Cant answer your question "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?"
Space group validation with Zanuda [image: image.png] CCP4 https://legacy.ccp4.ac.uk › newsletter48 › articles › zanuda <https://legacy.ccp4.ac.uk/newsletters/newsletter48/articles/Zanuda/zanuda.html> The program Zanuda presented in this article was developed to automate the validation of space group assignment in such circumstances. In addition, the program ... On Wed, 21 Feb 2024 at 15:40, Oganesyan, Vaheh < vaheh.oganes...@astrazeneca.com> wrote: > 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 > >> >> > >> >> 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 > >> >> > >> >> This message was issued to members of > http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by > http://www.jiscmail.ac.uk/, terms & conditions are available at > 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 > http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by > http://www.jiscmail.ac.uk/, terms & conditions are available at > 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 > >> > >> 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/ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> 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/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 > > > > Master Programme in Biochemistry for Health > > 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 > > ----- > 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 > > 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/ > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
