I run a python script, but it returns this error. I am working on an environment and I believe that I have to install the pymol module. I am not familiar with these things and I have no idea how to solve this problem. Could anyone guide me?

This is the command I use to invoke the environment:

source env_prova/bin/activate

This is the command for the script:

python pymol_align.py --list1=list.txt --list2= template.txt --out= pr.txt

This is the error:

Traceback (most recent call last): File "pymol_align.py", line 4, in import pymol ImportError: No module named pymol

Could someone help me?

1 Answer 1


apt install pymol should do it if you are on a debian-based system (ubuntu, mint, ...).

Otherwise pip install pymol .

edit: If I remember correctly pymol uses python 3, so make sure you are not using 2

  • If I try with pip, this is the result: Could not find a version that satisfies the requirement pymol (from versions: ) No matching distribution found for pymol
    – Tommaso
    Jul 30, 2020 at 13:12
  • What distro are you using, apt install was one example, but other large distro's will also have this package in their repo. It's best to use it from their repo's instead of using pip (compatibility is better)
    – Garo
    Jul 30, 2020 at 13:16
  • How I can see which python I'm using?
    – Tommaso
    Jul 30, 2020 at 13:17
  • python --version
    – Garo
    Jul 30, 2020 at 13:17
  • 2.7.5 but I have also python3, how I can change it?
    – Tommaso
    Jul 30, 2020 at 13:18

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