Re: [ccp4bb]: estimated error of occupancy

[Petrus Hendrik Zwart <Zwart@embl-hamburg.de>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

> - plot your R-factor versus occupancy.

What about plotting the value of the likelihood vs the occupancy?
Normalisation of the likelihood values later on gives you a nice
distribution, so you don't run into problems that your fitted gaussian
distribution will give you non-zero probabilities for occupancies bigger
then 1 or smaller then 0.

> You are also fighting a different problem, the occupancy and the 
> B-factor of your metal will be very highly correlated. In other words if 
> you decrease the B-factor your occupancy will go down as well. So make 
> sure that you have a reasonable B-factor and keep that one fixed in the 
> refinement.

You can make a 2D likelihood plot of occupancy and Bfactor if desired...
 
> To get a good B-factor for the metal, take the average B-factor
> of atoms around the metal for which you know that the occupancy is 1
> (i.e. side chain atoms that have only one conformation).

Or use those b-factors to build a prior of your ion bfactor, assume
uniform prior on occupancy and go bayesian ..... ;-)

Peter