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Dear Herman,
you provided a nice pictorial explanation of the term 'correlation'.
I'll leave it to you to run the experiment - I spent a couple of weeks
on this project because the separation is quite tricky.
Apologies for being sloppy, I referred to the unit of the y-axis on
Bernhards plot, not the physical reduction of electrons.
Regards.
To,
On 05/07/2014 05:20 PM, [log in to unmask] wrote:
> Dear Tim,
>
> As I see it, the issue is not how good the overall correlation is,
> but whether the differences in distribution of the electrons
> (narrow vs. broader) will show up in difference maps, which often
> show up at the edge of the ion. To make such calculations, I would
> calculate a difference map between say a model with a Zn with full
> occupancy and high B-factor vs. a model with a Zn with say 80%
> occupancy and a matching lower B-factor.
>
> Only if you do not see any significant features is such a map, I
> will be convinced there is not a great difference in changing
> occupancy or B-factor. Besides, it is new to me that increasing the
> B-factor would reduce the number of electrons. I always assumed
> they only would get distributed differently.
>
> Best, Herman
>
>
>
> -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board
> [mailto:[log in to unmask]] Im Auftrag von Tim Gruene Gesendet:
> Mittwoch, 7. Mai 2014 16:52 An: [log in to unmask] Betreff: Re:
> [ccp4bb] AW: [ccp4bb] Refining Metal Ion Occupancy
>
> 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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