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

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: