Upon displaying an output rmf3 file on Chimera, I am getting a number of
large, radially distributed spheres as part of the model. Within the
rmf3 file hierarchy, they are not part of the System or States within
(meaning I can exclude these spheres from visualization by showing only
"System" in the rmf3 file hierarchy panel). I wonder exactly what they
mean. If anyone has experienced these before I'd appreciate any help
interpreting and/or addressing this issue.
Without seeing your RMF file or knowing how you generated it, I can only
guess, but if at some point you make a rigid body using
IMP.atom.create_rigid_body() this will rigidify all of the leaves
(usually atoms or beads) but also add bounding spheres for any non-leaf
(e.g. chain). So if you rigidify an entire protein you'll see a large
sphere for each chain (within which you'll see spheres for each bead).
If you don't want to see these, they should be easy to select and hide
in ChimeraX (using the RMF tool from the ChimeraX toolshed). Not sure if
you can do that in legacy Chimera; the Chimera developers aren't working
on that code any more.