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Feedback Wanted: Layer system in Avogadro v2

Marc Masó is a master’s student at UPC in Barcelona. He’s working on Avogadro v2 as part of this year’s Google Summer of Code on a project he called “Tools for visualization and efficient editing.”

One thing Marc would like to add is a system of “layers” for fragments. This would be similar to tools in graphics editing programs (Photoshop, Blender, etc.) and make it easier to edit or change graphics styles on different disconnected pieces (e.g., ligand + protein, molecule + surface, two molecules, etc.)

He’s looking for some feedback on then concept and how the UI should work.

When finished, the layers would also be available to commands / input generation (e.g., fragment-based calculations).

Thoughts? Ideas? Suggestions?

I am not sure I get the concept. Is the idea that one can group molecules and then use different display styles - like VDW or ball and stick - for different groups, so that they are easily distinguishable or that one can more easily see a molecule in a solvent?

Certainly all of the above:

  • molecules and fragments can have different display styles
  • one can more easily see a molecule in a solvent (e.g., hide the solvent layer / layers)
  • layers can be exposed to other programs (e.g., use QM for a molecule and MM for the solvent, etc.)
  • you could lock / freeze a layer during optimization as a constraint

I like the idea very much! It seems so obvious, but somehow did not come to my mind before :upside_down_face:
Would love to have it for material science projects, when we have sandwiched materials or water + nanotubes or graphene. It will make life so much easier to be able to modify only part of the system without fear to spoil the rest. Ideally, selection and editing must be limited to the current layer if a user do not select the opposite.

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