On 18 Apr 2007, at 14:39, Eva Kirchner wrote:
(But I'm still curious about the B-factor refinement when there is
no "REFI BREF ISOT" in the com-file...)
Eva,
Refmac internal default is REFI BREF ISOT
that's why even if you remove the above line from the com file (or
deselect that option from the interface) it still does ISOT BREF
refinement.
It does tell you that though....
if you look at the log file there's a bit that says
.......
Method of minimisation : Sparse Matrix
Experimental sigmas used for weighting
Number of Bins and width: 20 0.0080
Refinement of individual isotropic Bfactors
..........
what do you have there when you deselect the B fact option from the
interface?
I agree with Herman that at 3.2 A isotropic B values refinement can
be useful.
Roberto
Eva
2007/4/18, Mischa Machius <[EMAIL PROTECTED]>:
Like Harry said, it is not justified to do individual B factor
refinement at that resolution. Well, you can do it, but you'll end
up with funny results, such as what are observing right now. Still,
from a pragmatic point of view, individual B factor refinement in
cases like these can have a positive effect on the electron
density. However, keep in mind that the resulting B factors may
physically not be very meaningful. In the end, you'll have to
switch to grouped B factor refinement, or you risk nasty comments
from an attentive mentor or reviewer (and rightly so). Hope that
helps. Best - MM
On Apr 18, 2007, at 7:20 AM, Eva Kirchner wrote:
Hi,
I have a little problem with B-factor refinement. I'm using the
CCP4i interface, Refmac 5.2.0019, a resolution of 30-3.2 A (I
tried 8-3.2 A as well, it doesn't make a big difference for this
problem), and a current Rfree of 30.4%.
Refmac refines the B-factors so that they are nearly the same for
main chain and side chain, and I don't like that (or could it make
sense in any way?). Moreover, my structure is a protein complex,
and Refmac is mainly doing this for one component of the complex.
If I take the B-factors from the original uncomplexed protein
(around 18, 1.75 A) and add 44 to them with moleman to get them in
the range they are in the complex, Refmac "flattens" them
remarkably in only 5 cycles of restricted refinement. Does anyone
have an explanation for this? I am pretty sure that the complex
components are in the right place, I see beautiful density and
everything I should see at this resolution.
Here is what I tried further:
* I de-selected "Refine isotropic temperature factors" in the
Refmac interface. There was no REFI BREF ISOT any more in the com
file. But there was also no difference in the B-factors compared
to when there _was_ REFI BREF ISOT in the com file... So does
Refmac just _ignore_ my wish not to refine B-factors? (The REFI
keywords were as follows: type REST - resi MLKF - meth CGMAT - is
there any B-factor-thing hidden in this?)
* I played around with the geometric parameters. If I select the B-
factor values there (the keywords are TEMP|BFAC
<wbskal><sigb1><sigb2><sigb3><sigb4>), it does not make _any_
difference, what values I fill in there, the resulting B-factors
are always the same (but different from when I don't use the TEMP
keyword, and even "flatter"). Default for WBSCAL is 1.0, I tried
10, 1.0, 0.1, 0.01, and the equivalent numbers for the sigbs.
Thanks for any thoughts on this,
Eva
----------------------------------------------------------------------
----------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
---
Dr. Roberto Steiner
Randall Division of Cell and Molecular Biophysics
New Hunt's House
King's College London
Guy's Campus
London, SE1 1UL
Phone +44 (0)20-7848-8216
Fax +44 (0)20-7848-6435
e-mail [EMAIL PROTECTED]
