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 <[email protected]> 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 <[email protected]> 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 <[email protected]> > > 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 > > > > >
