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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.
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7 comments:

  1. FelixMarch 31, 2011 at 6:40 AM

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

    ReplyDelete
  2. Jan JensenMarch 31, 2011 at 10:18 AM

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

    ReplyDelete
  3. AnonymousApril 17, 2011 at 9:06 AM

    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

    ReplyDelete
  4. Jan JensenApril 17, 2011 at 11:39 AM

    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.

    ReplyDelete
  5. AnonymousApril 18, 2011 at 1:27 AM

    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

    ReplyDelete
  6. AnonymousOctober 3, 2012 at 9:56 AM

    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 ...

    ReplyDelete
  7. Jan JensenOctober 3, 2012 at 10:25 AM

    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).

    ReplyDelete