Avogadro trunk now supports custom labels, colors, and radii for individual atoms

Avogadro from my trunk now supports custom labels, colors, and radii for individual atoms. To change these parameters, switch to select tool and right-click on atom.
You need trunk of OpenBabel for writing these new parameters to CML and reading of them

Known issues: 1) color of atom changes to default when you rotate molecule in Quick Render mode, and if you set transparency (color map behavior should be changed to prevent massive code duplication)
2) I don’t like how menu looks like (maybe “Reset all” is better?)


19.05.10, 18:53, “Shlomo Katz” shlomokatz00@gmail.com:

Which version of Python do you recommend, re Avogadro: Python 2.6.5 and Python 3.1.2?

Python 3 differ significantly, it’s not supported by Avogadro and not widely used in other projects
Stay with python 2

Is there a specific focus relating to learning Python programming and Avogadro plugins?


I’ve listed links in order you’ll need to read them while you’re moving forward. Also, you may want to take a look on other pages from


On Sun, 23 May 2010 10:11:06 -0400
Shlomo Katz shlomokatz00@gmail.com wrote:

Hi Konstantin,

Finally have some time to get back to this!!

I’ve installed the recommended dependencies, using the LinuxMint
package manager. Do I still make clean and cmake as you have
recommended, or forget those commands since I used the mint package

Jumping ahead a bit…


I’ve opened terminal and typed,

import Avogadro

class Engine():

def renderOpaque(self, pd):
pd.painter.drawText(50, 50, “Hello World”)

Is the terminal the place to try these commands, where is the output
(please excuse my ignorance at this stage!)

You’d better ask such thing on mailing list. Maybe Tim can help you
much better than me…

To check if terminal works properly, type help(Avogadro)