Jmol/Cavities pockets and tunnels: Difference between revisions

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Eric Martz

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 The following script generates a pocket isosurface (open mouths) and an interior isosurface (closed pieces) for the spike protein, and saves each isosurface as a jvxl file. You can run this script: copy it and save it as a [[Help:Plain text editors|plain text file]] with a filename ending '''.spt'''. Drop the script file into the molecular display window of Jmol. Execution may take several minutes.
+====Write JVXL Files====
 <pre>
-x
+# In the Jmol Java application,
-x
+# This script took 2 min 25 sec on a mid-2014 MacBook Pro.
-x
+# It would likely take ~20 min in JSmol.
+zap # Deletes any molecule present in Jmol.
+print # Clears the Jmol Script Console.
+load =6zgi # Fetches PDB file from the RCSB Protein Data Bank.
+# RENDER MOLECULE
+background white
+rotate x -90
+restrict protein # Selects protein and hides non-protein, e.g. glycosylation.
+backbone only
+backbone 0.7
+color chain
+set translucent false # Shows only the front-most surface of translucent objects.
+color translucent 5 # Chain-colored backbones are now translucent.
+refresh # Unnecessary, but shows the molecule.
+# MAKE POCKETS
+isosurface minset 50 pocket cavity 2.5 # Cavity probe radius 2.5 Å.
+refresh
+isosurface map property surfacedistance # Color pockets by depth.
+refresh
+write "poc.jvxl"
+isosurface delete
+# MAKE INTERIOR CAVITY NOT DISPLAYED IN THE POCKETS ISOSURFACE.
+isosurface minset 100 interior cavity 2.5
+refresh
+isosurface map property surfacedistance
+refresh
+write "bur.jvxl" # Buried.
 </pre>