Re: [ccp4bb]: need estimated error of occupancy

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

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

Susan Heffron wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Hi all.
> 
> We are looking for a method to calculate the "estimated error" for the
> occupancy values of the ions in our protein structure.  The occupancy
> was refined in X-PLOR or CNS.  A reviewer of our paper is requiring an
> "estimated error" of these values.  All suggestions for how to calculate
> this are appreciated.
> 
>                          Sincerely,
>                          Susan
> 
> --
> ------------------------------------------------------------------
>         Susan Heffron
> Dept. of Physiology and Biophysics
> University of California, Irvine
>  Irvine, CA  92697-4560   U.S.A.
>     phone:  (949) 824-4625
>     FAX:    (949) 824-8540
> ------------------------------------------------------------------


 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