Dear Arko,
An average B-factor of 25 does not exclude that certain atoms have
B-factors of 150 or more, as long as this is compensated by atoms with a
low B-factor (say 5-10). If you select in coot <Measures> - <residue
info> and then click on a residue, you will get a listing of the
occupancies and temperature factors of the individual atoms in the
residue. This should give you a handle on how to interpret the temp
factor variance plot.
Best,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Arka Chakraborty
Sent: Sunday, April 22, 2012 9:18 AM
To: [email protected]
Subject: Re: [ccp4bb] high temp factor in coot!
Hi Dr. Bernhard,
I was actually confused because the baverage program in ccp4
gave average bfactor of 25.0 for the residue but coot is showing 150!
Also its a high resolution structure(res 1.6 ang) and the density after
refinement is lovely and does not indicate any disorder. So I was
wandering if I am interpreting the temp factor variance plot in coot in
a wrong way!
Regards
ARKO
On Sat, Apr 21, 2012 at 11:58 PM, Bernhard Rupp
<[email protected]> wrote:
Don't worry. High B-factor just means that the
probability of the atoms being at the specified coordinate position is
low, for whatever reason.
In most cases this is completely normal and often
indicative of solvent exposed surface residues, and a look at the
electron density will
show whether this uncertainty is due to absence of
electron density or a result of poor modeling. Remember that cranking up
the B-factor is the
'emergency exit' for the refinement program if an atom
is located at an incorrect coordinate position from which it cannot be
expelled (due to
stereochemical restraints).
BR
From: CCP4 bulletin board [mailto:[email protected]]
On Behalf Of Arka Chakraborty
Sent: Saturday, April 21, 2012 11:14 AM
To: [email protected]
Subject: [ccp4bb] high temp factor in coot!
Hi all,
I have solved the structure of a decamer dna
oligonucleotide. Analysis in CCP4 using baverage shows acceptable(<30)
avg b factors for all the residues. However temperature factor variance
analysis option in coot gives a figure of 150 for one of the residues
with a huge red bar. I would like to ask how should this be interpreted?
What exactly does the bfactor plot in coot signify?
Thanks in advance,
ARKO
--
ARKA CHAKRABORTY
CAS in Crystallography and Biophysics
University of Madras
Chennai,India
--
ARKA CHAKRABORTY
CAS in Crystallography and Biophysics
University of Madras
Chennai,India
