paiardin
Python error when trying to prepare receptor
Hi,
I am trying to use the DockingPie plugin with open-source Py MOL version 3.1.0, installed via a conda environment. When trying to prepare a receptor for Vina I get the following error message. I am a bit puzzled by the - Has Conda: False statement, since I installed PyMOL using Conda.
Please advise.
Thank you,
Evert
PyMOL(TM) Molecular Graphics System, Version 3.1.0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org".
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 4.6. Shaders available.
Detected GLSL version 4.60.
OpenGL graphics engine:
GL_VENDOR: NVIDIA Corporation
GL_RENDERER: NVIDIA GeForce RTX 3060/PCIe/SSE2
GL_VERSION: 4.6.0 NVIDIA 550.120
Detected 12 CPU cores. Enabled multithreaded rendering.
PyMOL>set assembly, ""
Setting: assembly set to .
PyMOL>fetch 1dhfA
TITLE CRYSTAL STRUCTURES OF RECOMBINANT HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE AND 5-DEAZOFOLATE
ExecutiveLoad-Detail: Detected mmCIF
CmdLoad: "./1dhf.cif" loaded as "1dhfA".
Traceback (most recent call last):
File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/docking_program_gui/tabs.py", line 1822, in generate_receptor_func
generated_receptor = Generate_Object(self, dict = self.docking_programs_child_tabs.docking_programs.vina_receptors_dict,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 284, in __init__
self.generate_receptor()
File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 306, in generate_receptor
self.generate_checked_object()
File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 404, in generate_checked_object
self.generate_receptor_pdbqt(self.strc)
File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 444, in generate_receptor_pdbqt
subprocess.run(self.receptors_settings)
File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python'
My environment:
# DockingPie
- Version: 1.2.1
- Plugin path: /home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main
- Config directory: /home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/config
# PyMOL
- Version: 3.1.0
- Path: /home/evehom/Programs/miniconda3/envs/pymol/bin/python
- Qt: PyQt5
- Has Conda: False
# Python
- Version: 3.11.11 | packaged by conda-forge | (main, Dec 5 2024, 14:17:24) [GCC 13.3.0]
- Arch: 64
- Path: /home/evehom/Programs/miniconda3/envs/pymol/bin/python
# Operating system
- Platform: linux
- Arch: 64
# Python libs
- PyQt5: 5.15.9
- Conda version: 25.1.1
- Numpy version: 2.2.3
- Biopython version: 1.85
(pymol) evehom@mjolnir:~/Programs$ conda list python
# packages in environment at /home/evehom/Programs/miniconda3/envs/pymol:
#
# Name Version Build Channel
biopython 1.85 py311h9ecbd09_1 conda-forge
brotli-python 1.1.0 py311hfdbb021_2 conda-forge
python 3.11.11 h9e4cc4f_1_cpython conda-forge
python_abi 3.11 5_cp311 conda-forge
Hi Evert, Thank you for your interest in DockingPie.
The open-source versions of PyMOL do not incorporate Conda, that is why you are reading "Has Conda: False". For this reason we provide a different installation for this scenario, which you can find in the User's Guide https://github.com/paiardin/DockingPie/releases/download/versioning/DockingPie_User_Guide.pdf at Section 3.2.
However, the error suggests that python is not found when the subprocess is executed. While your system does have Python installed, the issue might be that the path to python is not correctly set or inherited by the subprocess call.
You may check if python is accessible by running: $ which python $ echo $PATH
Best Regards, Serena
Il giorno gio 20 feb 2025 alle ore 11:54 Evert-Homan < @.***> ha scritto:
Hi,
I am trying to use the DockingPie plugin with open-source Py MOL version 3.1.0, installed via a conda environment. When trying to prepare a receptor for Vina I get the following error message. I am a bit puzzled by the - Has Conda: False statement, since I installed PyMOL using Conda.
Please advise.
Thank you,
Evert
PyMOL(TM) Molecular Graphics System, Version 3.1.0. Copyright (c) Schrodinger, LLC. All Rights Reserved.
Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command.Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 4.6. Shaders available. Detected GLSL version 4.60. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce RTX 3060/PCIe/SSE2 GL_VERSION: 4.6.0 NVIDIA 550.120 Detected 12 CPU cores. Enabled multithreaded rendering.
PyMOL>set assembly, "" Setting: assembly set to . PyMOL>fetch 1dhfA TITLE CRYSTAL STRUCTURES OF RECOMBINANT HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE AND 5-DEAZOFOLATE ExecutiveLoad-Detail: Detected mmCIF CmdLoad: "./1dhf.cif" loaded as "1dhfA". Traceback (most recent call last): File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/docking_program_gui/tabs.py", line 1822, in generate_receptor_func generated_receptor = Generate_Object(self, dict = self.docking_programs_child_tabs.docking_programs.vina_receptors_dict, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 284, in init self.generate_receptor() File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 306, in generate_receptor self.generate_checked_object() File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 404, in generate_checked_object self.generate_receptor_pdbqt(self.strc) File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 444, in generate_receptor_pdbqt subprocess.run(self.receptors_settings) File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 548, in run with Popen(*popenargs, **kwargs) as process: ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 1026, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 1955, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'python'
My environment:
DockingPie
- Version: 1.2.1
- Plugin path: /home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main
- Config directory: /home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/config
PyMOL
- Version: 3.1.0
- Path: /home/evehom/Programs/miniconda3/envs/pymol/bin/python
- Qt: PyQt5
- Has Conda: False
Python
- Version: 3.11.11 | packaged by conda-forge | (main, Dec 5 2024, 14:17:24) [GCC 13.3.0]
- Arch: 64
- Path: /home/evehom/Programs/miniconda3/envs/pymol/bin/python
Operating system
- Platform: linux
- Arch: 64
Python libs
- PyQt5: 5.15.9
- Conda version: 25.1.1
- Numpy version: 2.2.3
- Biopython version: 1.85
(pymol) @.***:~/Programs$ conda list python
packages in environment at /home/evehom/Programs/miniconda3/envs/pymol:
Name Version Build Channel
biopython 1.85 py311h9ecbd09_1 conda-forge brotli-python 1.1.0 py311hfdbb021_2 conda-forge python 3.11.11 h9e4cc4f_1_cpython conda-forge python_abi 3.11 5_cp311 conda-forge
— Reply to this email directly, view it on GitHub https://github.com/paiardin/DockingPie/issues/9, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQIJQFANI4V63KYBZAUBVOL2QWX5HAVCNFSM6AAAAABXQOIDICVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3DKOBQGE3TANI . You are receiving this because you are subscribed to this thread.Message ID: @.***> [image: Evert-Homan]Evert-Homan created an issue (paiardin/DockingPie#9) https://github.com/paiardin/DockingPie/issues/9
Hi,
I am trying to use the DockingPie plugin with open-source Py MOL version 3.1.0, installed via a conda environment. When trying to prepare a receptor for Vina I get the following error message. I am a bit puzzled by the - Has Conda: False statement, since I installed PyMOL using Conda.
Please advise.
Thank you,
Evert
PyMOL(TM) Molecular Graphics System, Version 3.1.0. Copyright (c) Schrodinger, LLC. All Rights Reserved.
Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help <command-name>" for information on a specific command.Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 4.6. Shaders available. Detected GLSL version 4.60. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce RTX 3060/PCIe/SSE2 GL_VERSION: 4.6.0 NVIDIA 550.120 Detected 12 CPU cores. Enabled multithreaded rendering.
PyMOL>set assembly, "" Setting: assembly set to . PyMOL>fetch 1dhfA TITLE CRYSTAL STRUCTURES OF RECOMBINANT HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH FOLATE AND 5-DEAZOFOLATE ExecutiveLoad-Detail: Detected mmCIF CmdLoad: "./1dhf.cif" loaded as "1dhfA". Traceback (most recent call last): File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/docking_program_gui/tabs.py", line 1822, in generate_receptor_func generated_receptor = Generate_Object(self, dict = self.docking_programs_child_tabs.docking_programs.vina_receptors_dict, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 284, in init self.generate_receptor() File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 306, in generate_receptor self.generate_checked_object() File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 404, in generate_checked_object self.generate_receptor_pdbqt(self.strc) File "/home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/Functions/general_docking_func.py", line 444, in generate_receptor_pdbqt subprocess.run(self.receptors_settings) File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 548, in run with Popen(*popenargs, **kwargs) as process: ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 1026, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/home/evehom/Programs/miniconda3/envs/pymol/lib/python3.11/subprocess.py", line 1955, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'python'
My environment:
DockingPie
- Version: 1.2.1
- Plugin path: /home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main
- Config directory: /home/evehom/.pymol/startup/DockingPie1/lib/docking_program_main/config
PyMOL
- Version: 3.1.0
- Path: /home/evehom/Programs/miniconda3/envs/pymol/bin/python
- Qt: PyQt5
- Has Conda: False
Python
- Version: 3.11.11 | packaged by conda-forge | (main, Dec 5 2024, 14:17:24) [GCC 13.3.0]
- Arch: 64
- Path: /home/evehom/Programs/miniconda3/envs/pymol/bin/python
Operating system
- Platform: linux
- Arch: 64
Python libs
- PyQt5: 5.15.9
- Conda version: 25.1.1
- Numpy version: 2.2.3
- Biopython version: 1.85
(pymol) @.***:~/Programs$ conda list python
packages in environment at /home/evehom/Programs/miniconda3/envs/pymol:
Name Version Build Channel
biopython 1.85 py311h9ecbd09_1 conda-forge brotli-python 1.1.0 py311hfdbb021_2 conda-forge python 3.11.11 h9e4cc4f_1_cpython conda-forge python_abi 3.11 5_cp311 conda-forge
— Reply to this email directly, view it on GitHub https://github.com/paiardin/DockingPie/issues/9, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQIJQFANI4V63KYBZAUBVOL2QWX5HAVCNFSM6AAAAABXQOIDICVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA3DKOBQGE3TANI . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hi,
This is exactly how I Installed PyMOL.
With the PyMOL Conda environment activated I get:
(pymol) evehom@mjolnir:~/Data/Sandbox$ which python
/home/evehom/Programs/miniconda3/envs/pymol/bin/python
(pymol) evehom@mjolnir:~/Data/Sandbox$ echo $PATH
/home/evehom/Programs/miniconda3/envs/pymol/bin:/home/evehom/Programs/miniconda3/condabin:/usr/local/cuda/bin:/home/evehom/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/thinlinc/bin
I also installed SpyRMD, Openbabel and RxDock as outlined under 3.2. All modules except RxDock are showing as 'already installed' under the Configuration tab in DockingPie, despite RxDock being installed:
conda install bioconda::rxdock
Channels:
- conda-forge
- defaults
- bioconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
# All requested packages already installed.
Any clues?
BW/Evert
Hi,
I wiped PyMOL, created a new Conda environment and reinstalled PyMOL with
conda install conda-forge::pymol-open-source
After this everything works as it should.
Thanks for pointing me to the manual, I have a grown tendency not to read these.
BW/Evert