[phenixbb] rotamers

Phil Jeffrey pjeffrey at princeton.edu
Thu Mar 24 08:35:32 PDT 2011

```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.
>

```