From: Ashar Malik (
Date: Wed Mar 10 2021 - 18:01:10 CST


Try vectdist

On Thu, 11 Mar 2021 at 7:50 AM, William Howe <> wrote:

> I'd like to know if theres a way to select two points in space (not atoms,
> just a point in space) using a set of X, Y, Z coordinates from each of
> those points in space and then measure the distance ( in angstroms) between
> them.
> Say I wanted to measure the distance from point (117.445 , Y: 157.465 ,
> Z: 110.487) to point (X: 109.364 , Y: 129.146 , Z: 106.429) (both of
> these are geometric centers)
> Because what I'm trying to do is measure the distance between the
> geometric center (average of every X, Y and Z coordinate of every atom
> within the molecule or file) for a ligand (Diazepam) within a PDB structure
> (6HUP) and the geometric center of 240 ligands outputted from a molecular
> docking server as single PDB output file.
> I can calculate the geometric center by reading the file with python
> scripts, but I'm not sure how I would get VMD to register the X, Y, Z
> coordinates I calculated.
> Thank you!