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yep, thats the problem. at first time i thought i
should have at least
few atoms from the main chain with B-factors under
20 or less. But, the
data are the data. This is it!
thanks everyone for helping.
all the best,
fred
Eric Toth wrote:
The average B is within ~2 of the Wilson B. That's pretty good agreement.
Is your problem that the distribution of B factors is too tightly clustered
around the mean? The data are the data.
_____________________________________________
Eric A. Toth, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
Marlene and Stewart Greenebaum Cancer Center
University of Maryland School of Medicine
108 North Greene St.
Baltimore, MD 21201
Email: [EMAIL PROTECTED]
Phone: x-410-706-5345
Fax: x-410-706-8297
http://www.umaryland.edu/bmb/faculty/toth.html
http://crystal.umaryland.edu
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of
Frederico Moraes Ferreira
Sent: Friday, March 17, 2006 1:34 PM
To: [EMAIL PROTECTED]; ccP4 bulletin board
Subject: Re: [ccp4bb]: hi b-factor on refmac refinement
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Res. 1.75 ang
current Rfactor .1620
wilson plot Bfactor 29.8 (from sfcheck)
the coot electron density fit looks fine with few
outliers.
I think it must be something wrong. Bmins should
be 5-9
fred, still puzzled
Bernhard Rupp wrote:
Seems perfectly ok. depends on overall B scaling as well.
Resolution was what?
best, br
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-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of
Frederico Moraes Ferreira
Sent: Friday, March 17, 2006 9:38 AM
To: CCP4 bulletin board
Subject: [ccp4bb]: hi b-factor on refmac refinement
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hi everybody,
I've got too hight B-factors for main chain atoms on refinement with refmac
- the latest version.
The refinement
settings are essentially the defaults from GUI.
Reset B-factors to 20.00 or to
0.00 didn't help anything. I was waiting main chains Baves around 10-20
and
Bmins around 5-10 (see results bellow).
Is there something else
to do? Clues are appreciated.
Thanks in advance,
fred
MOLEMAN2 > sel and cla main
AND atom selection
With atoms for which : (CLA)
Equals : (MAIN)
Selection history : (NON-HYDROGEN | AND CLass =
Main |)
Nr of selected atoms : ( 2816)
MOLEMAN2 > bf st
Chain name Atoms Bave Bsdv Bmin
Bmax Brms Bharm.av
A<-> 1496 27.06 4.54
21.15 48.39 27.44 26.45
B<-> 1320 27.83 4.73
20.35 51.10 28.23 27.18
Nr of chains encountered : ( 4)
