> 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
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