At the moment there's not a solution to that problem that I'm aware of.
The constraints imposed by the alignment to the pattern end up confusing
the rest of the coordinate generation code.


-greg


On Fri, Sep 15, 2017 at 4:08 PM, Michał Nowotka <mmm...@gmail.com> wrote:

> Hi,
>
> Thanks for all the help with 'forcing' molecule highlighing. I have a
> different (hopefully the last) problem now.
> When I align a structure to the pattern and highlight it I'm getting
> the attached result. The substructure is correctly aligned and
> highlighted but the other part intersects with it.
>
> Can that be avoided?
>
> Michał
>
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