On Tue, 2021-07-27 at 15:20 +0100, Helge Paternoga wrote:
> Dear all,
>
> I have what feels like a trivial question about modelling in coot, but
> unfortunately I have not managed to solve it
> myself.
>
> I would like to create a bond between a P-tRNA and nascent chain and then
> subsequently use RSR in Coot for modelling.
>
> What I gathered so far is that I should use acedrg to create the restraints
> of the linked unit (in my case "A" to
> "VAL"). Therefore, I first followed the tutorial in the Coot development blog
> which worked well.
>
> But when I try to do the "real world" example with my model, acedrg crashes
> (and I could not find a useful error
> message).
>
> What I could figure out is that it has something to do with the
> RNA-nucleotide being referred to as "A", because
> linking an imported "AMP" molecule to valine as well as my whole nascent
> chain works as it should.
>
> Therefore, I wanted to ask if you could briefly tell me what is the correct
> way to achieve this type of linkage in
> Coot?
>
> Many thanks for reading and best wishes,
>
> Helge
>
>
> P. S. I have modified Oli Clarke's trimmings to automatically load the
> "Restraints" menu with
> "add_module_restraints()", but this is only partially working as the menu is
> not showing all entries upon starting
> coot. I have to still manually load "Calculate -> Modules -> Restraints" to
> get the rest of the entries to show. Is
> there something I could do to have the full menu from the get go?
>
>
Hello Helge,
It is not a trivial question.
I suggest that you use CCP4i2 interface for now - it is more featureful than
the Coot interface.
You can see Rob demoing the interface here:
https://www.youtube.com/watch?v=p4oTJ0bjD3M
https://onlinelibrary.wiley.com/iucr/doi/10.1107/S2059798321001753
But IIRC, your problem is more tricky yet, because one of the chains is
"backwards" relative to the other. I don't think
that I ever solved that.
As for auto-loading the module, this is what I have in my
~/.coot-preferences/modules.scm
(if (defined? 'coot-main-menubar)
(begin
(add-module-prosmart)
(add-module-restraints)
(add-module-cryo-em)))
Paul.
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