As already mentioned by jrh, I again want to impress that B-factor and occupancy are in principle two entirely different parameters.

They may appear as achieving the same thing upon refinement at the resolution we deal with in most macromolecular structures.

The fact is that reduced occupancy just *scales down* the entire scattering function at a given B, while an increased B-factor *changes the shape* of the scattering curve, i.e. makes it narrower in reciprocal space and thus in direct space gives a broader electron density. Reduced occupancy just reduces electron density levels. Those are physically distinctly different although not easily separable effects. I have an applet that can be used to see the point

http://www.ruppweb.org/cgi-bin/webscat.exe?E1=O&B=50.0&Occupation_factor=0.5&B1=Submit

(disregard the core dump in the cgi)

and a figure from the book also shows this:

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-06.htm

Note that by reducing occupancy I can achieve a *similar* overall effect than by increasing B, but not the *same* electron density distribution!

If the data are good enough (and reasonably high resolution), a refinement program can refine both parameters simultaneously, although with a high covariance.

In summary, similar appearance is not caused by the same effect.

Best, BR

PS: Partial occupancy is not the same as disorder. You can have well-ordered different occupancies that manifest themselves then in superstructure

patterns. Common in small molecule/materials.

PPS: Neither n or B have anything to do with reflection spot width, btw!

From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Pavel Afonine
Sent: Monday, November 19, 2012 3:54 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] occupancy vs. Bfactors

Hi Grant,

sounds like you did the right thing (as far as I can guess given the amount of information you provided).

In a nutshell, both, B-factors and occupancies, model disorder. The difference is that occupancies model larger scale disorder (such as distinct conformations) than B-factors (smearing due to temperature vibrations, etc).

Perhaps in you case the side chain has several conformations among which you can see only one, and therefore it's valid to model it with occupancy less than 1 (I presume you refined one occupancy per all atoms in that side chain).

Pavel

On Mon, Nov 19, 2012 at 3:36 PM, GRANT MILLS <[log in to unmask]> wrote:

Hello all,

I'm currently working on a structure which if I stub a certain side chain phenix/coot shows me a large green blob which looks strikingly similar to the side chain, when I put it in and run another refinement the blob turns red.

Basically I was just playing around and I changed the occupancy of the side chain and now there are no complaints. But I was thinking, should I haven changed the Bfactors instead? Should I have left well enough alone? If I lower the occupancy manually and do not include alternate confirmations have I introduced modelling bias?

Could someone recommend some good articles I could read on exactly how to correctly fix this problem.

Thanks,
GM