----- Original Message ----- From: "E.L. Willighagen (Egon)" <[EMAIL PROTECTED]> Date: Wednesday, October 29, 2003 1:15 pm
> > > Phillip Barak of the University of Wisconsin USA recently sent me > > > a link > > > that shows some excellent web pages with inorganic molecules. You > > > shouldtake a look at them: > > > http://www.soils.wisc.edu/virtual_museum/ > > > > Just to jump in here about our use of pdb files for the minerals > on our > > site: > > > > Using pdb was not our first choice. We would have prefered CIF > format,> files with the barest minimum of spatial information, > since symmetry > > operators allow 'tiling' out in any direction per user > parameters, but that > > was not to be with Chime. > > 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 P 0.0000 0.9931 0.0019 O 0.0000 0.9764 0.8649 O 0.0000 0.7618 0.0558 O 0.1823 0.1139 0.0436 Mg 0.0000 0.3766 0.3741 O 0.0000 0.6829 0.2878 H 0.0000 0.7192 0.2017 H 0.0000 0.8174 0.3299 O 0.0000 0.0768 0.4664 H 0.1157 0.0070 0.4999 O 0.2115 0.4852 0.4874 H 0.1989 0.2007 0.1824 H 0.3169 0.1702 0.3020 O 0.2179 0.2618 0.2643 H 0.3200 0.3904 0.5120 H 0.2511 0.6354 0.5027 N 0.0000 0.3657 0.7351 H 0.0000 0.2186 0.7832 H 0.0000 0.3311 0.6473 H 0.1148 0.4557 0.7535 Full description of file format at http://www.iucr.ac.uk/iucr-top/cif/ . 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 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 SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
