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VMD visualization of CaviTracer - #2279
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jamesmkrieger
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Sep 18, 2026
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jamesmkrieger
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A few minor things that I don’t need to check on. Otherwise everything looks good
| if object_type == 'connected_cavities_channels': | ||
| if isinstance(objects, dict): | ||
| objects = [objects] | ||
| elif not isinstance(objects, list): |
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This is redundant. The same happens in both if branches
| elif not isinstance(objects, list): | ||
| objects = [objects] | ||
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| if len(objects) == 0: |
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This will never happen unless an empty list is explicitly provided because of wrapping into a list giving length 1
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| # ------------------------------------------------------------------ | ||
| # Save protein | ||
| # ------------------------------------------------------------------ |
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Remove these as there are no long blocks that need separating
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For the other ones they are fine but could be shorter
| # Display | ||
| # ---------------------------------------------------------------------- | ||
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| color Display Background white |
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Maybe make these arguments
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I created the writeVmdCaviTracerScript() function, which creates a VMD state for the results obtained by CaviTracer.
How to use it:
from prody import *
p = parsePDB('1tqn')
atoms = p.select("protein")
For channels:
channels, surface = calcChannels(atoms)
writeVmdCaviTracerScript(channels, atoms)
Surface cavities:
cavities, surface = calcSurfaceCavities(atoms)
writeVmdCaviTracerScript(cavities, atoms, object_type='surface_cavities', surface=surface)
It will also work for pores and reconstruction of channels+surface cavities.
The user is obtaining a TCL script (vis_channels.tcl for channels, vis_pores.tcl for pores, etc.) that contains a visualization-ready state of the analysis.
To run the script:
vmd -e vis_channels.tcl
Visualization:
