XYZ

Codename: xyz

Contents

• XYZ format
• Import options
• Export options

XYZ format

Marvin imports and exports XYZ molecule files that have the following format:

[	# optional comment line	]	not written but allowed at import
[	N	]	always written, but can be omitted in imported files
[	name\tE	]	always written, but can be omitted in imported files
	atom1 x y z
	atom2 x y z
	...
	atomN x y z

where N is the number of atoms and E is the energy (optional). If energy is set for the molecule, then it is separated from the molecule name with a TAB ("\t") character.

Restrictions of the XYZ format:

• 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. In Marvin, implicit hydrogens are automatically converted to explicit H atoms at XYZ export.
• Charges are not stored.
• Query properties and other extra features are not stored.

Import options

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

Import options can be specified in the applet 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 XYZ 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.

Export options

See also the basic export options.

WARNING: Do not export 2D drawings in XYZ! XYZ export in Marvin is only meaningful for 3D molecules with realistic atomic distances.