[PyMOL] about image generation limitation of the EDU license

[Yonghui Li <fen...@ya...>]

Dear pymol developer and users,

I recently ran into a problem in generating molecule structures with 
pymol. Pymol works great in generating about 100k small molecule images. 
But the problem is the watermark. I've received a EDU license and 
configured to pymol. But since the 6th image, the watermark begins to 
show in every image. Is it a limitation of the software or the license? 
BTW, I am using a server without a GUI, so I did the configuration with 
CLI. Any suggestions will be appreciated.

Here is the --diagnostics prints.

  PyMOL(TM) 3.1.3.1 - Incentive Product
  Copyright (C) Schrodinger, LLC

  This Executable Build integrates and extends Open-Source PyMOL.
  Detected 12 CPU cores.  Enabled multithreaded rendering.
PyMOL>diagnostics
PyMOL 3.1.3.1
build date: Wed Feb  5 07:42:22 2025 -0800
git sha: 698d66e4c6e73b53e79c3954053b380006455f15
conda build: py312h2dc6bc7_0 https://conda.anaconda.org/schrodinger/linux-64

License Information:
  License Expiry date: 2025-12-01

License Files:
/opt/Anaconda3-2024.10-mols/share/pymol/license.lic
/opt/schrodinger/licenses/pymol-edu-license.lic

Operating System:
Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
#1 SMP Thu Nov 8 23:39:32 UTC 2018

OpenGL Driver:
(none)
(none)
(none)
PyQt5 5.15.10 (Qt 5.15.2)

Python:
3.12.7 | packaged by conda-forge | (main, Oct  4 2024, 16:05:46) [GCC 
13.3.0]
prefix=/opt/Anaconda3-2024.10-mols
executable=/opt/Anaconda3-2024.10-mols/bin/python
filesystemencoding=utf-8

Startup Scripts:
(no pymolrc file found)

Qt, Python and PyMOL Environment Variables:
LANG=en_US.UTF-8
PYMOL_DATA=/opt/Anaconda3-2024.10-mols/share/pymol/data
PYMOL_LICENSE_FILE=/opt/Anaconda3-2024.10-mols/share/pymol/license.lic:/opt/schrodinger/licenses
PYMOL_PATH=/opt/Anaconda3-2024.10-mols/share/pymol
PYTHONEXECUTABLE=/opt/Anaconda3-2024.10-mols/bin/python
PYTHONPATH=/opt/intel2024.0.0/advisor/2024.0/pythonapi
QTDIR=/usr/lib64/qt-3.3
QTINC=/usr/lib64/qt-3.3/include
QTLIB=/usr/lib64/qt-3.3/lib
QT_API=pyqt5
QT_GRAPHICSSYSTEM_CHECKED=1
QT_XKB_CONFIG_ROOT=/opt/Anaconda3-2024.10-mols/lib

PATH:
/opt/Anaconda3-2024.10-
mols/bin:/opt/intel2024.0.0/vtune/2024.0/bin64:/opt/intel2024.0.0/mpi/2021.11/
opt/mpi/libfabric/bin:/opt/intel2024.0.0/mpi/2021.11/bin:/opt/intel2024.0.0/mk
l/2024.0/bin/:/opt/intel2024.0.0/itac/2022.0/bin:/opt/intel2024.0.0/inspector/
2024.0/bin64:/opt/intel2024.0.0/dpcpp-ct/2024.0/bin:/opt/intel2024.0.0/dev-uti
lities/2024.0/bin:/opt/intel2024.0.0/debugger/2024.0/opt/debugger/bin:/opt/int
el2024.0.0/compiler/2024.0/opt/oclfpga/bin:/opt/intel2024.0.0/compiler/2024.0/
bin:/opt/intel2024.0.0/advisor/2024.0/bin64:/usr/lib64/qt-
3.3/bin:/opt/enviroment-modules.5.0.1/bin:/usr/local/bin:/usr/bin:/usr/local/s
bin:/usr/sbin:/opt/ibutils/bin:/public/home/******/.local/bin:/public/home
/******//bin

Diagnostics collected on Sat May 24 19:46:40 2025 -0800

---------------------------------------------------------------------------------------------------------------

The python script is a bit complicate but it basically something like:

import os
#os.environ["PYMOL_LICENSE_FILE"]="/opt/license/pymol-edu-license.lic"
import importlib
import pymol
pymol.pymol_argv = ['pymol', '-qc']
from pymol import cmd

******#some pre-processing

pymol.finish_launching()

os.system("pymol --diagnostics")

for i in range(len(meta)):
     print(meta[i]["path"])
     filename = Path(meta[i]["path"]).stem
     prefix,p1,p2 = re.findall(r"(.+?)_\w+(\d{3})_\w+(\d{3})", 
Path(meta[i]["path"]).stem)[0]
     p1,p2 = int(p1)+1, int(p2)+1
     xyz_path = basedir / f"{filename}.xyz"
     get_xyz(meta[i]["path"]).write_file(xyz_path)
     #cmd.delete('all')
     cmd.reinitialize()
     destfile = imgdir / f"{filename}.png"
     cmd.load(f"{xyz_path}")

     cmd.show('sticks')
     cmd.show('spheres')
     cmd.color('gray')
     cmd.set('stick_radius', 0.15)
     cmd.set('sphere_scale', 0.3)
     cmd.color('gray', 'elem C')
     cmd.color('red', 'elem O')
     cmd.color('blue', 'elem N')
     cmd.color('white', 'elem H')

     L, R = f"id {p1}", f"id {p2}"
     cmd.bond(L, R)
     cmd.set_bond("stick_color", "orange", L, R)
     cmd.set_bond("stick_radius", 0.3, L, R)
     cmd.png(f"{destfile}", ray=1)