I agree with Harry that an ice ring should never require you to process the data in two separate runs, and hopefully this does not become a standard approach..........
How did you present those data to aimless so it could scale the two datasets that have no overlap at all? Johan On Tue, 9 Apr 2019 at 10:07, Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi Sam > > Did you use the ice-ring exclusion option in iMosflm (a button that has an > image like a snowflake)? It should exclude data in _narrow_ resolution > rings (substantially less than 0.2Å!) around the ice rings, and can be set > for any combination of indexing, refinement and integration. There should > not be any need to process the data twice, once for the low resolution data > and once for the high. > > Harry > -- > Dr Harry Powell > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > On 8 Apr 2019, at 19:50, Sam Tang wrote: > > Hello everyone > > Thanks a lot for your input and advices. To report on how we tackled the > issue - > > (1) We used imosflm to integrate the data. > (2) We eventually integrated the data in two resolution ranges, say > 45A-3.5A, and 3.3A-3A, and merge them by Aimless. I must add that indeed > from the log file for our initial round the program had already identified > some ice ring regions. > > Aimless statistics looked fine and we were able to get a MR solution which > was refined to much better Rf/Rw. > > This is definitely not a smart solution because we effectively 'throw > away' useful data between 3.5A-3.3A, but for the purpose of MR and > refinement, it seems we have solved (or simply bypassed?) the problem. > > Suggestions on XDS/DIALS are appreciated. We are actually using this > dataset as a test set for XDS/DIALS to deal with ice rings. Will further > report if we've got anything interesting. > > Thanks again! > > Sam > > > > > On Thu, 4 Apr 2019 at 20:54, Clemens Vonrhein <vonrh...@globalphasing.com> > wrote: > >> 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. >> If you are not the intended addressee or an authorised recipient of the >> addressee please notify us of receipt by returning the e-mail and do not >> use, copy, retain, distribute or disclose the information in or attached to >> the e-mail. >> > Any opinions expressed within this e-mail are those of the individual >> and not necessarily of Diamond Light Source Ltd. >> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any >> attachments are free from viruses and we cannot accept liability for any >> damage which you may sustain as a result of software viruses which may be >> transmitted in or with the message. >> > Diamond Light Source Limited (company no. 4375679). 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 >> > > ------------------------------ > > 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 > -- Dr. Johan P. 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