Yes, that is about what one would expect. I also checked a few of the extreme outliers, and almost always can come up with a reasonable value. Which does not remove my curiosity regarding the B_sol 70 cutoff and its purpose.
Cheers, BR From: Pavel Afonine [mailto:[email protected]] Sent: Monday, January 30, 2012 11:33 AM To: [email protected] Cc: [email protected] Subject: Re: [ccp4bb] B_sol from EDS Hi Bernhard, I just calculated k_sol and B_sol for all PDB entries that - have reflection data available, - I could re-compute the R-factor within 5%, and - R-work<30% using a simple cctbx script. Here is what I get: Distribution of k_sol: 0.000 - 0.060 : 27 0.060 - 0.120 : 12 0.120 - 0.180 : 51 0.180 - 0.240 : 182 0.240 - 0.300 : 1770 0.300 - 0.360 : 13819 0.360 - 0.420 : 19731 0.420 - 0.480 : 3039 0.480 - 0.540 : 471 0.540 - 0.600 : 256 Distribution of B_sol: 0.000 - 31.300 : 4349 31.300 - 62.600 : 29425 62.600 - 93.900 : 4578 93.900 - 125.200 : 597 125.200 - 156.500 : 225 156.500 - 187.800 : 84 187.800 - 219.100 : 37 219.100 - 250.400 : 23 250.400 - 281.700 : 10 281.700 - 313.000 : 30 It seems like the result of similar exercise done by Fokine and Urzhumtsev (Acta Cryst. (2002). D58, 1387-1392) still holds (see figure 3 on page 1390 there). Pavel On Mon, Jan 30, 2012 at 11:10 AM, Bernhard Rupp (Hofkristallrat a.D.) <[email protected]> wrote: Dear All, when I plot bulk solvent B and K extracted from EDS, an improbable and bimodal distribution appears. In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears (B-axis left to right, 0-200). http://www.ruppweb.org/images/b_sol_contour.jpg http://www.ruppweb.org/images/b_sol_surface.jpg According to a quick peak at EDS instructions, it uses the REFMAC flat bulk solvent model throughout for bulk solvent correction. The main peak in fact has the expected distribution, but it seems that the sharp peak at B_sol=70 represents some cut-off that in a certain set of calculations was used. For data mining it would be useful to know where/when these cutoffs were used. Best regards, BR ----------------------------------------------------------------- Bernhard Rupp http://www.ruppweb.org/ -----------------------------------------------------------------
