I’m trying to select the residue conformation by using Pdb-tools.
Even though I’ve installed the package successfully (Requirement already satisfied: pdb-tools in c:\programdata\pymol\lib\site-packages (2.0.0)), and tried "python pdb_selaltloc.py myfile.pdb ",
I don’t know how to run selaltloc.py on pymol for windows.
Thanks in advance,
Without more information it’s very hard to help you.
On windows, after installing with
pip, you should be able to run the tools just by calling their name, e.g.
pdb_selaltloc.exe myfile.pdb from the command line. You cannot run them from within PyMOL.
From your output it seems that you somehow installed the tools using the Python version bundled with PyMOL. I would not recommend this. Instead, install Miniconda/Anaconda to have your own Python installation that does not depend on the version on PyMOL, etc. Then install the pdb-tools again against this Python version and they should be accessible when you load the Anaconda prompt.