Hello Kenneth,
On 06/05/2022 23:48, Kenneth Satyshur wrote:
I use the sphere refine in coot all the time. It's great. And when I
turn on 'Environmental Distances'. I can see the H-bonding to the
residue. Great. I have recently been using Isolde in ChimeraX to fit 3
A CryoEM density. When I select a residue, turn on H-bonding, it shows
all the nearest H-bonding. And when I run the MD to fix up the
problems, the H-bonds move in real time with the MD. Thus I can see
where the H-bonds of a neighbor may in fact be messing up the phi/psi
in question. Sometimes it is a sidechain that decides to pick a fight
with the backbone. Pulling on the offending group can resolve the
phi/psi. This is especially true of beta sheets with its alternating
peptide bonds.
My question is, can coot display the H bonds within a 'sphere refine'
radius so I can see all the H-bonding, and watch it more in real time.
Short answer no.
Longer answer...
One can add hydrogen bonds to the refinement
(set_refine_hydrogen_bonds(1)), but one can't see them during refinement.
coot 1 users can visualize the hydrogen bonds using
coot.calculate_hydrogen_bonds(imol).
I have recently been working on the interactive non-bonded contacts, so
it may not be much more work to add interactive hydrogen bond
representation also.
What I have not yet done (but is on the list) is dynamic updating of
non-bonded contacts list (and thus hydrogen bonds) during refinement
(this is the sort of thing that has been delayed ~3 years by me having
to do the infrastructure/gui/graphics work as a result of the Python 3
upgrade (for what that's worth)).
Is there a 'radius' parameter for 'environmental distances'?
No, it applies the the residue at the centre of the screen.
p.s. coot is so powerful I keep learning new things the more I use it.
Thanks Paul.
:-)
Paul.
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