Dear Refmac developers group,
I am trying to understand a small detail in the refmac log listing. In the
bulk
solvent section just below the restraint table (I use monitor MANY in
general):
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Overall : scale = 0.891, B = -0.266
Partial structure 1: scale = 0.375, B = 24.388
Overall anisotropic scale factors
B11 = -0.39 B22 = 0.09 B33 = 0.33 B12 = -0.00 B13 = 0.48 B23 = 0.00
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Is the listing indeed containing the flat bulk solvent model ('simple model'
in refmac gui, SOLVENT YES) k and B in the first 2 lines?
If so, I am curious
a) what exactly is 'Overall' versus 'partial structure'? What is the
relative magnitude of the scale and B telling me in each case?
b) would it not be useful to have it reported in the PDB header?
All I find there is the anisotropic B scaling matrix and a
mean (overall) B value (of unspecified origin - how exactly is that
computed?)
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.711
Explanation/intuition would be much appreciated.
Best regards, BR
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Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
[email protected]
[email protected]
http://www.hofkristallamt.org/
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Old and treacherous will beat young and skilled every time
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PS: The doc leaves me a little confused because SCAL type SIMP would imply
KB = K0*exp(-B0*s^2) (Simple Wilson scaling)
i.e. K1 = 0
while BULK (Babinet) which I did not specify
KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2))
gives me 2 Ks and Bs.
So I conclude that 'overall' and 'partial' lines do not list Babinet ks and
Bs (the B is also too small for that)
