Code name: xyz
Marvin imports and exports XYZ molecule files that have the following format:
Restrictions of the XYZ format:
[ # optional comment line ] not written but allowed at import [ N ] always written, but can be omitted in imported files [ molecule name ] always written, but can be omitted in imported files atom1 x y z atom2 x y z ... atomN x y z
Import options can be specified in the applet by writing "{options}" after the filename.
WARNING: Do not export 2D drawings in XYZ! XYZ export in Marvin is only meaningful for imported 3D molecules with realistic atomic distances.
{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 XYZ files do not contain bond information, these "guesses" can be different from the actual bond orders, especially in case ofThe user should check the calculated bonds after import.
- radicals - missing Hydrogen atoms - complexes