"Snap" to plane?

[Philip_Rhoades]

People,

Is there a convenient way to insert fragments and “snap” them to a
plane? eg I want to compare relatively “flat” molecules:

cytosine
thymine
uracil

side by side - I can insert the fragments, individually move, size and
rotate the fragments but I have trouble getting them to line up nicely
is there some way of laying them on the same plane?

Suggestions?

Thanks,

PHil.

Philip Rhoades

GPO Box 3411
Sydney NSW 2001
Australia
E-mail: phil@pricom.com.au

[mdigennaro]

Hello, I also would like to center a benzene molecule on the xy plane, with the center of mass in the origin.
Thank you

[ghutchis]

It’s a nice idea. At the moment, there isn’t a feature for that, but it would be relatively easy using the Python command scripts.

For example:

• FlattenZ: https://github.com/OpenChemistry/avogadro-commands/blob/000690a74633e5f300e5933e4645e3f3ec6758b5/flattenZ.py
• Centroid: https://github.com/OpenChemistry/avogadro-commands/blob/000690a74633e5f300e5933e4645e3f3ec6758b5/centroid.py

Basically, you’d just calculate the center of mass, translate the molecule, then rotate or flatten into the xy plane.

Not sure if I have time to modify the scripts for a bit, but hopefully that can give you a good starting point. This is exactly the use-case for the scripts.