[phenixbb] rotamers

Engin Özkan eozkan at stanford.edu
Thu Mar 24 10:24:51 PDT 2011

This topic generates very strong feelings, and everybody have their 
favorite and valid arguments. I usually favor placing side chains, but 
with occupancies left at the chemical reality of 1.0, and letting B 
factors take care of disorder. I would like to point out at least one 
case where placing side chain atoms with occ=1 makes very good sense: a 
high-resolution model placed in a low-resolution structure and map, 
where side chains for which density is lacking. This is a case where we 
have prior information where the atoms are, but we may not see them in 
our 4-Angstrom map. Obviously, how you do B factors for such structures 
is important.

The reason why we place some atoms in our models depends on how much 
prior information (i.e. geometry, chemical connectivity, and previously 
determined models) we have for that special set of atoms. If a long loop 
has no density for it, it will not be placed. However, this is usually 
not the case for side chains.

Low resolution structures are more common these days, especially for 
many large protein complexes (and it is great that we can get these 
structures). I guess Pavel will be testing different scenarios 
(hopefully including 4 A-ish resolution), and will let us know of his 


On 3/24/11 8:35 AM, Phil Jeffrey wrote:
> The occupancy is a scalar weighting term in the structure factor 
> equation (or if you prefer, the electron density equation).  That's 
> its actual meaning, and anything else is interpretation of the meaning.
> For example I think it's very unlikely that any refinement program 
> takes the occupancy as a probability and weight the geometric terms 
> accordingly.
> Ergo occupancy zero surely should be interpreted as meaning "this atom 
> doesn't contribute to the X-ray scattering in this model", which I 
> personally interpret as "I've got no idea where it is".  Geometry does 
> limit the "no idea part", naturally, but this might involve some 
> complex analysis of the ambiguity level of the backbone placement.
> I tend to go with putting the s/c in and letting the B-factors float, 
> but given the nature of PDB, whatever you do is wrong for some 
> applications if used by someone unaware of this issue.
> Cheers,
> Phil Jeffrey
> Princeton
> On 3/24/11 11:23 AM, Ed Pozharski wrote:
>> No, that is not what occ=0.00 says.  100% occupancy means in the
>> standard model that an atom has an average position at (x,y,z) and moves
>> around (dynamically and statically) in a harmonic fashion with the
>> amplitude defined by B-factor.  50% occupancy means that it is found 50%
>> of time in the "gaussian vicinity" of (x,y,z), and 50% of time it's
>> somewhere else (in the second location present as alternate conformation
>> or, if the latter is absent, everywhere else as allowed by geometry).
>> 10% means it is only found at (x,y,z) 10% of the time, etc.  What
>> happens at 0% depends on one's take on continuity of the occupancy as a
>> descriptor of physical reality.  Unless we redefine occupancy of
>> precisely 0.00 as a special case that actually means "I have no idea
>> where this atom is other than what I can deduce from geometry and by the
>> way, the coordinates provided are completely meaningless" then by
>> continuity it means that the probability to find this atom at (x,y,z) is
>> precisely 0.  Which, for a disordered side chain, is most likely
>> incorrect.
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Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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