Menu
▾
▴
Re: [Avogadro-Discuss] how to draw molecules on a plane
|
From: Philip R. <ph...@pr...> - 2010-08-01 21:32:31
|
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 <ph...@pr... > <mailto:ph...@pr...>> 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 > <ge...@ge... <mailto:ge...@ge...> > <mailto:ge...@ge... > <mailto:ge...@ge...>>> 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 > Avo...@li... > <mailto:Avo...@li...> > <mailto:Avo...@li... > <mailto:Avo...@li...>> > > 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 > Avo...@li... > <mailto:Avo...@li...> > https://lists.sourceforge.net/lists/listinfo/avogadro-discuss > > > -- > Philip Rhoades > > GPO Box 3411 > Sydney NSW 2001 > Australia > E-mail: ph...@pr... <mailto:ph...@pr...> > > -- Philip Rhoades GPO Box 3411 Sydney NSW 2001 Australia E-mail: ph...@pr... |