VMD-L Mailing List

From: William Howe (howew_at_mail.gvsu.edu)
Date: Wed Mar 10 2021 - 17:19:18 CST

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!