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 <fencing.he...@yandex.com> 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/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- *Jarrett Johnson* | Staff Developer, PyMOL
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
