BS"D
Dear All,
This topic has been discussed before, and if I recall correctly,
someone pointed out a very important thing about B-factors. Perhaps
I missed something, but I have not seen this point raised at this time.
Everyone (?) on this list knows the following:
B-factors measure displacement about an average position due
to thermal vibration. Thus, the bond between atoms should not be
regarded as a stick, rather a spring. Because most of us have poor
data/parameter ratios, we are forced to model this vibration
spherically. Small molecule people have a more accurate ellipsoid
model.
I think everyone should appreciate the following:
Missing side chain density is generally attributed to rotational
disorder. Imagine a serine side chain, where there is free rotation
about the Chi1 torsional angle. The Og will follow a circular path.
Another possibility is that the Og has 2 or more discrete
positions, and rotation about Chi1 is not free. Because of lack of
resolution, however, we don't see the Og, since it's occupancy at
each position is lowered.
So how can one consider taking a side chain for which there is no
density, presumably because it's moving (or was moving before it was
flash cooled...?) or assuming a few discrete conformations, and
assign very high thermal vibration parameters in the hope to model
this disorder? Seems rather incorrect to me.
Leave out the atoms you don't see.
As far as non crystallographers not understanding our data: caveat
emptor.
Harry
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Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
