Gaussian Cube

Codename: cube

Contents

• Cube format
• Import options
• Restrictions
• Limitation
• Basic export options

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

• Bonds are not stored.
• As a consequence, all the hydrogens must be explicit, otherwise the bond types can not be guessed reliably by the importing program.
• Charges are not stored.
• Query properties and other extra features are not stored.
• Volumetric data is skipped if import option 'M' is specified:
  • if volumetric data is read at import then data is stored and saved upon export but it is not processed by Marvin
  • if volumetric data is ignored at import then the corresponding fields are filled with defaults (a single voxel with zero volumetric value).

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

Limitation

• Volumetric data is not processed by Marvin but read in at import and written out at export. However, MarvinSpace uses the volumetric data. If the import option 'M' is specified then the volumetric data is skipped at import and filled with defaults (a single voxel with zero volumetric value) at export.