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
