thanks Ian - good to rediscover the wheel! E On Tue, 8 Oct 2024 at 18:28, Ian Tickle <ianj...@gmail.com> wrote:
> > In that thread Clemens reported his extensive investigation of datasets > processed by XDS and found serious issues with apparent twinning. Look for > "Warning about twinning (POINTLESS)" in > https://www.globalphasing.com/autoproc/wiki/index.cgi?ComparisonProcessing202409 > . > > I. > > > On Tue, Oct 8, 2024 at 6:21 PM Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > >> Yes - I read that but didn't attach pseudo-twinning problems to it.. >> E >> >> On Tue, 8 Oct 2024 at 18:18, Ian Tickle <ianj...@gmail.com> wrote: >> >>> >>> Dear Eleanor >>> There was a whole CCP4BB thread "[ccp4bb] Problem of data reprocessing >>> with XDS" on this last week (started by Yimin Hu on Oct 2). >>> >>> Cheers >>> >>> -- Ian >>> >>> >>> On Tue, Oct 8, 2024 at 6:08 PM Eleanor Dodson < >>> 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>>> Maybe we need the two BBs to cross fertalise? >>>> E >>>> >>>> On Tue, 8 Oct 2024 at 17:52, Rafael Marques <rafael_mmsi...@hotmail.com> >>>> wrote: >>>> >>>>> Hi Eleanor, >>>>> >>>>> I have been seeing complaints about the new XDS software quite a lot, >>>>> although I do not remember exactly where. If my memory is not failing me, >>>>> it is on the phenixbb. They even released a correction for the updated >>>>> XDS. >>>>> >>>>> Best wishes >>>>> >>>>> >>>>> >>>>> ______________________________________________________ >>>>> >>>>> Rafael Marques da Silva >>>>> >>>>> PhD Student – Structural Biology >>>>> >>>>> University of Leicester >>>>> >>>>> Mestrando em Física Biomolecular >>>>> Universidade de São Paulo >>>>> >>>>> Bacharel em Ciências Biológicas >>>>> Universidade Federal de São Carlos >>>>> >>>>> phone: +55 16 99766-0021 >>>>> >>>>> * "A sorte acompanha uma mente bem treinada"* >>>>> *________________________________________________* >>>>> ------------------------------ >>>>> *De:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> em nome de Eleanor >>>>> Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> >>>>> *Enviado:* terça-feira, 8 de outubro de 2024 17:46 >>>>> *Para:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>>>> *Assunto:* Re: [ccp4bb] a twinning question.. >>>>> >>>>> I think Gerard has probably hit the jackpot. The data was sent to me >>>>> by a student and here is a bit of the header: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> * OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: >>>>> 105456487_mx32736v69_xGSTPBBRETLGHA00BA54831_scaled_unmerged.mtz * Title: >>>>> From XDS file SCALED_SAD_SWEEP1.HKL, XDS run on 19-Sep-2024 from image* >>>>> >>>>> >>>>> I will check what version of XDS was used then but I suspect it is the >>>>> one recently updated! >>>>> The structure solves quite well in P212121 and refines to ~ 23% >>>>> Not good data - not a perfect structure but probably NOT twinned. >>>>> >>>>> Can someone warn the community about this? >>>>> >>>>> Eleanor >>>>> >>>>> >>>>> On Tue, 8 Oct 2024 at 17:38, Ian Tickle <ianj...@gmail.com> wrote: >>>>> >>>>> PS you'll find a link to a description of all the twinning tests it >>>>> runs on the server home page. >>>>> >>>>> I. >>>>> >>>>> >>>>> On Tue, Oct 8, 2024 at 4:20 PM Ian Tickle <ianj...@gmail.com> wrote: >>>>> >>>>> >>>>> Dear Eleanor >>>>> >>>>> Try submitting it to the STARANISO server? That does a whole slew of >>>>> twinning tests (so you can take your pick from sometimes totally different >>>>> twin fractions from the various tests!). Also it gives you the twin >>>>> fraction rather than having you understand how to use the tests! But I >>>>> agree that the L test is one of the best, and the server uses a variant of >>>>> it which gives more accurate estimates of the twin fraction. >>>>> >>>>> Cheers >>>>> >>>>> -- Ian >>>>> >>>>> >>>>> On Tue, Oct 8, 2024 at 4:01 PM Eleanor Dodson < >>>>> 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >>>>> >>>>> I have always had great faith in the L test and other statistics to >>>>> detect twinning.. >>>>> But now I have a puzzling data set. >>>>> Seems to be orthorhombic with a, b and c all different >>>>> One molecule/asymm unit and no NC translation.. >>>>> BUT clear indication of twinning given by second moments, etc.. >>>>> >>>>> I have seen this before when the spacegroup was actually monoclinic >>>>> and the pointless analysis of the two fold axes along a b or c showed one >>>>> was better than the other two and in fact the crystal proved not to be >>>>> twinned when the data was processed as monoclinic.. >>>>> >>>>> But in this case no amount of reprocessing gets rid of the twin >>>>> indicator .. >>>>> Does anyone have any suggestions of why this might be? >>>>> ( The data quality isnt great - 2.5A but the Rmerges are reasonable..) >>>>> Eleanor >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> To unsubscribe from the CCP4BB list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>>> >>>> >>>> ------------------------------ >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>>> >>> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
