Dear all, And if you want to process with XDS: autoPROC [1] will try to detect and exclude ice-rings automatically - if present [2].
If you know that you have ice-rings you can force it [3] to exclude all known ice-rings ranges - but this might not be the best solution if you have "just" diffuse ice-rings (where the special treatment of background within DIALS might be better). Something to test and compare maybe? Cheers Clemens [1] https://www.globalphasing.com/autoproc/ https://www.globalphasing.com/autoproc/wiki/index.cgi?IceRingHandling [2] https://www.globalphasing.com/autoproc/manual/autoPROC7.html#step1_spotnohkl https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Ice_rings [3] https://www.globalphasing.com/autoproc/manual/appendix1.html#SetvarParameter_XdsExcludeIceRingsAutomatically On Thu, Apr 04, 2019 at 10:51:19AM +0000, melanie.voll...@diamond.ac.uk wrote: > Dear Sam, > > > to continue from James Parkhurst's email... > > > You can do more analysis regarding ice rings using Auspex > (https://www.auspex.de/) if you already have some integrated file. > > Regarding re-integrating images, what did you use the first time round? I > think if you use DIALS it got some clever implementation in it that is better > in estimating the errors of reflections in proximity to ice rings. Hence you > should get better Rfactors without having to remove the effected resolution > range and the data it covers > (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619854/). > > > HTH > > > M > > > ________________________________ > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of > herman.schreu...@sanofi.com <herman.schreu...@sanofi.com> > Sent: 04 April 2019 10:26:09 > To: ccp4bb > Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring > > > 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<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 > > > > ________________________________ > > 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 > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. 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Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
