Hi, I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B-factors <25. Thanks for any help! -Jon
On Jan 19, 2010, at 6:13 PM, J. Fleming wrote:
I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B-factors <25. Thanks for any help!
K(sol) and B(sol) are the scale factor and overall B-factor for bulk solvent correction. They're properties of the crystal and not very sensitive to model quality - you shouldn't worry about them. (Including these statistics in the defaults for the Phenix version of POLYGON was a bad idea, and I've removed them in the current version.) I don't know what it means physically that the B(sol) is so low - you may just have weird crystals - but as long as K(sol) isn't zero, they don't indicate anything wrong with your data. For the record: the current version goes back to just R(work), R(free), average B, RMS(angles), and RMS(bonds). I'd like to have the clashscore in there too, but these are really the statistics that will be most interesting and informative to look at in POLYGON. -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
Hi Jon, for the Flat Balk solvent model: k_sol has a meaning of average solvent density, and its physically reasonable range is approximately from 0.2 to 0.6 e/A**3, with the average value ~0.35 (for all PDB entries). B_sol defines a smearing function that describes how deeply the bulk solvent penetrates into the model, and the value ranges from ~10-80A**2, with the mean ~46A**2. The contribution of the bulk solvent to the total structure factor Fmodel: Fmodel = scale_k1 * exp(-h*U_overall*ht) * (Fcalc + k_sol * exp(-B_sol*s^2) * Fmask) More details: - see "Relevant reading" section of phenix.refine manual (#4): http://www.phenix-online.org/documentation/refinement.htm#anch88 - slides #19-21 here: http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_p... For poor incomplete models B_sol typically tends to refine to nonsensical values above 100. Pavel. On 1/19/10 6:24 PM, Nathaniel Echols wrote:
On Jan 19, 2010, at 6:13 PM, J. Fleming wrote:
I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B-factors <25. Thanks for any help!
K(sol) and B(sol) are the scale factor and overall B-factor for bulk solvent correction. They're properties of the crystal and not very sensitive to model quality - you shouldn't worry about them. (Including these statistics in the defaults for the Phenix version of POLYGON was a bad idea, and I've removed them in the current version.) I don't know what it means physically that the B(sol) is so low - you may just have weird crystals - but as long as K(sol) isn't zero, they don't indicate anything wrong with your data.
For the record: the current version goes back to just R(work), R(free), average B, RMS(angles), and RMS(bonds). I'd like to have the clashscore in there too, but these are really the statistics that will be most interesting and informative to look at in POLYGON.
-Nat
-------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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The Bsol parameter will be influenced by model completeness (the B- factor of the solvent will tend to account for missing scattering in the atomic model). Given that your R-values are somewhat higher than usual it is possible that you need to complete the model further (adding ordered waters that have B-factors higher than 25 for example). On Jan 19, 2010, at 6:13 PM, J. Fleming wrote:
Hi,
I'm working on a structure but am having problems with K(sol) and B(sol). What are they and how do I get them into range? I thought they might have something to do with my waters but I have no water B- factors <25. Thanks for any help!
-Jon
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participants (4)
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J. Fleming -
Nathaniel Echols -
Paul Adams -
Pavel Afonine