On 25/08/2023 06:56, Daniel Larsson wrote:
Hi Paul,
I have some suggestions/requests for facilitating sidechain modelling.
* Option to have the rotamer tool default to the rotamer most
closely resembling the current rotamer (now it defaults to the
most common rotamer)
That seems like a marginal improvement in the user interface.
If you want to "just tighten up the probability to the closest rotamer"
then turn on rotamer restraints so that they are used during refinement
(set-refine-rotamers 1)
* Option to have the rotamer tool default to the rotamer with the
highest average map value for the atoms. Atoms closer to the Ca
should be weight higher (as an option).
This could be done quite easily. But it's getting quite close to
auto-fit-rotamer functionality.
* Perhaps also have an option to allow for a small rotation/translation.
The devil, is as Phil would say, in the detail.
* Show all rotamers in the rotamer library at the same time and then
you can click on the one that you want (“bouquet” mode)
I don't see how this is an improvement over the use of the dot and comma
keys.
* Automatically select the best rotamer in a chain/molecule
considering fit-to-density and clashes, but without touching the
backbone and not doing any refinement.
The backbone shrugs when the sidechain dances. There is no tool in Coot
for rotamer fitting that doesn't move the mainchain. It could be done
quite easily, but I am not convinced of the utility. It seems to me that
it is quite possible the the backbone atom positions have already been
compromised to account for the wrongly positioned sidechain rotamer and
so without variation in backbone orientation, the wrong rotamer is more
likely to be found.
Paul.
p.s. are you iDaniel?
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