Re: [Jmol-users] bug or not a bug -- select within()

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

I am completely swamped with other responsibilities ... I apologize.

Bob wrote:

> So, for example, when you say =22atomno=3D3=22, if there
> are 25 models, 25 atoms will be selected.

Correct.

> And then, after that, when you say,
> =22within(3.0, atomno=3D3)=22, then that original set is expanded based=

proximity. That proximity calculation COULD be checking only pairs of
atoms in the same model, but it isn't.

If this description of the behavior is correct, then I think that it is a=

bug.

> Personally, I think it should
> at least be an option.

I don't think it is an option, I think it is a bug.

> All the other =22within=22 options (group, chain,
> model, molecule, etc.) all work only within the same model
> because those constructs are within a model.
>
> The more I think about it, the more I think the default should be =22an=
d
within the same model.=22 The current situation is just too weird.

I agree.


Nico wrote:
>
> The implementation is probably really very simple, with one line
> modification.
> In Eval.withinDistance(), replacing:
> AtomIterator iterWithin =3D frame.getWithinAnyModelIterator(atom, dista=
nce);
> by
> AtomIterator iterWithin =3D frame.getWithinModelIterator(atom, distance=
);

In my opinion, this is the correct solution and the correct behavior.


Miguel