From: E.L. W. (Egon) <eg...@sc...> - 2003-10-30 07:17:45
|
On Wednesday 29 October 2003 22:41, PHILLIP W BARAK wrote: > > Jmol v8 has very limited support for PDB files... it reads only > > the atomic > > coordinates and the unit cell parameters, and symmetry operations > > are not yet > > supported... I am not sure what you mean with tiling, but what > > would the CIF > > file that would define the 'tiling' look like? > > A CIF file for struvite would (minimally) look like: > > data_struvite > _chemical_name_systematic > ; magnesium ammonium phosphate hexahydrate > ; > > _cell_length_a 6.955 > _cell_length_b 6.142 > _cell_length_c 11.218 > _cell_angle_alpha 90 > _cell_angle_beta 90 > _cell_angle_gamma 90 > > _symmetry_space_group_name_H-M 'P mn2(1)' > > loop_ > _atom_site_label > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z <snip> Good, all these but the _symmetry_space_group_name are supported... > Anyway, with the designated spacegroup 'P mn2(1)', the symmetry operations > are (a simple case): 1 x,y,z > 2 -x+1/2,-y,z+1/2 > 3 x+1/2,-y,z+1/2 > 4 -x,y,z We currently have no code that can take either the operations or the spacegroup name (in any convention) and convert this to new atoms... It would be good if someone could work this out (a student project?)... It's fairly easy, but it just takes a lot of time to write it... > On the basis of this information, a viewer should be able to designate a > single unit cell or any number of cells to be drawn in the a b c > directions, as specified by the user. This is possible too. Have a look at the crystal properties window in the application. I don't think setting the crystal box dimensions is setable by script commands yet, but that should be easy... Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html |