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 <eleanor.dod...@york.ac.uk>
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 <jganesh3...@gmail.com> 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 Malý <martin.maly...@email.cz>
> > 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 Å. 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
> > >>
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