Sunday, March 20, 2011

Building molecules: What's in a name?

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.


Felix said...

I just looked through the menu of Avogadro. it's amazing what kind of things they have ...

Jan Jensen said...

It really is. Sometimes I catch myself taking Avogadro for granted, but I really wouldn't want to be without it.

Anonymous said...

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.


Jan Jensen said...

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.

Anonymous said...

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

Anonymous said...

Hi Dr Jensen

Could you remind us how to set the labels of atoms so that the cartesian coordinates are re-numbered? Eg, consider ethanol, how do I have the oxygen as atom number 1 rather than one of the other atoms?

I seem to remember that you did this when you were manipulating some water molecules but I can't find the post.

Thanks ...

Jan Jensen said...

I don't think I have a post where I renumber atoms. If I have, I've forgotten where it is. I do have posts where I show the atom numbers (display settings -> labels).