#574 Cartesian coordinates are scaled according to the lattice constants in CIF

[Andrius Merkys]

Atom coordinates in CIF files, given in _atom_site_Cartn[xyz] tags, are scaled using the lattice constants, while Cartesian coordinates in CIFs are already given in angstroms (A) and therefore must not be scaled. An example MWE is attached, where "real" distances between adjacent vertices of regular icosahedron are 10 A, but are visualised as 100 A because of 10x10x10 A orthogonal lattice.

[Bob Hanson]

OK. This is fixed, however you will need to change your _geom_bond_distance fields to read the proper distance in Angstroms (10.0 in this case, not 100.0).

_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_ccdc_geom_bond_type
_geom_bond_distance
C01 C02 S 100.0

[Andrius Merkys]

Sure, 100.0 was in place only to demonstrate the issue.

[Bob Hanson]

Note: I am also enabling Jmol to read CIF files as simple as the following, without need for _geom_bond_distance

data_icosahedron
loop_
atom_site_label
_atom_site_Cartn_x
_atom_site_Cartn_y
_atom_site_Cartn_z
C01 0.0000000000 0.0000000000 9.5105651630
C02 8.5065080835 0.0000000000 4.2532540418
C03 2.6286555606 8.0901699437 4.2532540418
C04 -6.8819096024 5.0000000000 4.2532540418
C05 -6.8819096024 -5.0000000000 4.2532540418
C06 2.6286555606 -8.0901699437 4.2532540418
C07 6.8819096024 5.0000000000 -4.2532540418
C08 -2.6286555606 8.0901699437 -4.2532540418
C09 -8.5065080835 0.0000000000 -4.2532540418
C10 -2.6286555606 -8.0901699437 -4.2532540418
C11 6.8819096024 -5.0000000000 -4.2532540418
C12 0.0000000000 0.0000000000 -9.5105651630
loop
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_ccdc_geom_bond_type
C01 C02 S
C01 C03 S
C01 C04 S
C01 C05 S
C01 C06 S
C02 C03 S
C03 C04 S
C04 C05 S
C05 C06 S

[Bob Hanson]

and also without _ccdc_geom_bond_type

[Bob Hanson]

see http://chemapps.stolaf.edu/jmol/zip/jmol-14.4.3_2016.03.03b.zip

[Andrius Merkys]

Many thanks for the fix!