Re: [ccp4bb]: need estimated error of occupancy

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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> 
>  I have done this with MLPHARE - you run REFMAC5 for the structure
> without the ions, and that outputs  FC/PHIC and FOM;
> 
> Then you can run mlphare
>  LABI FP=FC PHIB=PHIC FOM=FOM FPH=Fobs SIGFPH=SIGFobs  ( Maybe you have
> to assign a SIGFP too, but it can be a dummy SIGFP=DELFWT or something..
> 
> Then the "heavy" atoms are the ions, and you need only refine the
> occupancies against the centric data. You will get and SD as well..
> You can us the the "convert coordinate utilities to chanfge the ions in
> the pdb to the ha format used by mlphare.
> Eleanor
>  It is pretty reliable I think - good enough for a reviewer!
> Eleanor

 After reading all the other contributions I will extend this a bit.
 1) MLPHARE is a full matrix method, you will refine the ions without
restraints, so the SDs are quite reliable
 2) Since you only need an SD for the ion occupancy, amd maybe
(anisotropic?) B factor if the resolution allows both occupancy and Bs
to be refined. you only need limited resolution
(If the sites are very anisotropic you may need to refine xyz, but prob.
not..)

 You do need a decent observation/parameter ratio, but by restricting
the refinement to the ions alone you will have this at lowish
resolution, and in many space groups using the centric data alone..

3) Partitioned refinement like this (ie taking the protein as fixed and
refining ions alone)  is quite acceptable practice.

If you have an anomalous signal this refinement could be carried out for
the ions ( and any other anom scatters) alone. However that depends on
the accuracy of the ano diffs..

Eleanor