Dear Sam,
Cutting out reflections obviously means you lose information. If you are using dials to process your data, then an alternative would be to try the ice ring background modelling algorithm which may give you better results.
Taking the output of dials.integrate you can do this as follows:
dials.model_background integrated_experiments.json
dials.integrate refined.pickle integrated_experiments.json \
background.algorithm=gmodel \
background.gmodel.model=background.pickle
Then scale as normal.
You can also use auspex to look at your scaled intensities to see if the ice rings are causing systematic errors.
Best wishes
James
________________________________
From: CCP4 bulletin board <[log in to unmask]> on behalf of Frank von Delft <[log in to unmask]>
Sent: 04 April 2019 11:39:19
To: ccp4bb
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring
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, <[log in to unmask]<mailto:[log in to unmask]>> 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:[log in to unmask]<mailto:[log in to unmask]>] Im Auftrag von Sam Tang
Gesendet: Donnerstag, 4. April 2019 11:01
An: [log in to unmask]<mailto:[log in to unmask]>
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 <[log in to unmask]<mailto:[log in to unmask]>> 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 <[log in to unmask]<mailto:[log in to unmask]>> 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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