Dear Berhnard It seems there are only one or two questions remain to clarify.
On 31 Dec 2011, at 07:20, Bernhard Rupp (Hofkristallrat a.D.) wrote: > Dear Garib, > > thank you for the quick response despite (or because of) the holidays. I’ll > 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) > Overall in the pdb header is calculated from atominc B values. > 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 > Partial is mask bulk solvent. > Overall : scale = 0.891, B = -0.266 > > Now it gets interesting: what is this in terms of the above equation? I don’t > 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? > Again: Overall B value in the pdb header is from atominc B values. Bvalue here is remaining part. It should be 0 but because of differences between lsq scaling and ML it is not always 0. For refinenemnt we use ML and for scaling/Rfactor calculations ls scaling. > Ø Current version of refmac does not calculate Wilson B value > > I think we can get that readily from say truncate. But that won’t be in the > PDB REMARK 3 then… > Yes. It would not be in the pdb header after refmac. It needs to be sorted out. I.e. refmac should calculate/read and write tot the pdb header > 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 > Regards and Happy New Year Garib > From: Garib Murshudov [mailto:garib.murshu...@gmail.com] On Behalf Of Garib N > Murshudov > Sent: Thursday, December 29, 2011 4:47 PM > To: b...@hofkristallamt.org > Cc: CCP4BB@JISCMAIL.AC.UK > 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 > > Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
