I dont think REFMAC can refine occupancy, but the way I would tackle it
is to first refine B factors, then if those for the ligand are much
higher than for the protein maybe test changing those occupancies to 0.7
, 0,5 and so on..
But in fact B factors and occupancies are highly correlated, and you
would probably expect a ligand soaking in after crystallisation to have
higher B factors, so it is very difficult to get a definitive answer.
Eleanor
nkamiya wrote:
> Dear all,
>
> This is my first mail to CCP4BB.
>
> I'm now refining crystal structures of an enzyme at a resolution of
> 1.5A using refmac5 through CCP4i. Before X-ray data collections,
> the substrate and co-factor ions were soaked into the crystals. Their
> occupancies seem to be less than the unity because negative peaks
> can be found around the substrate and co-factors in the difference
> Fourier maps.
>
> I found "Developers Options" in the CCP4i window of refmac5 to
> specify an external keyword script file. If refmac5 can refine
> occupancies of substrate and co-facotrs independently, by using the
> script file, under the condition of fixed temperature factors, please
> let me know examples of the script files and how to use them.
>
> Best wishes,
>
> Nobuo Kamiya
>
>
> *********
> Prof. Nobuo Kamiya
> email: [log in to unmask]
> fax: +81-6-6605-2557
> tel: +81-6-6605-3131
> Osaka City University
> 3-3-138, Sugimoto, Sumiyoshi, Osaka
> Osaka 558-8585, Japan
> *********
>
>
|