Então eu encontrei meu jetbrains-pycharm-ce.desktop e usei o gksudo
[Desktop Entry]
Version=1.0
Type=Application
Name=PyCharm Community Edition
Icon=/usr/lib/pycharm-community/bin/pycharm.png
Exec= gksudo -k -u root "/usr/lib/pycharm-community/bin/pycharm.sh" %f
Comment=The Drive to Develop
Categories=Development;IDE;
Terminal=false
StartupWMClass=jetbrains-pycharm-ce