[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: need estimated error of occupancy
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
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
------------------------------------------------------------------