Hi Eleanor According to the peak search the 3 highest peaks on the chi=180 section are at:
| 3 90.00 -52.26 180.00 0.49 | | 4 90.00 -73.73 180.00 0.47 | | 5 90.00 -66.55 180.00 0.44 | plus a lot of lower peaks on that section which are clearly in the noise. However eyeballing that contoured section that's clearly not right: there are no clear peaks at those positions and I bet the ones above would vanish with higher contour levels. The highest peaks are elsewhere on the contoured chi=180 section, i.e. due to the 3 crystallographic 2-folds at: 90 0 180 (2_x) 90 90 180 (2_y) 0 0 180 (2_z) The other peaks in the peak search could be similarly in error: it would probably work better with a noise threshold. I would have more confidence in the results if I saw the contoured sections for myself ! A peak on the chi=90 section doesn't necessarily imply a 4-fold axis (i.e. a closed group). It could simply be 2 (or even 3) subunits related by a 90 deg. rotation (i.e. not a closed group). A 4-fold axis gives rise to multiple overlapping peaks on the chi=90 and chi=180 sections (so the peak heights would be greater). Cheers -- Ian On Sat, 22 May 2021 at 18:14, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Ian - I read the log file - agree, you cant get much from the pictures.. > But the peak heat of the translation vector is 50% od the origin - ie > pretty strong.. > And ditto for the rotation angles - all 50% of origin too > But of course any set of rotation angles does not have to generate a > closed rotation system - they could be relating distant monomers.. > Cheers Eleanor > > > > On Sat, 22 May 2021 at 17:50, Ian Tickle <ianj...@gmail.com> wrote: > >> >> Hi Eleanor >> >> On Sat, 22 May 2021 at 14:55, Eleanor Dodson < >> 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: >> >>> And several strong rotations >>> 180 0 90. - ie a 4 fold round the c axis? >>> 0 0 60 - ie a 6 fold round the c axis? >>> >> >> How can you tell that from the meagre information provided by MOLREP? An >> NCS point group doesn't have to be a crystallographic one: it could be >> 5-fold, 7-fold, 19-fold or indeed anything-fold and we're not given the >> relevant sections to make a decision on that. MOLREP has an option to >> choose a different angle for the 60 deg. section, but to sample the chi >> angle at 5 deg. intervals would require running 32 jobs! It's much easier >> to run POLARRFN once and get all the sections in one job. >> >> Also NCS doesn't even have to form a closed group, i.e. assuming there >> are 2 subunits they don't have to be related by a 180 deg rotation (or 90 >> deg for 4 subunits, or 60 deg for 6). It could be any angle of rotation >> relating 2 (or more) subunits. >> >> Then numerous two folds in the a b plane. >>> >> >> Isn't that just noise because MOLREP has used a contour level that's much >> too low? If you raise the contour levels that noise will disappear, and >> maybe the c axis rotations as well (though I doubt that: the c axis peaks >> look quite strong). I couldn't see how to change the contour levels in >> MOLREP: again POLARRFN allows you to do that. >> >> Cheers >> >> -- Ian >> >> ######################################################################## 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/