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: [EMAIL PROTECTED]
fax: +81-6-6605-2557
tel: +81-6-6605-3131
Osaka City University
3-3-138, Sugimoto, Sumiyoshi, Osaka
Osaka 558-8585, Japan
*********
