> The result is that multiple rotamers of one residue are displayed in the
> molecule.
> Unfortunately, Jmol starts to make bonds between those rotamer atoms, and
> that's not really what I want. It gets pretty messy that way.
>
> Is there a way to get this fixed? Or a workaround somewhere?

I don't know what a rotamer is but ...

Put them in separate models and they won't bond.

Then use 'model all' to show all the models at the same time.

If you want to select the base model plus the individual 'rotamer-things'
then you will need to say something like:

  restrict model=1,model=2


Miguel



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