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..
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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