On 2nd thoughts I guess you could do it in a space group that's a supergroup of the plane group say with all l and all z = 0. Then you could use symm x,y,z and it would just ignore the z components (I think?).
I. On 12 April 2012 12:11, Ian Tickle <ianj...@gmail.com> wrote: > 'echo symm x,y | cad' gives: > > Data line--- symm x,y > > **SYMMETRY OPERATOR ERROR** > > Error in interpreting symop "X,Y" > > I. > > On 12 April 2012 12:03, Eleanor Dodson <eleanor.dod...@york.ac.uk> 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 >>> > >>> > >> >>
