[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: CNS to Refmac anomalous scatter library
*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html ***
Jeff Vargason wrote:
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html ***
>
> While I was moving my refinement from CNS to Refmac, I wasn't able to find
> a way to add anomalous f' f'' scattering values. CNS allows me to use
> Cu, Mo, or a user defined anomalous f' f'' library file. I am refining
> this structure at a wavelength with substantial anomalous signal, and
> therefore, I would like to add alternate f' f'' values to improve my
> refinement. Can this be done in Refmac or added to protin.dic? For those
> questioning whether this is important, in CNS I see an approximate
> increase of 2% in both R and Rfree when using the Cu f' f'' values
> relative to f' f'' values based on my wavelength.
>
> Thanks,
>
> Jeff
> _______________________________________
>
> Jeff Vargason
> Department of Biochemistry & Biophysics
> ALS 2011
> Oregon State University
> Corvallis, OR 97331
> (541)737-1870
There is no way to use the f" value at present - fuure plans!..
But it is important to assign Cu Cu+1 or Cu+2 correctly - you need to
enter the atom name in the Pdb - eg
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 831 ZN+2 IUM Z 2 1 0.000 0.000 -8.039 0.33
11.00 Zn+2
ATOM 1 N MET A 1 57.252 -9.729 -43.817 1.00
40.00 N
Is that OK?
To change f'
This is rather clumsy, but you can edit the Cu formfactor in
$CLIBD/atomsf.lib
to include the f' difference then assign ATOMSF myatoms.lib on the
command line:
The extract about Cus is here:
Cu
29 29 1.191000
13.337999 7.167600 5.615800 1.673500
3.582800 0.247000 11.396600 64.812599
-2.019000 0.589000 0.263000 1.266000
Cu+1
29 28 0.890000
11.947500 7.357300 6.245500 1.557800
3.366900 0.227400 8.662500 25.848700
-2.019000 0.589000 0.263000 1.266000
Cu+2
29 27 1.144310
11.816800 7.111810 5.781350 1.145230
3.374840 0.244078 7.987600 19.896999
-2.019000 0.589000 0.263000 1.266000
and you need to modify the 3rd number on this line to 1.191000 +f' (
assuming f' is negative..)
Cu
29 29 1.191000
Eleanor Dodson