of O10, while the other
changes O9. What I would like to do is to manually make the O9 and
O10 in the same plane with aromatic ring if possible. I was able
to rotate O10 along the C07-N08 bond but not 09, which I shall be
able to do in coot?
If I understand correctly what you are saying then that's a bug.
C06-C07-N08-O09 defines a rotatable bond (C07-N08) about which one
side of the fragment (the smaller side) is rotated - i.e. you cannot
move O10 without moving O09 also. That's how it should work. It seems
that you are saying that that is not how it's working for you.
By the way, I was able to make O9 and O10 in the same plane with
the aromatic ring by adding planar restraint. I would like to know
why I could not rotate O9 along the N08-C07 bond if possible.
Me too. It does seem very curious. Is there a missing bond restraint -
what happens when you display using colour-by-chain?
Paul.
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