Changing atom types

General Discussion
1

Hi,

I imported a graphitic cluster from a .mol file, and cut it down to
the size I want (C_96). Now I want to add hydrogens to cap the edges.
The atom types or bonds were not specified in the input, so when I
select add hydrogens I get two hydrogens on each edge carbon instead
of one. One hydrogen, of course, is the appropriate choice. What is
the easiest way to handle this? I would like to be able to tell
Avogadro that I have all sp2 carbons. Is this possible?

Thanks,
Gary

2

of one. One hydrogen, of course, is the appropriate choice. What is
the easiest way to handle this? I would like to be able to tell
Avogadro that I have all sp2 carbons. Is this possible?

You can manually edit atom types in the View->Properties->Atom Properties window. But with 96 atoms, that’s tedious.

My suggestion would be to save the current structure as an XYZ format file (e.g., C96.xyz) and then re-read it. This will force bond re-perception.

Hope that helps,
-Geoff