Re: [PyMOL] about image generation limitation of the EDU license

[Jarrett J. <jar...@sc...>]

Hello,

This issue, I believe, should have already been addressed in our latest
patch (3.1.5.1). Can you upgrade and see if you still observe this issue?

Thanks,
Jarrett J.

On Sat, May 24, 2025 at 8:38 AM Yonghui Li <fen...@ya...> wrote:

> 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)
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Staff Developer, PyMOL