price at uchicago.edu
Thu Mar 24 08:26:07 PDT 2011
I'm moderately in favor of the "just let B go through the roof" option. Here's why:
Most "user friendly" programs like pymol have an option to color the atoms by B but not by occupancy.
Most end-users I interact with know enough to see if coloring by B makes a side chain flaming red, but they'd never think (or know how) to check occupancy. (So if you do set occ to zero, please set B to the max!)
And truncating side chains screws up simple electrostatics calculations, which matters if you deal with nucleic acid-binding proteins.
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
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