XYZ Plugin, Version 1.3
This plugin reads and writes XYZ files, a minimalistic plain text format for storing molecular coordinates. The format basically follows the format, that was read and written by the old XMol program, but also tries to be as compatible as possible to other variations of the XYZ format.
A brief summary of the format, as read by VMD follows:
XYZ molecule file format: XYZ files are a simple molecule file format suitable for output by homegrown software since they are very minimalistic. They don't even include bonding information. [ # optional comment line ] comment line (can be blank) ^^^ NOTE: comment lines aren't supported by the current version of this plugin. [ N ] # of atoms, required by this xyz reader plugin [ molecule name ] name of molecule (can be blank) atom1 x y z [optional data] atom name followed by xyz coords atom2 x y z [ ... ] and and (optionally) other data. ... instead of atom name the atom number in atomN x y z [ ... ] the PTE can be given. Note that this plugin currently ignores everything following the z coordinate (the optional data fields).
XYZ files can contain multiple timesteps. All timesteps, however have to have the same number of atoms (VMD does not support this currently anyways). Also the elements have to always be in the same order, only the first timestep will be used to read the element names. From all successive timesteps only the coordinates will be read.
This plugin only reads the label and coordinates for each atom. Any additional data recorded for an atom is ignored.
VMD requires that the first non-comment line of the file contain the number of atoms.
Atoms in an XYZ file can be labeled with either the atom name or ordinal number.
The plugin assigns masses to the atoms according to the natural isotope distribution of the elements (see e.g. http://www.webelements.com/). If an element name could not been recognized, a mass of 0 is assigned. To set the mass for those elements or assign a different mass for the other atoms, you have to use to create a selection with atomselect and then use the selection subcommands to set the mass.
XYZ file as they are produced by the Tinker package are not compatible to this plugin. Also some other XYZ format versions, that are missing the atom count or the title line will not work. You have to either convert them to a different format, that is understood by VMD or add the missing information.