But curiously, all the 4 best solutions correspond to a SG with a 21
screw along b.
And amazingly none of the TF solutions is rejected due to clashes.
On 21/02/2024 12:20, Eleanor Dodson 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..
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
<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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