Don't forget, metals with their many electrons behave a lot better in
refinement than light (CNOS) atoms, because scattering goes as square of
number electrons. So you ought to get good behaviour even for joint
occupancy and B-factor refinement even at quite rubbish resolutions.
On 07/05/2014 13:25, [email protected] wrote:
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
