Dear Kay This is a plot I sent to Eleanor yesterday, from her log file. The cumulative intensity plot shows I think that there are too few weak intensities, the opposite of twinning. I don;t know where it comes from but it’s not right! Best Phil
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> On 29 May 2025, at 12:03, Kay Diederichs <[email protected]> > wrote: > > CAUTION: This email originated from outside of the LMB: > [email protected]. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > If you think this is a phishing email, please forward it to > [email protected] > -- > > Dear Gerard, > > part of the problem was probably indeed due to the use of XDS BUILT=20240712 > (that version was used for CORRECT.LP that Janani Ganesh sent to me). I > obtained the raw data from Janani Ganesh and processed with both the current > XDS (BUILT=20250430), and the bad version from July last year. My findings: > - with the bad version the data appear twinned, whereas with the current > version the data appear untwinned > - Wilson B is 34 A^2 with the current version, and significantly (and > unrealistically) lower with the bad version > > The structure can be satisfactorily solved and refined with data from the > current XDS version. With data from the bad version, average B goes down to > 19 and the R-values stall at high values. > > This does not explain the weird B-values that were reported, though. So I > suspect another problem. > > Best, > Kay > > > > On Thu, 29 May 2025 11:37:14 +0100, Gerard Bricogne <[email protected]> > wrote: > >> Dear all, >> >> I wrote yesterday a contribution to this thread, but mistakenly >> used a simple Reply instead of a Group Reply, so that my message did >> not reach the BB while it intended to, as shown by the introductory >> "Dear all". >> >> I am including it below, as it contains a link to some material >> that is of general interest but that we had not yet found a way of >> disseminating to the whole community. Users of XDS, or of XDS-based >> pipelines, please take notice and do take a close look at this link, >> and ultimately at the BUILT= information about the exact XDS version >> used in producing your results - it can make a lot of difference. >> >> >> With best wishes, >> >> Gerard. >> >> -- >> Date: Wed, 28 May 2025 16:18:25 +0100 >> From: Gerard Bricogne <gb10> >> Subject: Re: [ccp4bb] Requesting help with twin refinement >> To: Eleanor Dodson <[email protected]> >> >> Dear all, >> >> These kinds of anomalies (overoptimistic estimates of resolution, >> unphysical persistence of signal at high resolution, spurious twinning >> diagnostics) are reminiscent of what we observed with some of the >> recent versions of XDS, as documented at >> >> https://www.globalphasing.com/autoproc/wiki/index.cgi?ComparisonProcessing202504 >> >> and three predecessor pages referenced from within this one. >> >> Only one version is currently available from the XDS download >> page (that we consider as being OK) but there was a succession of many >> problematic ones going back to July 2024. Perhaps the version used to >> process this dataset was one of the unlucky ones. >> >> Apologies if this is a red herring, but that check is worth >> making. >> >> >> Best wishes, >> >> Gerard >> >> -- >> On Thu, May 29, 2025 at 11:05:52AM +0100, Eleanor Dodson wrote: >>> After inspecting the log files it is obvious the problem is in the data >>> integration. (Wilson B negative! highest resolution shell stronger than low >>> res, etc..) >>> I think you used XDS for that? Do you have an alternative set of integrated >>> unmerged data, eg done with DIALS? >>> If so I would use that, or download a new version of XDS and try again.. >>> >>> On Wed, 28 May 2025 at 07:56, Janani Ganesh <[email protected]> wrote: >>> >>>> Dear Martin, >>>> >>>> Thank you for your suggestion. I will try it out and let you know. >>>> >>>> Regards, >>>> Janani Ganesh >>>> >>>> On Tue, 27 May 2025 09:01:06 +0100, Martin Mal� <[email protected]> >>>> wrote: >>>> >>>>> Dear Janani, >>>>> >>>>> There has been recently a significant development in twin refinement >>>>> algorithms in Servalcat. Could you try this program and let us know if >>>>> it helps? >>>>> You can find Servalcat in i2 in the most recent version of CCP4. You can >>>>> also run it in terminal/CCP4Console: >>>>> servalcat refine_xtal_norefmac --hklin data.mtz --model model.pdb -s >>>>> xray --labin I,IMEAN,FreeR_flag --twin >>>>> (Assuming your MTZ data file has columns I,IMEAN,FreeR_flag.) >>>>> >>>>> Full list of options: >>>>> servalcat refine_xtal_norefmac -h >>>>> >>>>> Please feel free to ask if anything was not clear. >>>>> Cheers, >>>>> Martin >>>>> >>>>> >>>>> On 27/05/2025 07:00, Janani Ganesh wrote: >>>>>> Hello, >>>>>> >>>>>> I recently collected diffraction data and I was able to do the data >>>> processing upto 1.88 �. I observed the R-merge remained the same throughout >>>> the resolution bins. I could solve the structure using Phaser in the space >>>> group P32 2 1 (no. 154). But when I refined the structure the R-factors >>>> remained ~ 35 % even after several cycles of refinement and model building. >>>>>> >>>>>> Then I looked for twinning in my data using Xtriage, Detwin, Pointless, >>>> etc which indicated twining. Subsequently, I started twin refinement with >>>> Refmac using twin law (-h, -k, l). The R-factors came down to ~25%. >>>> However, the B-factors refined to 0.5 for all the atoms. I tried redoing >>>> the data processing at lower symmetry space groups, P3, P31, P32, followed >>>> by twin refinement but the issue with the B-factors persisted. >>>>>> >>>>>> I would appreciate any suggestions and advice towards resolving this >>>> problem. >>>>>> >>>>>> Regards, >>>>>> Janani Ganesh >>>>>> >>>>>> ######################################################################## >>>>>> >>>>>> 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/ >>>>> >>>>> ######################################################################## >>>>> >>>>> 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/ >>>> >>>> ######################################################################## >>>> >>>> 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/ >>>> >>> >>> ######################################################################## >>> >>> 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/ >> >> ######################################################################## >> >> 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/ > > ######################################################################## > > 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/ ######################################################################## 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/
