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Dear Bernhard,
I just happen to collect the correlation between ADP and occupancy for
a publication I am involved in.
At 1.5A (!) resolution, the correlation for a single ion between both
figures is greater than 90% - there is certainly not a clear
difference between these factors.
One of the reasons might actually be visualised from the URL you
posted: At 2.5A resolution (the resolution this thread is about) the
number of electrons for Zn with B=30 drops from 30 to 25, which is not
so great a difference, at 1.5A it drops to about 20, which is still
not so great a difference, i.e. the B-factor weight is not too far off
from being constant at 'protein' resolution ranges.
Best,
Tim
On 05/07/2014 02:58 PM, Bernhard Rupp wrote:
>> 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:[log in to unmask]] On Behalf Of
> [log in to unmask] Sent: Mittwoch, 7. Mai 2014 14:25 To:
> [log in to unmask] 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:[log in to unmask]] Im Auftrag von Chris Fage Gesendet:
> Dienstag, 6. Mai 2014 19:03 An: [log in to unmask] 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
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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