[phenixbb] to leave atoms out of ADP restraints
Jorge Iulek
iulek at uepg.br
Tue Feb 13 12:11:32 PST 2024
Thanks, Pavel, I will recall this part of the article. I see I can have
just one set of R, p and q values for the whole structure (= all atoms).
Best,
Jorge
On 2/12/24 11:19, Pavel Afonine wrote:
> Hi Jorge,
>
>> The ADP restraints I refer to in this discussion are the ones
>> that would make B-factors of nearby atoms to influence (or more or
>> less resemble) each other.
>> For some very disordered side chains, I would like to test
>> "taking out" the "more disordered" atoms (maybe for high chi angle
>> variability) of these restraints, for them to be more free to
>> skyrocket, but also that they do not influence so much the main
>> chain, in some cases where the flexibility difference between main
>> and side chain seems to be significant.
>> Is there a way to do so?
>
> not really, you can't exclude selected atoms from ADP restraints
> calculation.
> However, the way the restraints function is defined sort of
> intrinsically allows for something similar to what you describe, see
> formula (6) here:
>
> https://journals.iucr.org/d/issues/2012/04/00/ba5180/index.html
>
> Pavel
>
> Pavel
>
>
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