Hi Graeme (I may well have mentioned this when we shared an office) et al I’ll add something from my small-molecule crystallography days, when we used point detectors - so this would be pre-1996 which was the last time I used one of these machines.
I don’t remember which structure it was (feel free to go through the CSD to check on my behalf, but many structures were not deposited in those days and languish in a PhD thesis!); I had a dataset with three 90º angles, but the processing statistics (and overall cell volume) indicated quite plainly that it was monoclinic (probably P21). I re-refined the unit cell as if it were triclinic and the “best” 90 degree angle with the smallest ESD was the one that corresponded to the monoclinic beta; the two 90º angles refined away from their true value more. A result of that experiment was that (since then) I never assumed that the values of the angles from the data processing showed unambiguously that I had a high symmetry solution. I believe that Pointless arose after a hexagonal/C-centred orthorhombic ambiguity arose (but my memory could be faulty here). Best wishes Harry > On 23 Feb 2024, at 09:58, Winter, Graeme (DLSLtd,RAL,LSCI) > <00006a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Huw > > (first: thank to Phil for picking this up; it caused much confusion) > > While I get where you are coming from, it is still from a mathematical > standpoint correct to consider e.g. a tetragonal crystal as monoclinic - P21 > is a subgroup of P43212 (say) so strictly it is possible and correct - if > experimentally unlikely - to have the situation we are discussing here occur. > > Also, under merging data to investigate twinning is a current bb topic. > > Telling users to “fiddle the parameters” so that the strict test is satisfied > feels like a non-ideal answer: a warning when importing such data could be > legitimate e.g. “hmm I note a = b and al=be=ga=90 _exactly_ this is unusual, > I hope you know what you are doing” rather than a flat out error. > > Literally I got involved as I had a dials user ask me how to do this > parameter fiddling in a more niche case and I thought that was a suboptimal > solution to an artificial problem :-) > > On a personal note, I think it is important that the tools we develop still > allow people to explore problems rather than railroading them down one true > route which is the only allowed way to look at a problem: we learn a lot by > exploring odd corners as here. > > Best wishes Graeme > >> On 23 Feb 2024, at 09:49, Huw Jenkins <h.t.jenk...@me.com> wrote: >> >> [You don't often get email from h.t.jenk...@me.com. Learn why this is >> important at https://aka.ms/LearnAboutSenderIdentification ] >> >> Hi Graeme, >> >>> On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) >>> <00006a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: >>> >>> Processing a data set in lower than necessary symmetry e.g. tetragonal as >>> monoclinic you _cannot_ import the merged MTZ file into i2 because it is >>> impossible to have 90 degree angles for P21 >> >> I had a look at the code in CCP4i2 that generates the errors in the >> screenshots you posted. The first one is only generated if two cell >> parameters are *exactly* equal and the second is generated when beta is >> between 89.9999 and 90.0001 degrees. >> >> I think these tests should only fail if the data were processed assuming >> higher symmetry so that unit cell parameters were restrained and then the >> space group changed to a lower symmetry one. Isn't the correct approach when >> the true symmetry is lower than originally assumed to repeat the data >> processing without applying constraints imposed by the higher symmetry - >> because, for example, cell parameters refined assuming cell length/angle >> constraints may not predict the reflection positions as well as if these >> restraints were not applied, reflections assumed to be symmetry equivalent >> when they weren't may lead to suboptimal scaling etc etc? >> >> >> Huw > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not use, > copy, retain, distribute or disclose the information in or attached to the > e-mail. > Any opinions expressed within this e-mail are those of the individual and not > necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England and > Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > ######################################################################## > > 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 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/
