Hi Paul,
Am 14.04.11 15:03, schrieb Paul Emsley:
> Let's be clear what you mean, do I understand correctly?
>
> You are refining one residue and you want that residue to know about
> it's environment - i.e. residues that have not been selected for
> refinement and won't move, but will influence the refinement because
> they can provide vdW or H-bond restraints to the moving atoms?
yes, that's exactly what I want, but only if I'm convinced that the
fixed environment atoms are (more or less) in correct positions.
Otherwise, I would prefer to ignore them, because they might give false
VDW repulsions or false H-bonds attractions.
>
> You can do something like that with sphere refinement - and fixing the
> atoms that you don't want to move.
>
> Understanding hydrogen bonds in refinement though is not something
> that coot does at the moment. Some of the underlying code has been
> written but this feature is not available yet. It will be - keep
> poking :-)
I'm looking forward to this :-)
Best regards,
Dirk.
>
> Paul.
>
>
>
> On 14/04/11 10:37, Dirk Kostrewa wrote:
>> Another idea, that I propose from time to time, would be to have a
>> complete force-field like geometry term, including VDW repulsions and
>> hydrogen bonds. This would avoid refining atoms into already occupied
>> places and it would maintain secondary structures even at very low
>> resolution.
>>
>> Best regards,
>>
>> Dirk.
>>
>> Am 14.04.11 11:32, schrieb Bernhard Lohkamp:
>>> This is an idea I had for a while but never had the time to implement
>>> or test (it's still on my list though). For now torsion angle
>>> refinement and especially back-rub rotamer fitting of side chains
>>> (default for lower resolution; 2.8A IIRC) should help to prevent side
>>> chains from moving into the 'main' density.
>>>
>>> B
>>>
>>>> this one is for Paul, but maybe it's worth discussing it on the list.
>>>> If that
>>>> feature already exists, please let me know.
>>>>
>>>> Would it make sense to down-weight the side chain atoms in real space
>>>> refinement? At low resolution I often find that the side chain atoms
>>>> are dragged
>>>> into the density of where I suspect the main chain to run, and maybe
>>>> this effect
>>>> could be avoided by downweighting the X-ray 'force' on the side chain
>>>> atoms.
>>>> This might correspond to having different matrix values for main and
>>>> side chain
>>>> atoms.
>>>>
>>>> I am curious to hear comments about this idea.
>>>>
>>>> Cheers, Tim
>>>>
>>>
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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Germany
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