Q. I have calculated pockets using
ICMPocketFinder. How to calculate the distance from a pocket to a specific residue in the protein?
A.
Use the commands shown below where g_pocket_rec1 is your pocket and K132 is the residue in object a_rec.a
# distance between grob center and center of some resodue
Distance( Mean(Xyz(g_pocket_rec1 )) Mean(Xyz(a_rec.a/^K132/)))
# distance between grob center and specific atom
Distance( Mean(Xyz(g_pocket_rec1 ))Rarray(Xyz(a_rec.a/^K132/ca)))