Linking Pymol with Pyrosetta on windows 10 using UBUNTU

[Jacob199527]

Hello,

I am very new to protein modeling and I am trying to get stuck into some tutorials but I am having difficulties setting up.

I am using the windows subsystem for linux to run pyrosetta. I have gotten to the point where I can create a virutal enviroment via to run python 3.12, pyrosetta and pymol. When I open pymol I can successfully link pymol and rosetta together via the pymol mover. However, I am then stuck in the terminal not being able to input any commands (see attached). Is there anyway to get back to pyrosetta from this point in the same terminal to input commands? When I open a new terminal with pyrosetta it is not linked with pymol.

any help would be appreciated.

[roccomoretti]

Generally speaking, I'd recommend launching PyMol and PyRosetta in separate terminal windows. As you see, once you launch PyMol, it "takes over" the terminal. If you leave that terminal running and switch to a new one, (reactivating the Conda environment as necessary), you can then launch PyRosetta.

I'm not sure why you're not able to link the separate terminals. If I had to guess, it may have to do with using Windows Subsystem for Linux. It may be the way you're launching the terminals causes Windows to launch two separate copies of Linux. Ideally, you'll launch another terminal with the same copy of Linux. I'm not entirely familiar with WSL, but from a quick web search, I think you should be able to shift-click the taskbar icon of the currently running terminal to launch a new terminal in the same session.

Failing that, you can always try launching PyMol in the background of the first terminal. PyMol is a bit chatty, so you'll want to redirect the output. Something like pymol &> /dev/null & should launch in the background (last &) and discard the output normally printed to the terminal by redirecting it to /dev/null (&> /dev/null).

Alternatively, there are several "virtual terminal" managers, including tmux and screen, which should allow you to have multiple effective terminals within a single terminal window.

[Jacob199527]

Turns out, I could open another terminal and the pyrosetta and pymol were still linked. I can use the PyMOL_Mover() function to place pose from pyrosetta into pymol. I will experiment more tomorrow but exciting stuff.