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MembraneDepthMapping

Map the depth on a PDB file. The depth, here, correspond to the distance between the upper phosphate (COM*) plane and the protein (COM).

  • COM = center of mass

Usage

python MapDepth.py -pdb my.pdb -Up [optional] -Low [optional]

  • pdb: the PDB file of your peripheral membrane protein in complex with a bilayer
  • Up: If your protein bound to the upperleaflet
  • Low: If your protein bound to the lowerleaflet

output: a pdb file with the depth instaead of the B-factor. You can use Pymol or Chimera to visualize it:

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