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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