Thanks Jarrett! I've updated it via conda and the water marks are gone.
Thanks for your help!
Best,
Yonghui Li
On 5/30/2025 8:32 AM, Jarrett Johnson wrote:
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)
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*Jarrett Johnson* | Staff Developer, PyMOL
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