[Jmol-developers] no bonds between models

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

Rene wrote:
> On an aside I wonder whether it is possible to create an input file
> that has bonds between atoms that are part of different models. I don't=

> see a reason to do that, but I also think it should not be possible...

It is not possible to create bonds between atoms that are in different
models.

Each model is supposed to be in its own world.

The auto-bonding code will not allow it.

If, by some accident, a bond were created between atoms in two different
models then I am sure that some things would break.

In PDB files the atoms are identified by numbers. In some (all?) pdb file=
s
the atom numbering does not restart when a new model begins. Bonds can be=

declared in PDB files using CONECT records. CONECT records refer to atom
numbers. Therefore, it is possible to have a CONECT record that created a=

bond that spanned two different models. This would be a *BAD* thing. If
(at some point in the future) it happens then we should modify the
PdbReader (or the frame building code) to prevent it from happening. I di=
d
not try it.

Miguel