How to draw molecules on a plane

Claudiu,

On 2010-08-02 02:12, Claudiu Bucur wrote:

the align function has an “everything” and “molecule” setting.
i just played around with 2 short molecules to check if it works and it
allows me to orient both molecules to the axes i need based on the 1->2
center->end atoms i select.

I think the 1->2 > center->end atoms idea needs to be extended to:

(1->2->3) * n => n molecules aligned on a line (1->2) and plane (1->2->3)

if you are dealing with several molecule which you are trying
to align to a plane, ( so on 2 axes instead of 1) then i suggest you use
packmol:
http://www.ime.unicamp.br/~martinez/packmol/quickguide/index.html along
with avogadro.

Looks interesting but I think it is too non-graphical for what I want to
do - which (at the moment) is to just align a number of molecules side
by side for structural comparison.

i was able to get really fancy figures with films/hydrated, ions in
solution, etc fixed to Si or Ge, etc surfaces. For large files i had
better luck with .xyz files instead of .pdb

Thanks - I will have a look at this later as I get more familiar with
Avogadro.

Regards,

Phil.

hope this helps

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562
www.claudiubucur.com http://www.claudiubucur.com
http://www.linkedin.com/in/claudiubucur

On Sat, Jul 31, 2010 at 9:12 PM, Philip Rhoades <phil@pricom.com.au
mailto:phil@pricom.com.au> wrote:

Claudiu,

How did you use the align tool to do that? - it seems that it can
only align one molecule at a time to a particular axis.  It seems
quite difficult to me to align more than one molecule to a plane.

Thanks,

Phil.



On 2010-07-30 01:26, Claudiu Bucur wrote:

    thank you,
    i was able to allign my polymer chains to a plane and then use
    gimp to
    "mount" that layer on top of a "substrate" layer and get an
    image of an
    "adsorbed" film.

    Claudiu Bucur, PhD
    USDA-NCAUR
    850-566-1562
    www.claudiubucur.com <http://www.claudiubucur.com>
    <http://www.claudiubucur.com>

    http://www.linkedin.com/in/claudiubucur


    On Mon, Jun 28, 2010 at 3:01 PM, Geoffrey Hutchison
    <geoff.hutchison@gmail.com <mailto:geoff@geoffhutchison.net>
    <mailto:geoff.hutchison@gmail.com
    <mailto:geoff.hutchison@gmail.com>>> wrote:

     > is it possible to draw a plane and mount molecule on it, to
        simulate the deposition of a film on a substrate?

        No, not really. The first part of that "draw a plane" is the
        sticking point. It *is* possible to align molecules in
    particular
        planes and/or simulate depositing molecules on a substrate.

        To align a molecule, use the Align tool:
    http://avogadro.openmolecules.net/wiki/Align_Tool

        Hope that helps,
        -Geoff



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E-mail: phil@pricom.com.au <mailto:phil@pricom.com.au>


Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au