Dear Garib,
thank you for the quick response despite (or because of) the holidays. Ill try to summarize because I am not sure I understand yet, and it might be useful for all : Ø Partial structure mask bulk solvent parameters. Mask bulk solvent B value is in addition to protein B value. Not quite clear what you are saying here how does that answer what the Overall means versus the Partial? (some guessing below) Ø Full scaling is like this: Fscaled = scale_protein exp(-B s^2/4) exp(-s^T U s) (F_protein + scale_mask exp(-B_mask s^2/4) Fmask) (1-scale_babinet exp(-B_babinet s^2/4)) Ok then I see that I can use either _mask or _babinet terms because only one set of terms is in effect if the other one is zero. If I turn both off, I get basic k, B scaling, plus anisotropic B correction. Makes perfect sense. Based on that I will try to determine which line in the printout is actually the bulk solvent contribution. For the Partial structure part: Partial structure 1: scale = 0.375, B = 24.388 If I recall correctly, for the flat bulk solvent model the scale_mask and B_mask are generally in the order of 0.4 and 40AA, so then this ought to be scale_mask and B_mask of the solvent contribution? Yes? No? Now for Overall : scale = 0.891, B = -0.266 Now it gets interesting: what is this in terms of the above equation? I dont seem to be able to factor out a single overall scale and B correction from your eqn, but it sure looks like a correction term from bulk to be applied to the overall k and B . Can you clarify please? Ø Current version of refmac does not calculate Wilson B value I think we can get that readily from say truncate. But that wont be in the PDB REMARK 3 then Ø Note: Overall Bvalue may correspond to residual overall B value if you are using TLS refinement Understood. Ø If you use simple scaling then mask solvent is still on. Yes that is consistent with the doc. Ø You can turn it off by "Calculate the contribution of from the solvent region" Yes, that can be done by unclicking the box "Calculate the contribution from the solvent region". Handy if one needs to check certain things Ø To turn Babient's bulk solvent you need to use Babinet's scaling instead of simple. Yep, understood. Thx, BR From: Garib Murshudov [mailto:[email protected]] On Behalf Of Garib N Murshudov Sent: Thursday, December 29, 2011 4:47 PM To: [email protected] Cc: [email protected] Subject: Re: [ccp4bb] refmac Bsol Partial structure mask bulk solvent parameters. If you use simple scaling then mask solvent is still on. You can turn it off by "Calculate the contribution of from the solvent region" To turn Babient's bulk solvent you need to use Babinet's scaling instead of simple. I hope it helps regards Garib
