[Jmol-users] Tech note: extended XYZ file support in Jmol

[Miguel <mi...@jm...>]

> In other words, is there a standard specification for
> vibrations similar to the standardised formats PDB,
> MOL, XYZ, etc for atoms, coords, bonds, ...

John's question prompted me to write a short tech note regarding support
for XYZ files in Jmol v10.

Jmol supports extended XYZ files which may contain formal charges and/or
force vectors.

XYZ files also can contain multiple models. So one could have multiple
vibrational frequencies stored in an XYZ file with vectors for each
frequency.

XYZ files have a name line, followed by an atom count line, followed by
atom records.

The atom records contain an element symbol followed by decimal/numeric
fields. Fields are separate by one or more spaces/tabs.

The first three numeric fields represent the cartesian coordinates in
angstroms.

  {elementSymbol} x.coord y.coord z.coord

If there is one additional field (symbol + 4 numeric fields), it is
assumed to be a formal charge.

  {elementSymbol} x.coord y.coord z.coord f.charge

If there are three additional fields, (symbol + 6 numeric fields) then the
three additional fields are assumed to be vectors

  {elementSymbol} x.coord y.coord z.coord x.vect y.vect z.vect

If there are four additional fields (symbol + 7 numeric fields) then the 4
additional fields are assumed to be a formal charge followed by the vector
values

  {elementSymbol} x.coord y.coord z.coord f.charge x.vect y.vect z.vect



Miguel