We are getting off topic a little bit.
Original topic: is it better to not build disordered sidechains or
build them and let B-factors take care of it?
Ed's poll got almost a 50:50 split.
Question still unanswered.
Second topic introduced by Pavel: "Your B-factors are valid within a
harmonic (small) approximation of atomic vibrations. Larger scale
motions you are talking about go beyond the harmonic approximation,
and using the B-factor to model them is abusing the corresponding
mathematical model."
And that these large scale motions (disorders) are better represented
by "alternative conformations and associated with them occupancies".
My question is, how many people here do this?
If you're currently doing what Pavel suggested here, how do you decide
where to keep the upper limit of B-factors and what the occupancies
are for each atom (data with resolution of 2.0A or worse)? I mean, do
you cap the B-factor at a reasonable number to represent natural
atomic vibrations (which is very small as Pavel pointed out) and then
let the occupancies pick up the slack? More importantly, what is your
reason for doing this?
Cheers and thanks for your contribution,
Quyen
On Mar 30, 2011, at 5:20 PM, Pavel Afonine wrote:
Mark,
alternative conformations and associated with them occupancies are
to describe the larger scale disorder (the one that goes beyond the
B-factor's capability to cope with).
Multi-model PDB files is another option.
Best,
Pavel.
On Wed, Mar 30, 2011 at 2:15 PM, VAN RAAIJ , MARK JOHAN <mjvanra...@cnb.csic.es
> wrote:
yet, apart from (and additionally to) modelling two conformations of
the side-chain, the B-factor is the only tool we have (now).
Quoting Pavel Afonine:
> Hi Quyen,
>
>
> (...) And if B-factor is an estimate of thermo-motion (or static
disorder),
>> then would it not be reasonable to accept that building the side-
chain and
>> let B-factor sky rocket might reflect reality more so than not
building it?
>>
>
> NO. Your B-factors are valid within a harmonic (small)
approximation of
> atomic vibrations. Larger scale motions you are talking about go
beyond the
> harmonic approximation, and using the B-factor to model them is
abusing the
> corresponding mathematical model.
> http://www.phenix-online.org/newsletter/CCN_2010_07.pdf
>
> Pavel.
>
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es
