Dear Quyen,
I am afraid you won't get any better answers than you got so far. There is no
holy bible telling you what to do with disordered side chains. I fully agree
with James that you should try to get the best possible model, which best
explains your data and that will be your decision. Here are my 2 cents:
-If you see alternative positions, you have to build them.
-If you do not see alternative positions, I would not replace one fantasy (some
call it most likely) orientation with 2 or 3 fantasy orientations.
-I personally belong to the "let the B-factors take care of it" camp, but that
is my personal opinion. Leaving side chains out could lead to
misinterpretations by slightly less savy users of our data, especially when
charge distributions are being studied. Besides, we know (almost) for sure that
the side chain is there, it is only disordered and as we just learned, even
slightly less savy users know what flaming red side chains mean. Even if they
may not be mathematically entirely correct, huge B-factors clearly indicate
that there is disorder involved.
-I would not let occupancies take up the slack since even very savy users have
never heard of them and again, the side chain is fully occupied, only
disordered. Of course if you build alternate positions, you have to divede the
occupancies amongst them.
Best,
Herman
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Quyen Hoang
Sent: Thursday, March 31, 2011 3:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] what to do with disordered side chains
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
