Gaussian Cube

Codename: cube

Contents:

Cube format:

Marvin imports and exports Gaussian Cube molecule files that have the following format:
comment line          (always written, ignored at import)
comment line          (always written, ignored at import)
N vx vy vz          number of atoms,
         followed by the position of the origin
         of the volumetric data (the latter is not read in case of import option 'M',
in which case it is set to 0 0 0 at export)
M1 vx1 vy1 vz1          number of voxels along the first axis,
         followed by the first axis vector
(if volumetric data is ignored at import then this is set to 1 1 0 0 at export)
M2 vx2 vy2 vz2          number of voxels along the second axis,
         followed by the second axis vector
(if volumetric data is ignored at import then this is set to 1 0 1 0 at export))
M3 vx3 vy3 vz3          number of voxels along the third axis,
         followed by the third axis vector
(if volumetric data is ignored at import then this is set to 1 0 0 1 at export))
atom1 x y z
atom2 x y z
...
atomN x y z
volumetric data lines          (if volumetric data is ignored at import then this is set to a single 0 at export)

Gaussian Cube format import/export in Marvin:

Import options can be specified by writing "{options}" after the filename.
f...      Bond length cut-off. Two atoms can be connected if they are closer than the sum of their covalent radii times the cut-off value. Default: "{f1.12}"
Z#      Set maximum number of connections for element Z.
Example: "{f1.4,C4,H1}". This setting increases the cut-off value, but does not let Carbons to have more than 4 connections, and Hydrogens to have more than 1 connection.
b      Try to guess bond types, atom charges and implicit hydrogens from atom distances and valence rules.
Warning: This is an experimental feature. Since Gaussian Cube files do not contain bond information, these "guesses" can be different from the actual bond orders, especially in case of
-  radicals
-  missing Hydrogen atoms
-  complexes
The user should check the calculated bonds after import.
M      Read only molecule, skip volumetric data.
Warning: This data is not processed by Marvin but only written upon export. MarvinSpace uses the volumetric data.

See also the basic export options.

Restrictions:

The default behavior is to use the "any" bond type for all bonds, 0 charge for each atom, no implicit hydrogens.

Limitation: