On 05/07/2014 10:52 AM, Tim Gruene wrote:
>  At 2.5A resolution (the resolution this thread is about)

But maps ae not made "at 2.5 A" but from say 30A to 2.5 A.
In principle (i.e. if the 0,0,0 reflection were used), the effect
of diminishing the amplitude of high resolution terms is not to
decrease the total electron density but to smooth the features:
If the electron density profile going through the atom were a
rectangular box, the sharp corners would be rounded resulting in
less density inside the box and more outside, with the integrated
electron density the same. Which is exactly what you would expect
for an atom with increased rms displacement.

Now when the 0,0,0 reflection is absent so that the map is "floating"
with average value zero, and also the object is smaller than the
bragg spacing of the reflection, the 2.5 A reflection may contribute to
total electron density - I'm not sure.

Still the main effect of increasing the B factor should be to
spread out the density, while decreasing occupancy reduces
the total electron density without affecting the shape.
I can readily imagine that refinement programs can successfully
deconvolute the two. 90% correlation may be manageable.

eab


On 05/07/2014 10:52 AM, Tim Gruene wrote:
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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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