On Wednesday, March 30, 2011 08:29:11 am 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.

But this "knowledge" may be quite wrong.  If the flaming red really indicates 
large vibrational motion then yes, one whould not bet on stable H-bonds.
But if the flaming red indicates that a well-ordered sidechain was incorrectly
modeled at full occupancy when in fact it is only present at half-occupancy
then no, the H-bond could be strong but only present in that half-occupancy
conformation.  One presumes that the other half-occupancy location (perhaps
missing from the model) would have its own H-bonding network.

> - None of them would ever think to look at occupancy and they don't know how anyway.

A big part of the problem is that the needs of the community that produces
PDB files are different from those of the community that consumes them.  
Polling the two different communities will highlight points of difference, 
but not necessarily indicate a workable resolution.

Here's my take on letting the B factors absorb uncertainties in tracing,
rotamer assignment, multiple conformations, etc:

   ==> Don't do it if at all possible

Why?

The resulting model is not physically realistic.  I.e., it fails our
overarching validation criterion: "The model should not violate known physical/chemical/biological properties of the molecule".

To take a problem area close to my heart, consider the use of B in TLSMD and TLS
refinement.  Both TLSMD and TLS refinement itself are predicated on the assumption
that the B factors represent vibrational amplitudes.  Not uncertainty, not multiple
conformations, not incorrect rotamers - vibration.  If the model [mis]uses the 
B factors to indicate something else, then the TLSMD analysis is invalid, 
and TLS refinement is unlikely to work well either.

Both the refinement and analysis programs can correctly handle a half-occupancy
segment with reasonable B-factors.  At best, it is unclear what results from 
treating the same segment as full occupancy with B-factors that are unreasonably 
large by a factor of 2. [Or is that 2^2? or sqrt(2)? or or some exponential?]
At worst, improper description of this poorly ordered segment may degrade the
description of the well-ordered parts of your model.

The IUCr document defining atomic displacement nomenclature is
[Trueblood, et al, 1996; Acta Cryst. A52, 770-781] 
http://dx.doi.org/10.1107/S0108767396005697

From Section 1.5:
   [...] we shall try to summarize and describe briefly the most important
   components of the displacement. The best known is the displacement
   arising from atomic vibrations. When these result from the motion of
   molecules or molecular fragments (e.g. Willis & Pryor, 1975), they are
   usually characterized by relatively large amplitudes. In crystals
   containing relatively strongly bonded atoms (e.g. molecular and
   ionic crystals), much smaller displacement amplitudes result from the
   ever-present internal vibrations, such as bond stretching and bending
   [...] Other effective displacements from the mean position may arise as
   a result of a variety of possible types of disorder.
   These include small deviations from ideal periodicity, present in all
   real crystals; orientational disorder, present in many molecular crystals;
   density and displacement modulations; and short- and long-range displacive
   correlations.

From the Recommendations:
1. The term anisotropic displacement parameters (abbreviated ADPs) should
   be used in referring to the individual atomic coefficients in the
   exponent of the factor that describes the effects of atomic motion and
   static displacement.

My comments on the IUCr recommendations (EAM):
Although the definition of ADP refers to "anisotropic" displacements, 
the document itself considers both the isotropic and anisotropic cases.
The term "displacement" signifies displacement about a mean position, 
not a set of N discrete conformations.  The mathematical treatments
deal with representing displacements as [pseudo]Gaussian PDFs.  This representation/assumption is violated if the ADPs are [mis]used
to denote multiple conformations or incorrect positional assignments.

	cheers,

		Ethan


> - 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 <[log in to unmask]> (on behalf of Ed Pozharski <[log in to unmask]>)
> >Subject: [ccp4bb] what to do with disordered side chains  
> >To: [log in to unmask]
> >
> >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.
> >
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742