Hi All,
Interesting discussion as I have a similar case. In my case molecular
replacement solution can be found easily in P21, P212121, with very similar
looking electron densities. However, R-factors remain relatively high (mid
30s). In P1 completeness suffers (75% completeness), maps look decent, R
factors are in high 20's. Resolution limit is 1.9A with CC1/2 in high res.
shell ~0.7.
This might be a silly question, but I do not know the answer: After refinement
in P1 how do I distinguish which axis is crystallographic and which one in
non-crystallographic?
Vaheh
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Randy John Read
<rj...@cam.ac.uk>
Sent: Wednesday, February 21, 2024 9:18 AM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Difficult Molecular replacement
Hi,
It’s possible the true space group is P2(1) with the b-axis unique, and that
subset of true symmetry is found repeatedly with different incorrect
backgrounds of other copies. But I think the easiest way to resolve this
unambiguously is to solve in P1, and let that uncover the true symmetry.
Best wishes,
Randy
> On 21 Feb 2024, at 13:56, Pedro Matias <mat...@itqb.unl.pt> wrote:
>
> 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.
>> >>
>> >> ########################################################################
>> >>
>> >> To unsubscribe from the CCP4BB list, click the following link:
>> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
>> >>
>> >> This message was issued to members of
>> >> http://www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a
>> >> mailing list hosted by
>> >> http://www.jiscmail.ac.uk/<http://www.jiscmail.ac.uk>, terms & conditions
>> >> are available at
>> >> https://www.jiscmail.ac.uk/policyandsecurity/<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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
>> >
>> > This message was issued to members of
>> > http://www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a
>> > mailing list hosted by
>> > http://www.jiscmail.ac.uk/<http://www.jiscmail.ac.uk/>, terms & conditions
>> > are available at
>> > https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity/>
>>
>> -----
>> 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
>>
>>
>> ########################################################################
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list
>> hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions
>> are available at
>> https://www.jiscmail.ac.uk/policyandsecurity/<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<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
> --
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___________________________________
> Phones : (351-21) 446-9100 Ext. 1669
> (351-21) 446-9669 (direct)
> Fax : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt
>
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography<http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography>
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit<http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit>
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhD
> https://youtu.be/de6j-aaTWNQ<https://youtu.be/de6j-aaTWNQ>
>
> Master Programme in Biochemistry for Health
> https://youtu.be/UKstDCFjYI8<https://youtu.be/UKstDCFjYI8>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
-----
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
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list
hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are
available at
https://www.jiscmail.ac.uk/policyandsecurity/<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/
