Hi Felipe,

If your aim is to get a measure of the size of the ligand you could use “measure inertia ligand”. That shows an ellipsoid that matches the inertia of the atoms which is usually a decent approximation to the shape, and the radii along the 3 ellipse axes are reported in the Reply Log (in menu Favorites) as a, b, c.

open 2gbp

measure inertia ligand

Inertia axes for 2gbp 12 atoms

v1 = 0.710 0.376 -0.595 a = 4.106 r1 = 1.511

v2 = -0.671 0.106 -0.734 b = 3.321 r2 = 1.857

v3 = -0.213 0.921 0.328 c = 0.619 r3 = 2.362

center = 37.399 30.587 49.61

Longest axis is 2*a = 8.2 Angstroms.

If you really want the maximum pairwise distance then a simple Python script (attached) will do this.

open 2gbp

select ligand

open maxdist.py

Reply Log shows

Maximum distance between pairs of atoms among 12 atoms is 6.31 for #0:310.A@O6 and #0:310.A@O2

Tom