BS"D
Dear Eva,
You should be refining an overall temperature factor at that
resolution. It's one of the choices in the list, instead of
"isotropic".
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
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Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
