You can use sftools to set a shell of reflections to MNF - then Refmac
will fill those in with DFc, and that'll presumably be much better than
having very wrong reflections.
Whether that will fix your Rfactor is a different story.
phx
On 04/04/2019 11:05, Eleanor Dodson wrote:
You cant exclude one resolution ring in REFMAC - there would be ways
to fudge the exclusion from your current file, but much safer to use a
data integration tool
On Thu, 4 Apr 2019 at 10:27, <herman.schreu...@sanofi.com
<mailto:herman.schreu...@sanofi.com>> wrote:
Dear Sam,
I would remove the ice ring and reprocess the data. Ice rings may
wreak havoc with scaling so at minimum you have to redo the scaling.
Best,
Herman
*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>] *Im Auftrag von *Sam Tang
*Gesendet:* Donnerstag, 4. April 2019 11:01
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
Dear Eleanor and Eric
Thanks for your replies.
Yes indeed when we looked at the plots e.g. R factor vs resln
there was a sharp peak near 3.6 - 3.8 A which is where we visibly
saw an ice ring on the image. Thus our first thought was to remove
the ic ring. (either reprocess or can we bypass this resolution
range during refinement?)
The protein is 50 kDa, two molecule in the ASU, seemingly no
obvious density was unassigned. We got ~30000 total observations,
~15000 unique observations. NCS restraints was applied.
Best regards
Sam
On Thu, 4 Apr 2019 at 08:57, Eric Montemayor
<montemayor.e...@gmail.com <mailto:montemayor.e...@gmail.com>> wrote:
That’s a rather large gap between Rwork and Rfree. I suspect
you have mis-assigned your space group and as a result have a
large number of copies in your asymmetric unit. Any structure
can be solved in P1, but that does not mean the true space
group is indeed P1. If you use P1 when it’s not actually P1,
you will have an unnecessarily overparamerized model, hence
the large gap between Rwork and Rfree.
Questions:
1- how many copies in your asymmetric unit in P1?
2- how many atoms in your model vs number of unique reflections?
3- if more than one copy per asymmetric unit, are you imposing
NCS restraints during refinement?
-Eric
On Wed, Apr 3, 2019 at 1:41 PM Sam Tang <samtys0...@gmail.com
<mailto:samtys0...@gmail.com>> wrote:
Hi everyone again
Hmmm I think we have solved a structure in P1 space, to
2.5 A. However after refinement the Rfree stuck at 33%-35%
with Rwork around 26%. The structure was solved by MR and
current model seems to fit density well. In Refmac log I
found that at the resolution corresponding to high R there
may be a solvent/ice ring. Since imosflm should be able to
exclude ice rings, I am not 100% sure whether it's the
cause to high R. But if this is actually the case, is
there a way I can exclude certain resolution bins during
Refmac (and is it an appropriate way to do so?)
PS - the data is not affected by twining or pseudosymmetry
as checked by Xtriage.
Many thanks!
Sam
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