On Mon, 10 Nov 2025 10:20:44 +0000, Dawn Duan <[email protected]> wrote:
>Dear community members, > >I recently received a different opinion regarding whether one sample should be >C121 or I121. > >I am trying to integrate automatic data processing and displaying resutls to >users. In the pipeline, I run pointless to get the best space group solution, >in the end of this message comes the detailed pointless output related to >space group determination that I got for one of the samples. I took the best >solution from pointless, i.e. I121 (Cell: 81.74 67.10 86.75 90.00 > 98.20 90.00). However, I later also extracted the space group and unit >cell result from the phenix.xtriage output and got C121 (Cell: 110.377 67.1 >81.744 90 128.931 90). The space group number indicates space group 5 from >both cases, and according to the International Tables for Crystallography >Volume A: Space-group symmetry Second online edition (2016) [ISBN: >978-0-470-97423-0 (https://it.iucr.org/services/purchase/)[doi: >10.1107/97809553602060000114](http://dx.doi.org/10.1107/97809553602060000114), >space group 5 should be C121. > >Could I receive some wisdom from the community regarding whether one is >correct, and if so, which one, or whether both are correct? Any further >comments/opinion regarding whether I should display both options (I121 and >C121 with their corresponding unit cell parameters) would be helpful. > >Thank you so much in advance! > >Best, >Dawn ( ... pointless output removed ...) Dawn, yes this is confusing. In fact, I121 with (Cell: 81.74 67.10 86.75 90.00 98.20 90.00) and C121 (Cell: 110.377 67.1 81.744 90 128.931 90) describe the same diffraction pattern, so both are correct. You can verify this by feeding the C121 cell and lattice type C into CCP4 othercell The "problem" is described in the pointless documentation (https://www.ccp4.ac.uk/html/pointless.html): "A note on setting conventions In some space-groups there may be a difference between the IUCr “standard” setting and the “reference” setting given in given as the principle setting in International Tables. For chiral space groups, this affects only primitive orthorhombic (P 2x 2x 2x) and centred monoclinic (C2) groups. For primitive orthorhombic space groups the conventional standard setting has a < b < c irrespective of which axes are screws, eg space group 18 may be P 2 21 21 rather than the reference setting P 21 21 2. This convention allows the indexing program (eg Mosflm) to label the axes with a < b < c, without you needing to reindex the data at a later stage when the correct space group becomes clear. For a centred monoclinic cell, the choice for the standard is either C2 (side-centred) or I2 (body-centred), whichever has the smaller beta angle. Pointless offers a choice of using the standard (CELL-BASED) or the reference (SYMMETRY-BASED) settings, see the SETTING command." That the IUCr and the IT don't fully align, is confusing. Personally, I don't agree with the default choice of pointless, which is the standard (CELL-BASED) setting. To me, the shortcomings of the standard (CELL-BASED) setting are worse than those of the reference (SYMMETRY-BASED) setting. You find my argument at https://wiki.uni-konstanz.de/xds/index.php/Pointless - no need to copy it here. I expect that if you run pointless with SYMMETRY-BASED, it will tell you that the data are in C121 (Cell: 110.377 67.1 81.744 90 128.931 90), in agreement with phenix.xtriage. This is also what I think you should use for deposition and publication. HTH, Kay ######################################################################## 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/
