Hi Eleanor,
> On 21 Feb 2024, at 12:20, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
>
> Lots of comments, but it would be easier to actually look at your integrated
> data!
> Some of the stats look a bit ropey -
> 621 reflections labelled as outliers by PHASER?
> Very anisotropic
> Moments go mad at the highest resolution..
These 3 observations are actually all consequences of the strong anisotropy.
Phaser flags reflections with very little information content as outliers,
because they’re being ignored (as they would have almost no effect on the
likelihood calculation), and these come from the data in the weak directions.
The moments go mad, but in a way that is predictable from the sigmas on the
intensities, as seen by the fact that the predicted and observed moments track
each other as a function of resolution.
Best wishes,
Randy
>
> The good news - extremely strong signal from the rotation function means the
> model is probably a good one.
> Bad news - translation function results do not select a definitive solution..
> Possible reasons
> Unit Cell: 72.61 73.73 147.23 90.00 90.00 90.00
> Most likely data problems - a axis ~ = b axis so twinning is possible
>
> I could add more comments if either you could share the unmerged data, or at
> least a pointless logfile..
> Cheers Eleanor
>
>
>
>
>
> On Wed, 21 Feb 2024 at 11:06, Randy John Read <rj...@cam.ac.uk> wrote:
> Hi Marco,
>
> To add to what Kay has said:
>
> The intensity moments from Phaser (between 1.5 and 2 for the second moments
> after correcting for anisotropy) are indicative of likely twinning. With the
> cell dimensions, it might be possible to have pseudomerohedral twinning in an
> orthorhombic space group, but given the lack of distinction among possible
> choices of orthorhombic spac group (noted by Kay), it seems much more likely
> that the true symmetry is lower and that you have pseudosymmetry combined
> with perfect twinning.
>
> Judging from the strong and unambiguous rotation peak, your model is clearly
> very good, so I think it would be easy to ask Phaser to solve this by looking
> for 4 copies in space group P1. You can get P1 data either by expanding the
> orthorhombic data to P1 or by re-merging the data in P1. If the merging
> statistics were good, that would indicate that any twinning would be close to
> perfect, so just expanding the data would be a reasonable choice.
> Alternatively, you have reasonable redundancy so merging in P1 would be a
> plausible choice. I would probably go with expanding the data, figuring out
> from the MR solution what the real symmetry is, and then merging the data
> with that symmetry.
>
> Unless there are some other pathologies, I think the MR in P1 is very likely
> to give a clear answer (or maybe 2 answers related by the twin operator).
> It’s formally possible that you could have a different number of copies (e.g.
> 6 in the unit cell) if the true symmetry were monoclinic, so keep an open
> mind on that question. You could just try finding the largest domain from
> splitting the AlphaFold model (presumably the domain for which you sent the
> log file), work out the symmetry from that solution, and then run a job to
> search for all the domains in the right space group. It’s generally a good
> idea, by the way, to ask Phaser to look for everything you expect to find in
> one job, because it has built-in logic to predict the best search order but
> then update it on the basis of preliminary results.
>
> There are different ways to sort out the true symmetry from the MR solution,
> but within CCP4 the Zanuda procedure is a very effective choice.
>
> Get in touch if you have any difficulties following this procedure, and it
> would be great to let the BB know the outcome!
>
> Best wishes,
>
> Randy Read
>
> > On 21 Feb 2024, at 08:42, Kay Diederichs <kay.diederi...@uni-konstanz.de>
> > wrote:
> >
> > Hi Marco:
> >
> > short comments (I sent you also a private mail):
> > - the stats in CORRECT.LP look ok, but I'd like to know what ISa is, and
> > what the number of outliers is ("misfits"). Seeing the delta-CC1/2 stats as
> > a function of frame number is also useful for judging e.g. the radiation
> > damage - this is available from XDSGUI in the "statistics" tab. Another
> > remark: SPOT_RANGE=1 11 in COLSPOT will sample reciprocal space poorly - I
> > always use the first half of the DATA_RANGE as SPOT_RANGE, at a negligible
> > cost in CPU time.
> > - the Phaser logfile shows that the rotation function (table at line 1344)
> > has only a single solution, but the translation function (table at line
> > 7028) does not even allow to determine the space group - there is very
> > little contrast difference between potential "solutions".
> >
> > Best wishes,
> > Kay
> >
> > On Tue, 20 Feb 2024 21:45:12 +0000, Marco Bravo <mbrav...@ucr.edu> wrote:
> >
> >> https://www.dropbox.com/scl/fo/pmw9nisdmq53yir2jqcmu/h?rlkey=zaj6cnknkjgkowrzf0vrmqdyf&dl=0
> >>
> >> Here is a link to my Molecular replacement and asymmetric unit contents
> >> logfiles.
> >>
> >> I ran Simple molecular replacement phaser MR through ccp4 cloud with my
> >> .mtz that was auto-processed at the ALS light source Beamline 831. I
> >> truncated my Alphaphold model into several domains as suggested and ran
> >> separate MR jobs. All of them are still running but one MR job for just
> >> one of the helicase domains finished and that is the molecular replacement
> >> job logfile i have posted.
> >>
> >> I also posted my Data collection output for the crystal in the dropbox
> >> file.
> >>
> >> I also attached my XDS.INP and XDSCONV.INP files for more troubleshooting
> >> help.
> >>
> >> Thank you all for helping me I hope this provides more information to help
> >> figure out what is going on. I can post more information if needed.
> >>
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> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>
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-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road E-mail:
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
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