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Re: [ccp4bb]: need estimated error of occupancy



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Eleanor, (and CCP4ers): 

I'm making progress, but still need a little advice.

"Eleanor J. Dodson" wrote:
>  To begin with I think I would not use the PHIC at all. For centric data
> it should be the same as the FC(CA)
> What happens if you simply say
> FP =FC (I think you will have to assign SIGFP to something! maybe SIGFP
> but that might fail..
> 
> FPH1 to FP SIGFPH1 to SIGFP?
> 
> then just refine the CA sites andsee what the occupancies become.
> 

Mlphare now runs, but the refined occupancy is too high.  Here's what I
did:

Ran CAD with the Refmac output mtz file as input, and made a new mtz
file with FP, SIGFP, FC, and a second copy of SIGFP with column label
SIGFP2.

Ran mlphare using FP=FC SIGFP=SIGFP2    FPH1=FP SIGFPH1=SIGFP.
And started with the occupancy and b-factor of the ion set at the values
that they refined to in X-PLOR: 
 ATOM  CA+2   0.38223   0.26070  -0.06327    0.89 0.0 BFAC     16.210
Also, this was run using no resolution cuts, so the program is using all
data 2.0-15.0A.  Ran 10 cycles refining x,y,z and occ.

Now it runs (major progress!), but the final occupancy value is 1.327
(with S.D.= 0.066).  Does this indicate that there is some scaling that
I should be applying?  

I also tried running 10 cycles, alternately refining B and occ, and the
results are even further from what I was hoping for:  final occ=1.601
with B=22.84.

Again, what I am actually after in all of this is the S.D. of the
occupancy, which mlphare does give me, but the final occupancy value
from mlphare is not realistic because it is > 1.0.  The "expected"
occupancy value for this data set is ~0.9, and it certainly should be <=
1.0.

Any suggestions?

                                With thanks,
                                Susan

P.S.  I re-installed CCP4 vers. 4.2 last Friday, and now everything
works fine. I don't know what was causing the memory fault problems that
we were having initially.

> 
> > Sorry for this lengthy message... Any help you can give will be greatly
> > appreciated!  BTW, I'm running CCP4 version 4.1.1 of mlphare using a
> > script, because the recently installed version 4.2 exits with a memory
> > fault for this particular program.  My ccp4i is the 4.2 version.
> 
>  Oh shivers! It may be woreth checking on the ccp4 bug pages if there is
> a fix.
> Eleanor



-- 
------------------------------------------------------------------
        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
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