On 4/1/2011 10:18 AM, Robert Hanson wrote:
On Fri, Apr 1, 2011 at 9:10 AM, Pshemak Maslak <[email protected]
<mailto:[email protected]>> wrote:
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?
exactly
That would mean that Jmol has maximum bonding distances stored for all
element combinations. Is that correct?
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
Sure, but use Mn instead of Au in that last line ;)
Duh....that what happens when one does it "manually". :-)
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?
In principal, yes. Always safer to go with explicit operators, but
Jmol should be able to read the space group, especially if you use a
Hall name. The problem is with settings and origin offsets.
I like the brevity of that file format. Is there a good source of cif
files for (crystalline) elements somewhere? This would help to avoid
"manual" mistakes and cases where origins are not at 0,0,0. What do you
mean by "problems with settings"?
Can one "invent" unit cells for "hypothetical" atoms or does the atom
size (stored in Jmol?) and cell dimensions have to be consistent?
Thanks for your help,
PM
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