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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
https://pymol.org/
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apbs plugin issue #328

Closed Vcald closed 6 months ago

Vcald commented 8 months ago

I have installed open source pymol on windows 11 through conda (Miniconda_latest) and with cctbx with the following command: conda.exe create -n opensource -c conda-forge cctbx pymol-open source

After successful installation I have installed apbs plugin, then apbs and pdb2pqr. When trying to use the plugin I get the following error: Any hint?

PyMOL>fetch 1rmz TITLE Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH at 1.3 A resolution ExecutiveLoad-Detail: Detected mmCIF CmdLoad: ".\1rmz.cif" loaded as "1rmz". GENERATING PQR FILE via PDB2PQR Erasing contents of C:\Users\Vito\AppData\Local\Temp\pymol-generated.pdb in order to generate new PDB file TESTING DONE TESTING args are now converted to string: C:\Miniconda3_latest\envs\opensource\Scripts\pdb2pqr30.exe --ff=AMBER C:\Users\Vito\AppData\Local\Temp\pymol-generated.pdb C:\Users\Vito\AppData\Local\Temp\pymol-generated.pqr b'' b'Traceback (most recent call last):\r\n File "", line 198, in _run_module_as_main\r\n File "", line 88, in _run_code\r\n File "C:\Miniconda3_latest\envs\opensource\Scripts\pdb2pqr30.exe\main.py", line 4, in \r\n File "C:\Miniconda3_latest\envs\opensource\Lib\site-packages\pdb2pqr\init.py", line 10, in \r\n from .main import main\r\n File "C:\Miniconda3_latest\envs\opensource\Lib\site-packages\pdb2pqr\main.py", line 21, in \r\n from . import debump\r\n File "C:\Miniconda3_latest\envs\opensource\Lib\site-packages\pdb2pqr\debump.py", line 11, in \r\n from . import io\r\n File "C:\Miniconda3_latest\envs\opensource\Lib\site-packages\pdb2pqr\io.py", line 12, in \r\n from . import cif\r\n File "C:\Miniconda3_latest\envs\opensource\Lib\site-packages\pdb2pqr\cif.py", line 12, in \r\n import pdbx\r\nModuleNotFoundError: No module named \'pdbx\'\r\n' PDB2PQR's mainCommand returned 1 In show error 2

speleo3 commented 8 months ago

How did you install pdb2pqr? Installing it with pip or conda should automatically install the mmcif_pdbx dependency.

Vcald commented 8 months ago

I installed it with conda and verified that mmcif_pdbx was installed as well. But still it does not work. Can it be because of a space between my name and surname in the temp directory?

Il giorno dom 21 gen 2024 alle ore 12:24 Thomas Holder < @.***> ha scritto:

How did you install pdb2pqr? Installing it with pip or conda should automatically install the mmcif_pdbx dependency.

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Vcald commented 8 months ago

I have deleted everything and reinstall from scratch...pmw does not work at the beginning (pmw2.0.0). I have to uninstall it and install pmw2.1.1 for getting the apbs plugin window working. After this tweak...it works.