-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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:[email protected]] On Behalf Of > [email protected] Sent: Mittwoch, 7. Mai 2014 14:25 To: > [email protected] 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:[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 > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTakicUxlJ7aRr7hoRAq9bAKCZURDNZxvfzuXpk0slF1vh6hkkLACfd5Ls s7OV453Zj63k1xMOo+qzTfA= =lpSS -----END PGP SIGNATURE-----
