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BradyAJohnston / MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.
https://bradyajohnston.github.io/MolecularNodes/
MIT License
798 stars 81 forks source link

v4.0.11 surface #483

Open Jojo109x opened 1 month ago

Jojo109x commented 1 month ago

Is your feature request related to a problem? Please describe. In v4.0.11 a new way to depict surfaces was introduced. As far as I can tell the old method was removed. I really liked the old one because it did a better job at 'isolating' sidechains. With a bit of tweaking one was able to generate almost realistically looking high resolution electron density maps with the style (example settings: quality 4, scale radii 0.1, probe size 0.9, separation True). Although not particularly scientific, I loved the aesthetics of this. It was also quite unique compared to surface depications of pymol, chimera etc.

Describe the solution you'd like Could we please get the old surface style back as an optional alternative to the new one?

rbdavid commented 4 weeks ago

Version control of geometry nodes is a very difficult nut to crack. I am whole-heartedly on your side about this though. I think the best solution I can suggest at the moment is:

  1. Download the v4.0.10 ~/molecularnodes/assets/MN_data_file.blend file (or any .blend file for a project where the geo node is working as you expect/want).
  2. Load that file into a blender instance that does not have the MN addon loaded. This avoids conflicts in node naming between blender imported geometry nodes and the nodes stored in the v4.0.10 blender file.
  3. Change the name of the geometry node(s) that you wish to use so they won't conflict with the new MN version's nodes. Save the .blend file.
  4. In a blender instance with the current MN addon version loaded, you can append geometry nodes from other .blend files via File -> Append. Then in the file browser, find your v4.0.10 .blend file and find the desired node(s) in that file's NodeTree subdirectory. Appending those nodes to your current project should make them accessible in the Geo Node Editor dropdown menus.

or just continue using v4.0.10 for the project. Neither option is really a solution.

Jojo109x commented 4 weeks ago

GABAA Thanks a lot! I will give this a try.

In the meantime, I have found alternative parameters that produce similar results (high resolution electron density like appearance) with the new surface style.

In case anyone is interested (Quality 4, Scale Radii 0.9, Probe Size 0.000, Separate True, Triangulate True, Relaxation steps 30)

rbdavid commented 4 weeks ago

To avoid this issue in the future, I think it might be worthwhile to suggest a geometry node naming format where version numbers are included so that previous nodes are not lost. This runs the risk of creating bloat in the imported nodes but would enable back-compatibility and reproducibility of scientific visualizations. Worthy causes to strive for imo.

For example, the geo node to draw a Cartoon style node is named MN_style_cartoon. I haven't dug through change logs to find when that node was last altered, so I'm gonna use placeholder text here. My suggestion for a new naming scheme is: the Cartoon style node to be renamed to MN_style_cartoon_vX.X.X to denote the node is "new as of version X.X.X". Then, when a new implementation of the Cartoon style node is pushed, that version is named MN_style_cartoon_vY.Y.Y. The old version of the node is moved from the Geometry Node Editor's Add -> MolecularNodes menu to the Geometry Node Editor's Add -> Unassigned menu tree to keep clutter down.

Also, dope image! I really need to start testing out the surface representations. Everyone seems to be heavily using those instead of cartoon reps.