This is the diagnostics log. Please keep reading at the end of the log: ------------------------------------------------------------------------------------------------
PyMOL(TM) 2.3.4 - Incentive Product Copyright (C) Schrodinger, LLC This Executable Build integrates and extends Open-Source PyMOL. Detected 40 CPU cores. Enabled multithreaded rendering. PyMOL>diagnostics PyMOL 2.3.4 build date: Wed Nov 6 20:04:05 2019 -0100 git sha: b5302154d05cd6c9f0ed78394d1ca2dcf91ebf8f conda build: py37h75f9260_0 file:///tmp/miniconda/conda-bld/linux-64 License Information: No License File - For Evaluation Only (0 days remaining) License Files: (no license file found) Operating System: Linux-4.4.0-178-generic-x86_64-with-debian-stretch-sid #208-Ubuntu SMP Sun Apr 5 23:45:10 UTC 2020 OpenGL Driver: (none) (none) (none) PyQt5 5.6 (Qt 5.6.2) Python: 3.7.5 (default, Oct 25 2019, 15:51:11) [GCC 7.3.0] prefix=/home/my_user/pymol executable=/home/my_user/pymol/bin/python filesystemencoding=utf-8 Startup Scripts: (no pymolrc file found) Qt, Python and PyMOL Environment Variables: LANG=es_ES.UTF-8 PYMOL_DATA=/home/my_user/pymol/share/pymol/data PYMOL_LICENSE_FILE= PYMOL_PATH=/home/my_user/pymol/share/pymol PYTHONEXECUTABLE=/home/my_user/pymol/bin/python PYTHONPATH=/home/my_user/envs/dqn_docking/RDKit:/home/my_user/envs/dqn_docking/lib:/home/my_user/envs/dqn_docking/local/lib:/home/my_user/envs/dqn_docking/bin/python:/home/my_user/miniconda3/bin/python PYTHONSTARTUP=/home/my_user/.startup.py QT_API=PyQt5 QT_QPA_PLATFORMTHEME=appmenu-qt5 QT_XKB_CONFIG_ROOT=/home/my_user/pymol/lib PATH: /home/my_user/pymol/bin:/home/my_user/envs/dqn_pymol/bin:/usr/local/MGLTools -1.5.6/bin:/home/my_user/miniconda3/bin:/home/my_user/projects/baselines/bas elines/deepq/mgltools/bin:/home/my_user/bin:/home/my_user/.local/bin:/usr/lo cal/MGLTools-1.5.6/bin:/home/my_user/miniconda3/bin/conda:/home/my_user/proj ects/baselines/baselines/deepq/mgltools/bin:/usr/local/sbin:/usr/local/bin:/us r/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/jdk-11.0.5 /bin:/snap/bin:/usr/local/cuda/bin:/usr/local/cuda/bin Diagnostics collected on Fri Jun 19 18:33:16 2020 -0100 ------------------------------------------------------------------------------------------------ So, no license file was found. My PyMol is installed in $HOME/pymol/. So, I moved the license file to $HOME/pymol/share/pymol/license.lic . Then I ran the diagnostics again: ------------------------------------------------------------------------------------------------ PyMOL(TM) 2.3.4 - Incentive Product Copyright (C) Schrodinger, LLC This Executable Build integrates and extends Open-Source PyMOL. Detected 40 CPU cores. Enabled multithreaded rendering. PyMOL>diagnostics PyMOL 2.3.4 build date: Wed Nov 6 20:04:05 2019 -0100 git sha: b5302154d05cd6c9f0ed78394d1ca2dcf91ebf8f conda build: py37h75f9260_0 file:///tmp/miniconda/conda-bld/linux-64 License Information: PyMOL for educational use only Expiry date: 01-jan-2021 License Files: /home/my_user/pymol/share/pymol/license.lic Operating System: Linux-4.4.0-178-generic-x86_64-with-debian-stretch-sid #208-Ubuntu SMP Sun Apr 5 23:45:10 UTC 2020 OpenGL Driver:(none)(none)(none) PyQt5 5.6 (Qt 5.6.2) Python: 3.7.5 (default, Oct 25 2019, 15:51:11) [GCC 7.3.0] prefix=/home/my_user/pymol executable=/home/my_user/pymol/bin/python filesystemencoding=utf-8 Startup Scripts: (no pymolrc file found) Qt, Python and PyMOL Environment Variables: LANG=es_ES.UTF-8 PYMOL_DATA=/home/my_user/pymol/share/pymol/data PYMOL_LICENSE_FILE=/home/my_user/pymol/share/pymol/license.lic PYMOL_PATH=/home/my_user/pymol/share/pymol PYTHONEXECUTABLE=/home/my_user/pymol/bin/python PYTHONPATH=/home/my_user/envs/dqn_docking/RDKit:/home/my_user/envs/dqn_docking/lib:/home/my_user/envs/dqn_docking/local/lib:/home/my_user/envs/dqn_docking/bin/python:/home/my_user/miniconda3/bin/python PYTHONSTARTUP=/home/my_user/.startup.py QT_API=PyQt5 QT_QPA_PLATFORMTHEME=appmenu-qt5 QT_XKB_CONFIG_ROOT=/home/my_user/pymol/lib PATH: /home/my_user/pymol/bin:/home/my_user/envs/dqn_pymol/bin:/usr/local/MGLTools -1.5.6/bin:/home/my_user/miniconda3/bin:/home/my_user/projects/baselines/bas elines/deepq/mgltools/bin:/home/my_user/bin:/home/my_user/.local/bin:/usr/lo cal/MGLTools-1.5.6/bin:/home/my_user/miniconda3/bin/conda:/home/my_user/proj ects/baselines/baselines/deepq/mgltools/bin:/usr/local/sbin:/usr/local/bin:/us r/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jvm/jdk-11.0.5 /bin:/snap/bin:/usr/local/cuda/bin:/usr/local/cuda/bin Diagnostics collected on Fri Jun 19 18:46:42 2020 -0100 ------------------------------------------------------------------------------------------------ Now the license file is recognized. So, apparently this problem should be solved. But unfortunately the warning message persists. It should be noted that I'm calling pymol through the Python's API. I'm working with a virtual environment. I wonder if the problem is related to this fact?? Thanks for your help, Thomas. I really appreciate it. Kind regards, El vie., 19 jun. 2020 a las 14:02, Thomas Holder (< thomas.hol...@schrodinger.com>) escribió: > That's unexpected. Can you send the output of the following command? > > pymol -cd diagnostics > > This will report the exact installation location, and also if a license > file was found. > > > > On Jun 19, 2020, at 10:33 AM, Antonio Serrano <aserra...@ucam.edu> > wrote: > > > > I changed the name of the license file as you said, but the warning > message keeps popping: > > > > <current_pos.png> > > > > > > > > > > > > > > El jue., 18 jun. 2020 a las 20:16, Thomas Holder (< > thomas.hol...@schrodinger.com>) escribió: > > Hi Antonio, > > > > Rename the file to "license.lic". > > > > Cheers, > > Thomas > > > > > On Jun 18, 2020, at 6:08 PM, Antonio Serrano <aserra...@ucam.edu> > wrote: > > > > > > Hi Thomas. Thanks for your quick response. I installed Miniconda, so I > put the license file (pymol-edu-license.lic) in the following path: > $HOME/miniconda3/share/pymol/ . But a warning text stating "No License File > - For evaluation Only (0 days remaining)" still appears when rendering PNG > files with PyMol. Any suggestions? > > > > > > El jue., 18 jun. 2020 a las 12:44, Thomas Holder (< > thomas.hol...@schrodinger.com>) escribió: > > > Hi Antonio, > > > > > > Did you install PyMOL into $HOME/anaconda3 ? If you installed into a > different location, then that path to the license file will differ of > course. Basically, path-to-pymol-dir/share/pymol/license.lic is the path. > > > > > > Cheers, > > > Thomas > > > > > > > On Jun 17, 2020, at 2:15 PM, Antonio Serrano <aserra...@ucam.edu> > wrote: > > > > > > > > Hi: > > > > > > > > I'm working with PyMol installed on a remote server, so I don't have > access to the GUI. I already have an educational license. According to your > FAQ at https://pymol.org/2/support.html?, the license file should be > placed in $HOME/anaconda3/share/pymol/license.lic on a Linux computer. I > already did it but PyMol isn't still activated. Any idea on how to > completely install the license file using only the Command Line Interface? > Many thx. > > > > > > > > BR, > > > > Antonio Serrano > > > > -- > > Thomas Holder > > PyMOL Principal Developer > > Schrödinger, Inc. > > > > > > > > -- > > Antonio Serrano > > Predoctoral researcher - Contratado predoctoral > > > > UCAM Universidad Católica de Murcia > > Phone: +34 968 278 821 > > Email: aserra...@ucam.edu > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > -- Antonio Serrano Predoctoral researcher - Contratado predoctoral *UCAM Universidad Católica de Murcia* Phone: +34 968 278 821 Email: aserra...@ucam.edu <//aserra...@ucam.edu> <https://scholar.google.es/citations?user=ZEJJCuUAAAAJ&hl=en&authuser=1> <https://orcid.org/0000-0002-8121-5032> <https://www.researchgate.net/profile/Antonio_Serrano9?ev=hdr_xprf> -- "Este mensaje es privado y confidencial y se dirige exclusivamente a su destinatario. Si usted recibe este mensaje por error, no debe revelar, distribuir o copiar este e-mail. Por favor, comuníquelo al remitente y borre el mensaje y los archivos adjuntos de su sistema. No hay renuncia a la confidencialidad ni a ningún privilegio a causa de una transmisión errónea o por mal funcionamiento". "This message is private and confidential and it is intended exclusively for the addressee. If your receive this message by mistake, you should not disseminate, distribute or copy this e-mail. Please inform the sender and delete the message and attachments from your system. No confidentiality or any privilege regarding the information is waived or lost by any mistransmission or malfunction". No me imprimas si no es necesario.Don't print me unless it's necessary.
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