Dear Gerard,
I agree with you based on debates at some conferences.
But, based on what I have seen here so far, it seems to me that everybody knows exactly what to do with disordered side chains.
People that want to build structures to best fit the data tend to prefer omitting disordered side chains. On the other hand, people that want to build structures to best represent reality tend to prefer building them. I don't see any disagreement here nor do I see any problems with either approach. Different people collect the same data to study different things and I feel that they are entitle to view and interpret the data the way that they fine most meaningful.
Equations are attempts to describe reality, I don't see why we should constrain reality to fit equations.
Cheers,
Quyen
On Mar 31, 2011, at 12:21 PM, Gerard Bricogne wrote:
> 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 [log in to unmask] *
> * *
> * Global Phasing Ltd. *
> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
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> ===============================================================
>>
>>
>> On Mar 31, 2011, at 10:22 AM, [log in to unmask] 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:[log in to unmask]] On Behalf Of
>>> Quyen Hoang
>>> Sent: Thursday, March 31, 2011 3:55 PM
>>> To: [log in to unmask]
>>> 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
>>>> <[log in to unmask]> 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: [log in to unmask]
>>>>
>>>>
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