Re: [ccp4bb] what to do with disordered side chains

[Quyen Hoang]

I don't have strong preference either way, but if one has good density  
for backbone and no density for a corresponding side-chain, would it  
be reasonable to believe that the side-chain might actually exists and  
that it has no visible density at a certain contour level might be  
because it was moving around (or static disorder)? 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?

Cheers,
Quyen
_______________________________
Quyen Hoang, Ph.D
Assistant Professor
Department of Biochemistry and Molecular Biology,
Stark Neurosciences Research Institute
Indiana University School of Medicine
635 Barnhill Drive, Room MS0013D
Indianapolis, Indiana 46202-5122
Phone: 317-274-4371
Fax: 317-274-4686
email: qqho...@iupui.edu
Website: www.hoanglab.com



On Mar 30, 2011, at 2:04 PM, James Holton wrote:


I'm afraid this is not a problem that can be solved by  
"standardization".

Fundamentally, if you are a scientist who has collected some data  
(be it diffraction spot intensities, cell counts, or substrate  
concentration vs time), and you have built a "model" to explain that  
data (be it a constellation of atoms in a unit cell, exponential  
population growth, or a microscopic reaction mechanism), I think it  
is generally expected that your model explain the data "to within  
experimental error".  Unfortunately, this is never the case in  
macromolecular crystallography, where the model-data disagreement  
(Fobs-Fcalc) is ~4-5x bigger than the "error bars" (sigma(F)).

Now, there is nothing shameful about an incomplete model, especially  
when thousands of very intelligent people working over half a  
century have not been able to come up with a better way to build  
one.  In fact, perhaps a better name for the "disordered side chain  
problem" would be "dark density"?  This name would place it properly  
amongst "dark matter", "dark energy" and other fudge factors  
introduced to try and explain why our "standard model" is not  
consistent with observation?  That is, "dark density" is the stuff  
we can't see, but nonetheless must be there somewhere.

Whatever it is, I personally do hold a vain belief that perhaps  
someday soon the problem of "dark density" will be solved, and that  
presently instituting a "policy" requiring that all macromolecular  
models from this day forward remain at least as incomplete as  
yesterday's models is not a very good idea.  I say: if you think  
there is "something there" then you should build it in, especially  
if it is important to the conclusions you are trying to make.  You  
can defend your model the same way you would defend any other  
scientific model: by using established statistics to show that it  
agrees with the data better than an "alternative model" (like  
leaving it out).  It is YOUR model, after all!  Only you are  
responsible for how "right" it is.

I do appreciate that students and other novices may have a harder  
time defining "surfaces" and measuring hydrogen bond lengths in  
these pesky "floppy regions", but perhaps their education would be  
served better by learning the truth sooner than later?

-James Holton
MAD Scientist


On 3/30/2011 9:26 AM, Filip Van Petegem wrote:

Hello Mark,

I absolutely agree with this.  The worst thing is when everybody is  
following their own personal rules, and there are no major  
guidelines for end-users to figure out how to interpret those  
parts.  I assume there are no absolute guidelines simply because  
there isn't any consensus among crystallographers... (from what we  
can gather from this set of emails...). On the other hand, this  
discussion has flared up many times in the past, and maybe it's  
time for a powerful dictator at the PDB to create the law...

Filip Van Petegem



On Wed, Mar 30, 2011 at 8:37 AM, Mark J van Raaij <mjvanra...@cnb.csic.es 
> wrote:
perhaps the IUCr and/or PDB (Gerard K?) should issue some  
guidelines along these lines?
And oblige us all to follow them?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1



On 30 Mar 2011, at 17:29, Phoebe Rice wrote:

> I've now polled 4 fairly savvy "end users" of crystal structures  
and there seems to be a consensus:
>
> - they all know what B is and how to look for regions of high B  
(with, say, pymol) and they know not to make firm conclusions about  
H-bonds to flaming red side chains.
> - None of them would ever think to look at occupancy and they  
don't know how anyway.
> - they expect that loops with disordered backbones would not be  
included in the models, and can figure out truncated or fake-ala  
side chains with some additioanl effort, but that option makes  
viewing surfaces and e-stats more of a pain.
>
>  Phoebe
>
> =====================================
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> 
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
>
> ---- Original message ----
>> Date: Tue, 29 Mar 2011 17:43:49 -0400
>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of  
Ed Pozharski <epozh...@umaryland.edu>)
>> Subject: [ccp4bb] what to do with disordered side chains
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>> The results of the online survey on what to do with disordered  
side
>> chains (from total of 240 responses):
>>
>> Delete the atoms                                         43%
>> Let refinement take care of it by inflating B-factors    41%
>> Set occupancy to zero                                    12%
>> Other                                                     4%
>>
>> "Other" suggestions were:
>>
>> - Place atoms in most likely spot based on rotomer and contacts  
and
>> indicate high positional sigmas on ATMSIG records
>> - To invent refinement that will spread this residues over many  
rotamers
>> as this is what actually happened
>> - Delet the atoms but retain the original amino acid name
>> - choose the most common rotamer (B-factors don't "inflate",  
they just
>> rise slightly)
>> - Depends. if the disordered region is unteresting, delete atoms.
>> Otherwise, try to model it in one or more disordered model (and  
then
>> state it clearly in the pdb file)
>> - In case that no density is in the map, model several  
conformations of
>> the missing segment and insert it into the PDB file with zero
>> occupancies. It is equivalent what the NMR people do.
>> - Model it in and compare the MD simulations with SAXS
>> - I would assumne Dale Tronrod suggestion the best. Sigatm labels.
>> - Let the refinement inflate B-factors, then set occupancy to  
zero in
>> the last round.
>>
>> Thanks to all for participation,
>>
>> Ed.
>>
>> --
>> "I'd jump in myself, if I weren't so good at whistling."
>>                              Julian, King of Lemurs



--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
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