> /usr/local/avogadro/fragments. This is where I need the root password
> (Linux). Then, I can open my substrate file in Avogadro, and insert
> my molecule as a fragment.
You don't need to do this. There are copy/paste commands. Open up the molecule.
Choose "Edit->Copy". Open up the surface. Choose "Edit->Paste"
Done. In version 1.1, there's also a surface builder. Open up any CIF file,
including "File->Import->Crystal" (which has ~500 common crystal structures).
Then "Crystallography->Build->Slab" to generate the surface you want. The
surface will be placed in the xy plane, so one can easily align a molecule. The
next release will also include a manual translate/rotation option.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/
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