Well you can do this by going to the interpreter's dialogue box. Click on the interpreter that you are using, and underneath it, you should see two tabs, one called Packages, and the other called Path.
1)Open the Settings dialog box, and click Project Interpreter page.
2)In the Projects pane, choose the desired project.
3)For the selected project, choose SDK from the list of available Python interpreters and virtual environments.
In my experience, using a PYTHONPATH variable at all is usually the wrong approach, because it does not play nicely with VENV on windows. PYTHON on loading will prepare the path by prepending PYTHONPATH to the path, which can result in your carefully prepared Venv preferentially fetching global site packages.
Instead of using PYTHON path, include a pythonpath.pth file in the relevant site-packages directory (although beware custom pythons occasionally look for them in different locations, e.g. enthought looks in the same directory as python.exe for its .pth files) with each virtual environment. This will act like a PYTHONPATH only it will be specific to the python installation, so you can have a separate one for each python installation/environment. Pycharm integrates strongly with VENV if you just go to yse the VENV's python as your python installation.
checkboxes, as well as setting the "Working directory" field.
If you have set up your own Run/Debug Configurations then you might want to go to
Run > Edit Configuration > Python > [Whatever you called your config]
and edit it there.
My problem was that I wanted to have my whole repository included in my PyCharm 2016.2 project, but only a subfolder was the actual python source code root. I added it as "Source Root" by right clicking the folder then
Mark directory as > Source Root
Then unchecking "Add content roots to PYTHONPATH" and checking "Add source root to PYTHONPATH" in the Run/Debug config menu. I then checked the folder pathing by doing:
An update to the correct answer phil provided, for more recent versions of Pycharm (e.g. 2019.2).
Go to File > Settings and find your project, then select Project Interpreter. Now click the button with a cog to the right of the selected project interpreter (used to be a ...).
From the drop-down menu select Show All... and in the dialog that opens click the icon with a folder and two sub-folders.
You are presented with a dialog with the current interpreter paths, click on + to add one more.