-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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, [email protected] 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:[email protected]] Im Auftrag von Tim Gruene Gesendet: > Mittwoch, 7. Mai 2014 16:52 An: [email protected] 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:[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/ iD8DBQFTalFAUxlJ7aRr7hoRAptYAKCg+S7IxfZ876sDh2HV9junHkXJegCgt6WQ RWP85IflkYpVjFkxyL+0/sU= =YV02 -----END PGP SIGNATURE-----
