Selection based on MDAnalysis selection syntax

[mdpoleto]

Hello!

I was wondering if there are any plans to implement a selection tool based on MDAnalysis selection syntax, so users can use selection strings to select whatever atoms they need (e.g. "resname POT or resname CLA", or "segid PROA and resid 1-15").

It's somewhat frustrating when my topology does not use the same residue names as expected, and I end up not being able to use the tool for all my renderings (e.g., my Cl- ions are not picked up since they are named CLA).

I'm not sure how much work that would require, though.
Has that ever been considered?

[BradyAJohnston]

This is already possible! There is currently only a bit of documentation mentioning it (have been holding off on updating the docs for Blender 5.0): https://bradyajohnston.github.io/MolecularNodes/tutorials/trajectories.html#custom-selections

Internally it just creates a atom group through u.select_atoms() with the input selection string so all MDAnalysis selections are possible.

[mdpoleto]

That's great! Thanks!

A few questions: by using those selections, does that mean MN is using just the vertices corresponding to that selection? I'm wondering if other camera features like Track To or DOF focus can be used to that set of vertices without the hassle of creating a Vertex Group.

[mdpoleto]

Also, FYI:

I saved my session using those selections you mentioned above. When I had to reopen it and reload the Universe of each object, I got the following error:

Python: Traceback (most recent call last):
  File "/home/mdpoleto/.config/blender/4.5/extensions/blender_org/molecularnodes/ui/ops.py", line 689, in execute
    traj.set_frame(context.scene.frame_current)
  File "/home/mdpoleto/.config/blender/4.5/extensions/blender_org/molecularnodes/entities/trajectory/base.py", line 511, in set_frame
    self._update_selections()
  File "/home/mdpoleto/.config/blender/4.5/extensions/blender_org/molecularnodes/entities/trajectory/base.py", line 408, in _update_selections
    selection = self.selections[sel.name]
                ~~~~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'selection_0'

The Universe is loaded and I can see all frames but, ultimately, only the first object's positions are updated throughout the trajectory/timeline, while the others are basically frozen in space.

Any tips?

[BradyAJohnston]

This stores a boolean named attribute on the mesh vertices. All vertices remain in the mesh, just now some are true for usage inside of GN. This currently isn't directly compatible with other systems which can't read generic attributes and require the Vertex Group.

Coming in Blender 5.0 there is a new "Attribute Transform" constraint which will enable reading the attribute / transform data from a mesh for other modifiers / constraints to use.

[BradyAJohnston]

Are you able to give more details about reproducing the error you are getting?

The Universe is loaded and I can see all frames but, ultimately, only the first object's positions are updated throughout the trajectory/timeline, while the others are basically frozen in space.

I am also a little confused by what you mean with seeing "all frames" but only a single object is updated? Can you give mor edetails about this?

[mdpoleto]

This stores a boolean named attribute on the mesh vertices. All vertices remain in the mesh, just now some are true for usage inside of GN. This currently isn't directly compatible with other systems which can't read generic attributes and require the Vertex Group.

Thanks for the explanation. I may create a new issue about this but whenever I try creating a Vertex Group (Edit mode > manually select the vertices) after the trajectory is loaded, it seems to break something because atoms positions stop updating throughout the timeline (i.e. if I hit play in the timeline, atoms are frozen and not moving around as they would in the trajectory). No error is produced either.

[BradyAJohnston]

Hmm that's an interesting error - I can't immediately reproduce it so if you could come up with some example data for reproducing it would be great. Under the Molecular Nodes -> Object tab is there maybe a button / option to reload the trajectory?

[mdpoleto]

I did look for that button but I could not find it again. For all I can see, it seems the frames are loaded just fine (it says "This trajectory has X frames") but positions are not updated anymore.

I will work on a minimal reproducible example and will open a separated issue for this.

[mdpoleto]

Are you able to give more details about reproducing the error you are getting?

The Universe is loaded and I can see all frames but, ultimately, only the first object's positions are updated throughout the trajectory/timeline, while the others are basically frozen in space.

I am also a little confused by what you mean with seeing "all frames" but only a single object is updated? Can you give mor edetails about this?

About this error (sorry for sidetracking!):

I loaded my trajectory/topology in 3 different objects to control frame averaging differently (and also to apply different materials to each object). For each object, a selection_0 was created like you suggested above, so I ended up with:

• Object PROA (using selection string "segid PROA")
• Object CLA (using selection "resname CLA and around 35 segid PROA)
• Object POT (using selection "resname POT and around 35 segid PROA)

Then I applied some materials, positioned my camera, lights, etc. Once my session was ready to render, I saved it so I could render later. Once I opened the session again and tried to reload the trajectory/topology, I obtained the error below:

Python: Traceback (most recent call last):
  File "/home/mdpoleto/.config/blender/4.5/extensions/blender_org/molecularnodes/ui/ops.py", line 689, in execute
    traj.set_frame(context.scene.frame_current)
  File "/home/mdpoleto/.config/blender/4.5/extensions/blender_org/molecularnodes/entities/trajectory/base.py", line 511, in set_frame
    self._update_selections()
  File "/home/mdpoleto/.config/blender/4.5/extensions/blender_org/molecularnodes/entities/trajectory/base.py", line 408, in _update_selections
    selection = self.selections[sel.name]
                ~~~~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'selection_0'

For some weird reason, the atoms positions of the first object I tried to reload seem to update throughout the timeline, while the others did not (i.e. atoms are kept frozen as the timeline plays).

Perhaps the selection string is not being stored anywhere so Blender does not know what that attribute should be? Or perhaps it is trying to create an attribute before the universe is loaded by MDA? I may take a look into the code later.

[BradyAJohnston]

I did look for that button but I could not find it again. For all I can see, it seems the frames are loaded just fine (it says "This trajectory has X frames") but positions are not updated anymore.

Are properly entering & exiting Edit Mode? The positions won't change if you are still in edit mode (which is required to edit vertex groups)

[BradyAJohnston]

Okay thanks for the additional info around the issues. I can't currently replicate that exact issue (running into a different issue instead that isn't letting me save properly) but will definitely look into this.