Re: [ccp4bb] Expanding p4212 coordinates to p1

[Bart Hazes]

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 > >