Dear Chris, In my experience, modern refinement program manage quite well to deconvolute occupancy and B-factor. In your case the negative difference density surrounding your metal ion shows that the lower occupancy could not be fudged by a higher B-factor. I would just refine occupancy and B-factor at the same time and let the refinement program do the deconvolution. If your density maps would still indicate problems, you always can try to manually deconvolute.
By the way, your formulation <attempt to "flatten" the negative density> sounds like some cheap trick, when in fact you try to get a model that more accurately reflects your observed diffraction pattern. Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Chris Fage Gesendet: Dienstag, 6. Mai 2014 19:03 An: [email protected] Betreff: [ccp4bb] Refining Metal Ion Occupancy Hi Everyone, In my 2.5-angstrom structure, there is negative Fo-Fc density surrounding a metal ion after refining in Phenix. From anomalous diffraction I am certain of the metal's identity and position in each monomer. Also, the ion is appropriately coordinated by nearby side chains. Should I be refining the occupancy of the ion in attempt to "flatten" the negative density? I am considering soaking the metal ion into crystals or cocrystallizing and collecting additional datasets. Thanks for your help! Regards, Chris
