[phenixbb] zero B-factors

Pavel Afonine pafonine at lbl.gov
Mon Nov 18 13:38:24 PST 2013

If you see this problem using the latest Phenix version then please send 
me files (off-list) necessary to reproduce it and I will investigate.

If interested what was the "problem" causing zero B-factors please see 


In a nutshell the problem is this. Assuming total model structure factor 
is (for simplicity):

F ~ exp(-Boverall_scale * s**2) * exp(-Batoms * s**2)

it's clear that any combination of Boverall_scale and Batoms that 
maintains Boverall_scale+Batoms=const will not change total model 
structure factors (and therefore R-factors, maps, etc).

The new bulk-solvent and overall scaling algorithm that we implemented 
sometime in April 2012 and that went into 1.8_1069 originally did not 
care about returning isotropic component of Boverall_scale back to atoms 


In fact, it assumed that overall contribution (overall B that is equal 
for all atoms) should stay in Boverall_scale (indeed, why keep common B 
in all individual atomic B-factors!?), and the rest goes into Batoms.
This behavior typically generates user concerns about "too small" 

An alternative agreement is to postulate that the matrix Boverall_scale 
is traceless meaning that overall B-factor goes into individual atomic 
This behavior occasionally generates user concerns about "too large" 

A few months later (sometime in end summer/fall 2012) we changed scaling 
behavior such that overall B-factor stays in individual atomic B-factors.

All in all, either way is correct and a matter of agreement and 
preferences, but definitely not a bug.

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