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Hi Ed,
I guess it depends on what 'successfully' means. The large correlation
implies quite an error margin, and I find an occupancy range of +/-
0.2 - 0.3 quite a lot, although this impression may vary depending on
what you are discussing w.r.t. the refined occupancy.
Best,
Tim
On 05/07/2014 06:01 PM, Edward A. Berry wrote:
> 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: 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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