I am having an issue getting my Pycharm environment to match up with the environment that I have on the command line. I recently removed python and reinstalled it via home
Another approach is to source your script setting environmental variables (for example .bash_profile) by adding a line . /path/to/script into PY_CHARM_INSTALL_DIR/bin/pycharm.sh.
After that you can run pycharm using quick-lunch or whatever and you variables will be there.