Harry M. Greenblatt wrote:
You should be refining an overall temperature factor at that
resolution. It's one of the choices in the list, instead of "isotropic".
I disagree with this. At that (3.2 Angstrom) resolution I've often
found than a tightly restrained individual B-factor refinement gives a
significantly lower R-free than a single overall B-factor. I also
prefer it to grouped B-factors in CNS, because the latter are not
geometrically restrained and show a lot of physically unreasonable
waywardness (although often, similar R-free as B-individual).
Individual B's can also be restrained by non-crystallographic symmetry
and as far as I can tell grouped B's are not.
I think one has to explore all possibilities rather than take one fixed
approach to working at modest resolutions, and the optimal solution is
likely to be different for different structures.
Phil Jeffrey
Princeton, NJ
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
-------------------------------------------------------------------------
Harry M. Greenblatt
Staff Scientist
Dept of Structural Biology [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
Weizmann Institute of Science Phone: 972-8-934-3625
Rehovot, 76100 Facsimile: 972-8-934-4159
Israel
