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Re: [ccp4bb]: CNS to Refmac anomalous scatter library



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Jeff Vargason wrote:
> 
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> 
> 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