Installed - can't import _pmx as _p

I installed pmx on a cluster but was unable to get “pmx -h” to work.

I get this error:
Traceback (most recent call last):
File “/home/dburns/.local/bin/pmx”, line 5, in
from pmx.scripts.cli import entry_point
File “/work/LAS/potoyan-lab/Dan/SOFTWARE/pmx/pmx/”, line 46, in
from atom import *
File “/work/LAS/potoyan-lab/Dan/SOFTWARE/pmx/pmx/”, line 52, in
import _pmx as _p
ImportError: No module named _pmx

Thank you,


Guess I just needed to log out/in. Works now!

pmx requires an old version of rdkit - this is quite difficult to install on my cluster. Is there any suggested solution?

On the pmx master branch, now there is an updated script that uses a newer rdkit version:

Soon python3 based pmx will be released which will support the latest rdkit.