>the negative difference density surrounding your metal ion shows that the >lower occupancy could not be fudged by a higher B-factor
Because there is a clear difference between high B-factor and low occupancy: High B factor attenuates high resolution scattering most, while lower occupancy just evenly scales the scattering curve down. Ergo, the FT - the Electron density - also looks different, with a low occupancy causing a WIDER scattering curve than a comparable high B-factor, thus transforming into a NARROWER peak compared to high B-factor. So, you could adjust (within physically meaningful limits) B and n to 'reshape' the electron density. If you have a negative difference density 'ring', your 'observed' density there is less than the model density, and by reducing n you could reduce the wings of the model electron density peak, thus achieving a better match. There is also the possibility that you have - perhaps in addition - some truncation ripples, which are most prominent around heavy atoms. Figures 9-6 and 9-5 BMC. This app allows to generate the different scattering curve shapes, and a similar app lets you FT it. http://www.ruppweb.org/new_comp/scattering_factors.htm Best, BR -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of [email protected] Sent: Mittwoch, 7. Mai 2014 14:25 To: [email protected] Subject: [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy 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 -----Urspr�ngliche 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
