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
Claudiu B. Bucur - Piersica | LinkedInOn 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 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first <http://sprint.com/first> <http://sprint.com/first> -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net <mailto:Avogadro-Discuss@lists.sourceforge.net> <mailto:Avogadro-Discuss@lists.sourceforge.net <mailto:Avogadro-Discuss@lists.sourceforge.net>> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net <mailto:Avogadro-Discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: phil@pricom.com.au <mailto:phil@pricom.com.au>
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Philip Rhoades
GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au