I would also check carefully the other potential ice rings resolution ranges. I doubt there is just the one you can identify easily.
On Thu, Apr 4, 2019 at 12:07 PM Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 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> 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] *Im Auftrag >> von *Sam Tang >> *Gesendet:* Donnerstag, 4. April 2019 11:01 >> *An:* 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> >> 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> 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 >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=UECB-BTblxRTCrEA2arfPs5VNLr4ntyGxszsw_5Jaxc&s=QloAn3zc13ZQX64uxy6UZygomHXUigCIkpTw8ZhYpbk&e=> >> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=UECB-BTblxRTCrEA2arfPs5VNLr4ntyGxszsw_5Jaxc&s=QloAn3zc13ZQX64uxy6UZygomHXUigCIkpTw8ZhYpbk&e=> >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
