Yet Uaniso's are multiplied by 1 and stored as integers with no problem!
-- Ian
On Thu, Oct 13, 2011 at 1:44 AM, James Holton jmhol...@lbl.gov wrote:
I think the PDB decided to store B instead of U because unless the
B factor was 80, there would always be a leading 0. in that
column, and
I've been struggling a bit to understand the definition of B-factors,
particularly anisotropic Bs, and I think I've finally more-or-less got my head
around the various definitions of B, U, beta etc, but one thing puzzles me.
It seems to me that the natural measure of length in reciprocal space
Not sure if this is helpful Phil, but SCALEIT output includes various
definitions taken from the Willis and Prior book.
But then there is the problem of converting the amplitude B factors to
real space..
I attach my anisotropy notes..
It doesnt address the ? of sensible conventions!!
E
On
Hi Phil
My understanding is that when the B factor was devised it was believed
that it wouldn't represent any physical reality and was initially at
least widely regarded as a garbage dump for errors. So it made no
difference whether or not it was related to the natural length in
reciprocal
This may answer some of your questions or at least give pointers:
Grosse-Kunstleve RW, Adams PD:
On the handling of atomic anisotropic displacement parameters.
Journal of Applied Crystallography 2002, 35, 477-480.
http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf
Pavel
On Wed, Oct 12,
Indeed that paper does lay out clearly the various definitions, thank you, but
I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't
explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather
than d*^2). I think James Holton's reminder that the
I think the PDB decided to store B instead of U because unless the
B factor was 80, there would always be a leading 0. in that
column, and that would just be a pitiful waste of two bytes. At the
time the PDB was created, I understand bytes cost about $100 each!
(But that could be a slight
At this point I usually chime in with an explanation of why
the Protein Data Bank made some choice or other in the early
days but on the matter of U vs. B I have not information to
contribute.
I can point out the at that time characters were stored in
display code on a CDC 6600 and display code
