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.
Best,
Taka
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 https://discuss.avogadro.cc/)
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.
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At the moment, the Align tool is not in Avo2. If you could post an issue to https://github.com/openchemistry/avogadrolibs/issues 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?
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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.
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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.
Thanks!
-Geoff
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