Questions about Avogadro2

Hi all,

This is my first post to here.
I'm a physicist in Japan and having fun with Avogadro a lot!

I have several questions about Avogadro2.
(I afraid that it is suitable here. Should I post to devel? )
Today, I tried Avogadro2 first time, and had difficulties.

1) I could not find "Align tool". Where is it?
I utilize it very often. So, it is necessary for me.
To tell the truth, I want to align three atoms in a plane.
Do we have such a function in Avogadro2?

2)Can I display surface of molecular orbital in a cube file?
I could open cube file, and I could see "ball and stick".
But, I could not display orbital in it. How can I do it?
I could not find "Create surface" in Extensions menu.

3)Why there is no button for "Optimize geometry"?
I think this function is used frequently, since molecule
created by hand at the beginning has a nonsense geometry.
So, it is better to have a button for it, I think.
At least, it should be top level in menu.
In addition, why is it categorized in "Open Babel"?
To my understand, OB is a collection of converter of format
but is not a semi-empirical MO nor a molecular mechanics.
Hence, current menu design looks strange to me.

Sorry for sudden asking. Thanks.


Welcome! This is definitely a good place to ask questions. The developer list is mostly to coordinate development plans. (We have moved most of the discussions to the discussion forum

Avogadro v2 at the moment is an open beta as a work in progress. Not all features from Avogadro v1 have been ported to the new framework.

  1. At the moment, the Align tool is not in Avo2. If you could post an issue to it would be appreciated. If you can be a bit more specific about the 3-atom alignment that would help - you want to project them to the XY plane or something like that?

  2. If you open a cube file, go to Quantum ⇒ Calculate electronic surfaces to display MOs, electron density, etc. The user interface from this will be re-done this summer by an undergraduate here at the University of Pittsburgh.

  3. Open Babel has long had molecular mechanics (UFF, MMFF94, and GAFF) to support coordinate generation and conformer sampling. It’s the toolkit used by Avogadro v1. I’m currently working on a new force field framework for Avo2 but it won’t be in place for another few weeks. I understand the current menu design is a bit strange - this isn’t the final version.

We appreciate the feedback – it’s very helpful to know what needs improvement. Definitely if there are bugs or missing features, please post issues to the GitHub tracker above and post about them.


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