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