With Ubuntu 16.04, I used the “snap” installer, which doesn’t include an easily accessible icon (there’s probably one hidden inside the snap image, but it’s hard to get at). Instead it shows a grey question mark icon in the launcher instead. Also there doesn’t seem to be a Tools > Create Desktop Entry option in version 2017.3.3 as far as I can see – maybe it has been moved somewhere.

So I copied pycharm.png from an earlier non-snap Community installation, saved it somewhere, then created ~/.local/share/applications/jetbrains-pycharm-ce.desktop:

[Desktop Entry]
Version=1.0
Type=Application
Name=PyCharm Community Edition
Icon=/path/to/pycharm.png
Exec="/snap/bin/pycharm-community" %f
Comment=The Drive to Develop
Categories=Development;IDE;
Terminal=false
StartupWMClass=jetbrains-pycharm-ce

Then when I start PyCharm (from the command line), the launcher item appears with the correct icon, and then I right-click on it and choose “Lock to Launcher”, and it now persists.

A downside is that the icon will not be automatically updated with the app, so it might fall out of date.