Re: [Jmol-users] vibration AND charges in xyz format

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

Yves wrote:

> I try to use ionic radii AND vibrations in an xyz file, but it doesn t
> seem to work:

Yves,

The .xyz formats that are accepted are:

<elementSymbol> <x> <y> <z>
<elementSymbol> <x> <y> <z> <formalCharge>
<elementSymbol> <x> <y> <z> <x-vector> <y-vector> <z-vector>
<elementSymbol> <x> <y> <z> <formalCharge> <x-vector> <y-vector> <z-vecto=
r>

> In a previous message
> (http://sourceforge.net/mailarchive/message.php?msg_id=3D10608399),
> I have found that the charge must be in column 4 or 7 (with or without
> vibs).

I made a mistake in this message.

The formalCharge (if present) must come immediately after the atom
coordinates.

NOTE: If it is the case that this conflicts with the behavior of other
packages then please let me know and we can correct it.

>  Is the atom Symbol column 0? or is it in fact column 5 or 8?

Element symbol is always column 0

> Should all the atoms have a charge column? (I tried both)

No.
Each atom line is considered independently.
If an atom does not have a formal charge then it will be considered
uncharged (charge of 0)

Note that Jmol maintains a table of which formal charges are acceptable
for which elements. Atoms that have 'invalid' charges will be given a
charge of 0.

> Is there a way to unconnect atoms? For example in the same way as
> polyhedra
> (something like =22select silicon; nobond magnesium=22 or =22select oxy=
gen;
> nobond (2.1)=22 or =22select atmono=3D46; nobond atomno=3D23;=22)

One can disable all 'autobond' behavior by saying

  set autobond off

prior to loading a data file.

By default Jmol will run 'autobonding' if there is no bond information in=

the underlying file format. Pdb and mmcif files have special rules becaus=
e
the file format calls for specification of only 'unusual' bonds.

There is currently no way to add or remove specific bonds.

One can, however, turn off the display of specific bonds.

  set bondmode and;
  select atomno=3D46 OR atomno=3D23;
  wireframe off;



Miguel