How to create 2D output from Avogadro

This might be a stupid questions, but I haven’t found an answer so far:

I created e.g. an ethanol molecule, how can I get an output like this:


or this?:

I’m asking because I found here
http://avogadro.openmolecules.net/wiki/Avogadro_0.9.4
the statmenent: “2D cleanup code improvements for 2D molecule files.”

I’m interested in this feature because I have to draw a lot molecules like


and Avogadro is the only program I know that provides a calculation of the correct bond length and
coordination (vie the menu Extensions->Optimize geometry).
In the Wikipedia I often find there both versions, 3D and 2D:

So I gues that the 2D version is made out out of the 3D version - and that is exactly what I need.

thanks and regards
Uwe

I created e.g. an ethanol molecule, how can I get an output like this:
http://en.wikipedia.org/wiki/File:Ethanol-2D-skeletal.svg
or this?:
http://en.wikipedia.org/wiki/File:Ethanol_flat_structure.png

Avogadro doesn’t do that short of “Chemical 2D” drawing.

the statmenent: “2D cleanup code improvements for 2D molecule files.”

This is for importing 2D chemical files into Avogadro (and creating a
rough 3D structure).

In the Wikipedia I often find there both versions, 3D and 2D:
http://en.wikipedia.org/wiki/Tetraethyl_orthosilicate
So I gues that the 2D version is made out out of the 3D version -
and that is exactly what I need.

Actually, it’s probably the reverse – many people create the 2D
version, import into a program like Avogadro, optimize the geometry,
and then output the 3D graphic.

If you’d like suggestions on 2D drawing programs:

  • BKChem
  • SketchEl
  • MolSketch

On the proprietary side:

  • ChemSketch
  • ChemDraw

We can import 2D files from any of these programs.
-Geoff

Geoffrey Hutchison schrieb:

Actually, it’s probably the reverse – many people create the 2D
version, import into a program like Avogadro, optimize the geometry, and
then output the 3D graphic.

The problem is that non of the 2D drawing programs is able to check that the bonds have the right
length and angle. So it is often a long fiddling to get the molecules drawn as wanted and even then
the drawing is often physical incorrect. Avogadro is the only program I know that is able to
calculate the force fields to have correct bonds.

So in my opinion it would be a nice feature when one could create a molecule in Avogadro with the
calculated correct bonds and Avogadro is able to draw/export an adequate 2D image from this.

thanks for your help and regards
Uwe

On May 30, 2009, at 10:06 AM, Uwe Stöhr wrote:

The problem is that non of the 2D drawing programs is able to check
that the bonds have the right length and angle. So it is often a
long fiddling to get the molecules drawn as wanted and even then the
drawing is often physical incorrect. Avogadro is the only program I
know that is able to calculate the force fields to have correct bonds.

Well, 2D diagrams are stylized, but I’m sad to hear that none of the
open 2D programs have a “clean-up” feature. The proprietary ones do.

Do you already have SMILES for the compounds? If so, you could
probably use BKChem or another code to do 2D structure generation.

So in my opinion it would be a nice feature when one could create a
molecule in Avogadro with the calculated correct bonds and Avogadro
is able to draw/export an adequate 2D image from this.

It’s something we’ve considered, but so far no one has stepped forward
to do it.

Cheers,
-Geoff

Hi,

just found the following: http://bkchem.zirael.org/oasa_en.html
This seems to have some of the features requested …

Bye

Simon

Am Samstag, den 30.05.2009, 10:16 -0400 schrieb Geoffrey Hutchison:

On May 30, 2009, at 10:06 AM, Uwe Stöhr wrote:

The problem is that non of the 2D drawing programs is able to check
that the bonds have the right length and angle. So it is often a
long fiddling to get the molecules drawn as wanted and even then the
drawing is often physical incorrect. Avogadro is the only program I
know that is able to calculate the force fields to have correct bonds.

Well, 2D diagrams are stylized, but I’m sad to hear that none of the
open 2D programs have a “clean-up” feature. The proprietary ones do.

Do you already have SMILES for the compounds? If so, you could
probably use BKChem or another code to do 2D structure generation.

So in my opinion it would be a nice feature when one could create a
molecule in Avogadro with the calculated correct bonds and Avogadro
is able to draw/export an adequate 2D image from this.

It’s something we’ve considered, but so far no one has stepped forward
to do it.

Cheers,
-Geoff

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Geoffrey Hutchison schrieb:

Well, 2D diagrams are stylized, but I’m sad to hear that none of the
open 2D programs have a “clean-up” feature. The proprietary ones do.

OK, I’m checking out now the freeware version of ChemSketch.

Do you already have SMILES for the compounds?

Unfortunately not.

thanks for your help and regards
Uwe