Re: [Jmol-users] Default settings

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

Anthony wrote:

> I have been using JMol to display xyz files, and I have found that
> deuterium (element =22D=22) is set to have a much larger covalent radiu=
s
> than H.

Hmmm ... but there is no special support for deuterium ... so it must be
being treated as =22unknown=22

Q: Are they very large and colored 'hot pink' ?

If you say 'label %a' I suspect that these will be tagged as element 'Xx'=
.

> Presumably I could correct this using a script, but I would
> rather correct the default value.

In this case, we need to figure out what the correct treatment should be.=


> However there doesn't seem to be any
> accessible table of default values, or any way to change them from the
> JMol program.

You are correct. The table is compiled into Jmol.

> Have I missed something? I would like to see the default
> values (radii, colours and any other property) tabulated in an ASCII
> text file that is read in by the program. Then the default values
> could be changed easily without any need to incorporate code for doing
> it into JMol.

Others have asked for the same thing. It is a good feature to implement
after the official v10 release.

In the meantime, tell me some more about 'deuterium'.

Q: Is 'D' the accepted element symbol.

Q: What other elements have common 'alternate elements' for isotopes?

Implementing support for isotopes like this may not be straightforward.


Miguel