In the discussion of a previous blog post Geoff Hutchison and Marcus Hanwell made me aware of a really cool building feature in Avogadro: building by naming. I demonstrate this feature on the screencast above. All the hours spend learning organic nomenclature is finally coming in useful!
Notice that, just like in MolGrabber, you get 2D coordinates, so it is important to energy minimize the structure.
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Computational Chemistry Highlights: some numbers
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Excerpt from an email I sent out to the CCH editors:
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5 comments:
I just looked through the menu of Avogadro. it's amazing what kind of things they have ...
It really is. Sometimes I catch myself taking Avogadro for granted, but I really wouldn't want to be without it.
Dear Dr Jensen
One of my friends is wondering whether
Avogadro has a feature of symmetry-preserving atom manipulation. Is it available in the current version?
He is studying transition metal compounds with large organic ligands
with high symmetry.
...ty
Do you mean identifying symmetry unique atoms for an input file?
If so, there isn't a feature like that in Avogadro, but MacMolPlt has such an option (Molecule > Determine point group).
I have no direct experience with this option though.
Dear Dr Jensen
Thanks for your reply.
I was interested in whether
Avogadro can move
all the symmetry-equivalent atoms
automatically when one of them
is moved manually by the user
(given that the symmetry is
specified as input by the user).
I hope it will be supported in
future versions of Avogadro.
(I will check the homepage
of Avogadro if it is in a wish list.)
best regards...ty
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