Yes I was also confused by the fact that P4212 is obviously a space group (upper case 'P') whereas p4 and p1 are plane groups (lower case 'p'), as stated. Not sure what 'p2121' is though, I assumed it was somehow related to the p2gg plane group (no 8). Also there's no plane group 'p6212', but then there's no space group 'P6212' either.
Perhaps the original poster could clarify and take care with his P's and p's? Cheers -- Ian On 12 April 2012 16:51, Bart Hazes <bha...@ualberta.ca> wrote: > I am confused by the discussion on this message. Although it says plane > group I assume it really is a normal 3D tetragonal space group, P42(1)2 > > So Eleanor's suggestion should work and sftools expand command will do the > job as well. > > Bart > > > On 12-04-12 05:03 AM, Eleanor Dodson wrote: > > Apologies - I didn't notice the plane group.. > Although I think if the sym ops are correctly listed in the P4121 file they > will just be applied as given.. > Eleanor > > On 12 April 2012 11:58, Ian Tickle <ianj...@gmail.com> wrote: >> >> I didn't realise the CCP4 suite could handle the plane groups: where >> are they listed (they're not in symop.lib or syminfo.lib)? Or are >> they doing some clever projections of the space groups? >> >> Cheers >> >> -- Ian >> >> On 12 April 2012 11:48, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: >> > Cad will do this correctly >> > Reflection utilitied - merge mtz ( rather confusing job title - sorry..) >> > mtz in - the P4121.mtz data >> > Output - P41212-ext.mtz >> > >> > Defne mtz output >> > >> > Select define limit for refl;action by Laue code select P1 >> > >> > then you will get a list of all P1 reflections with phases correctly >> > modified. >> > >> > If you really want to work in P1 you will need to change the space group >> > in >> > P41212-ext.mtz >> > Easiest way is >> > mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz >> > SYMM P1 >> > end >> > >> > DONT change the G of P41212.mtz before doing the extension - the program >> > needs the P41212 sym ops to change the phases correctly.. >> > >> > If you want the coordinates extended too >> > use pdbset to get a P1 set of cds.. (Coordinate utilities >> > Edit pdb >> > select pdbset and "generate chains by symmetry operators" >> > eleanor >> > Eleanor >> > >> > >> > >> > >> > >> > On 12 April 2012 06:51, Henning Stahlberg <henning.stahlb...@unibas.ch> >> > wrote: >> >> >> >> Hi Everybody, >> >> >> >> I am working in a P4212 plane group, which is a p4 symmetric structure >> >> with a screw axis in addition. My map has in the unit cell two 4-fold >> >> symmetric structures, one if which is upside-down with respect to the >> >> other >> >> one. If using expand in sftools, then the resulting map is p4 >> >> symmetrized >> >> in the center between two p4-symmetric structures, which is wrong. This >> >> is >> >> probably the phase origin problem referred to here: >> >> http://www.ccp4.ac.uk/dist/html/sftools.html#expand >> >> >> >> Would anybody have a suggestion how I can expand the p4212 MTZ file to >> >> full p1, but with properly respecting the symmetry phase origin? >> >> >> >> My illiterate guess would be to either >> >> 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then >> >> use >> >> sftools with "expand 1" to create the full reflection sets in p1; then >> >> shift >> >> back by (180.0;0.0); or >> >> 2) use sftools with the command "expand 1", and then modify (invert?) >> >> the >> >> phases of the reflections in the quadrants that have wrong phases. >> >> >> >> In option 1) I am not sure if it is possible to shift phase origin, >> >> while >> >> staying in p4212 symmetry. How could I do that? >> >> In option 2) I would probably get into deep water the next time I work >> >> with another symmetry, like p6212, or p2121, where I would have to deal >> >> not >> >> with quadrants but with triangles of 60deg angle? >> >> >> >> Any suggestions would be highly appreciated. >> >> >> >> All the best, >> >> >> >> Henning. >> >> >> >> Henning Stahlberg, PhD >> >> Prof. for Structural Biology, C-CINA, Biozentrum, University Basel >> >> Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland >> >> http://c-cina.org | Tel. +41-61-387 32 62 >> > >> > > >
