I am just beginning to learn and explore display of crystal structures in Jmol.
For now, I am just looking at elements and their basic crystal lattices. I have started with excellent Jmol Crystal Symmetry Explorer (http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse/explore.htm) [Thank you Bob!] I looked at cif file of gold: data_global _chemical_name 'Diamond' _chemical_formula_sum 'Au' _cell_length_a 4.0786 _cell_length_b 4.0786 _cell_length_c 4.0786 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 67.85 _symmetry_space_group_name_H-M 'f m -3 m' loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z Au 0.00000 0.00000 0.00000 My questions: Where is the connectivity information in that file? The Jmol shows the nice tetrahedron "subunits" {1,1,1} with "bonds" between atoms. Is that based on proximity of these atoms? [please excuse my imprecise terminology, but I just started learning the subject] Could I manually generate a cif file for, let's say, manganese by doing the following: data_global _chemical_name 'Manganese' _chemical_formula_sum 'Mn' _cell_length_a 8.9125 _cell_length_b 8.9125 _cell_length_c 8.9125 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 707.94 _symmetry_space_group_name_H-M 'I -4 3 m' loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z Au 0.00000 0.00000 0.00000 In other words, can I generate correct displays for any element if I just know the cell parameters (a, b, c, alpha, beta, gamma) and the space group? Thank you for your help PM ------------------------------------------------------------------------------ Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
