GLTF: Cannot center nodes because a node has both a mesh and children

[mbopf@…]

As we discussed yesterday, I updated the NIH3D Workflows to yesterday’s daily build of ChimeraX to get the centering feature that Kristen requested. This throws and error (and segfault on MacOS) when we try to process PDB 3NIR.

I think this is the main error:

INFO prefect.ShellTask:shell.py:151 File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/gltf/gltf.py", line 633, in check_node_centering_possible
INFO prefect.ShellTask:shell.py:151 raise UserError('Cannot center nodes because a node has both a mesh and children')

[pett]

Session just before the error

[pett]

I had trouble reproducing this outside the workflows, but when I forced the workflow to poop out a session just before the problematic GLTF save, then the error could be reproduced...

[Tom Goddard]

Error output from Mike Bopf

[Tom Goddard]

Fixed.

Code now allows output GLTF with nodes centered when a ChimeraX drawing has both a mesh and child nodes. This happened when ribbons had tethers connected to the side chains. The ribbon model had a mesh which was the ribbon and a child drawing for the tethers. The fix turned the mesh into a separate node in GLTF. The GLTF node centering should now work on all scenes.

[Tom Goddard]

Another surprise I noticed while testing was that the new missing segment labels appear in the GLTF output. Those new labels show how many residues are missing above the dashed line representing the missing segment. I'm not sure whether this recent feature will cause the labels to appear in NIH3D models (probably undesired). Eric would know.

[pett]

They will only show up in "visualization" outputs. Printable outputs hide missing-structure pseudobonds.