Dear Quyen,
On Thu, Mar 31, 2011 at 11:27:58AM -0400, Quyen Hoang wrote:
> 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...
>
... but that might well be even harder than to decide what to do with
disordered side chains ... .
With best wishes,
Gerard.
--
===============================================================
* *
* Gerard Bricogne [email protected] *
* *
* Global Phasing Ltd. *
* Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
* Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
* *
===============================================================
>
>
> On Mar 31, 2011, at 10:22 AM, [email protected] 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:[email protected]] On Behalf Of
>> Quyen Hoang
>> Sent: Thursday, March 31, 2011 3:55 PM
>> To: [email protected]
>> 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
>>> <[email protected]> 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: [email protected]
>>>
>>>
