I installed pycharm normally via bin/pycharm.sh, but the mistake I made was doing bash pycharm.sh while the pycharm directory has inside the D
bin/pycharm.sh
bash pycharm.sh
In case you just want to update your launcher to point to an updated PyCharm, for me changing 4.0.4 to 4.0.6 in the following worked:
nano /usr/share/applications/jetbrains-pycharm.desktop