Thank you for your post, Herman.
Since there is no holy bible to provide guidance, perhaps we should
hold off the idea of electing a "powerful dictator" to enforce this?
- at least until we all can come to a consensus on how the "dictator"
should dictate...
Cheers,
Quyen
On Mar 31, 2011, at 10:22 AM, herman.schreu...@sanofi-aventis.com wrote:
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
