Pymol can not import python scripts when called in perl

[shengzizhang]

Hi, I tried to call pymol in perl for calculations with the following command:

perl -e 'system("/Applications/PyMOL.app/Contents/bin/pymol -c pymol.pml >test.txt")'

the pymol.pml script is below:

load 2nx5_DE_changepos.pdb
import elbow_angle
elbow_angle 2nx5_DE_changepos

The output is:

 PyMOL(TM) 2.3.1 - Incentive Product
 Copyright (C) Schrodinger, LLC
 
 This Executable Build integrates and extends Open-Source PyMOL.
 CmdLoad: PDB-string loaded into object "2nx5_DE_changepos", state 1.

Thus, pymol can only load the pdb but does not import the python elbow_angle script and do the calculation. In contrast, if running the same command in zsh shell, everything output well. It is unclear why this happens. I am using Mac with the macOS Catalina system.

[speleo3]

I can't reproduce this (macOS 10.14). Running from shell (bash) or from perl gives the same result for me.