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salilab / rmf_chimerax

ChimeraX plugin to read and visualize RMF files
MIT License
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Error reading IMP generated RMF files: UsageError: "Can't convert null value." processing decorator of type ParticleConst #1

Closed jaredsagendorf closed 1 year ago

jaredsagendorf commented 1 year ago

Hi, I'm looking at the IMP tutorials and trying to read some generated RMF output files, but keep getting the error (as per ChimeraX log):

open pbc_interacting_patches.py.rmf
Cannot open files: UsageError: "Can't convert null value." processing decorator of type ParticleConst

I've installed the latest version of both ChimeraX and this plugin, but still the error remains. As for the IMP code, I installed everything from scatch today via Conda.

I am running linux/Fedora 35

benmwebb commented 1 year ago

The problem here is that this tutorial creates an RMF file that contains a "Granules" node (this can be seen by running rmf_show -v on the file). This node has no attributes except for mass, which makes RMF think it's a Particle node. But Particle nodes are also supposed to have coordinates, so RMF gets confused when it tries to extract them and they're not there. The RMF code in Chimera can read this file though, so I'll steal a workaround from there.

benmwebb commented 1 year ago

The latest code here should now work for the initial reading of these files. However, reading a trajectory (rmf readtraj) uses similar code in RMF, so that won't work until we update the bundled copy of the RMF library here. Unfortunately we can't do that for Mac until Apple/VirtualBox fix VirtualBox ticket 21563.