-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>>> herman.schreu...@sanofi.com Sent: Mittwoch, 7. Mai 2014 14:25 >>>> To: CCP4BB@JISCMAIL.AC.UK 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Chris Fage >>>> Gesendet: Dienstag, 6. Mai 2014 19:03 An: >>>> CCP4BB@JISCMAIL.AC.UK 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/ iD8DBQFTamODUxlJ7aRr7hoRAmrMAJ9RvT4q2oUf1yGBXt9a1CgKm0t/FQCgslqq VOVuYvxPNeC8yeMMwFAx2oQ= =75DR -----END PGP SIGNATURE-----
