Hi !I would like to position a molecule on a surface with the mouse. I have managed to do it with Avogadro, but for this I need to be root. I wonder if there is another solution that would not need to be root.Here is the way I do it. I have to transfer first my molecule to /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.Is there an alternative without copying by hand the molecule in the fragment directory ?Best regardsDidier Sebilleau------------------------------------------------- Didier SEBILLEAU, Groupe Théorie, Département Matériaux-Nanosciences, Institut de Physique de Rennes, UMR UR1-CNRS 6251, Campus de Beaulieu, Universite de Rennes1, 35042 Rennes-cedex, Francetel : (33) 2-23-23-69-64 fax : (33) 2-23-23-61-98 e-mail : didier.sebilleau@univ-rennes1.fr website: http://www.ipr.univ-rennes1.fr/EN/MsSpec -------------------------------------------------
/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: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/