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i am reposting the message below. indeed, the ccp4bb software did not allow a
modestly sized gif to be attached, so to see the image instead aim your
browser at: http://xray.bmc.uu.se/gerard/embo2001/modval/owab_vs_bwilson.gif
mazzel tov and happy hanukka everybody !
--dvd
---------- Forwarded message ----------
Date: Thu, 21 Dec 2006 18:32:42 +0100 (CET)
From: Gerard DVD Kleywegt <[EMAIL PROTECTED]>
To: Paul Emsley <[EMAIL PROTECTED]>
Cc: CCP4BB <[email protected]>, Gerard Kleywegt <[EMAIL PROTECTED]>
Subject: Re: [ccp4bb]: high B-factors
A handful of misplaced waters with extremely high B-factors can shift the
average by several squared Angstroems. It is probably better to compare the
median temperature factor of the model with the value from the Wilson plot.
really ? assuming that a "handful" is 10 and "extremely high" is 100 A2, then
if you add $(handful) waters with a B of $(extremely high) and the average B of
your other 2000 atoms is 20 A2, they will increase the overall average B by
only ~0.4 A2
in EDS we leave out the waters when calculating the average B. if the ccp4bb
software allows attachments of 17 kB, then the attached box plot (>20,000 EDS
entries) shows that the correlation between average model B and Wilson B is
very good up to ~40 A2 - after that, the model B tends to underestimate the
Wilson B
(for an explanation of this type of plot, look here:
http://xray.bmc.uu.se/gerard/supmat/rfree2000/tie_fi.gif )
--dvd
******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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The opinions in this message are fictional. Any similarity
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