[SOLVED]---- Trouble saving edited files in Pycharm 4.5

I am using the free version Pycharm Community 4.5 with Ubuntu 14.04.02 64 bit.

I am using Pycharm to edit Robot Operating System(ROS) files in my home directory, but it won't let me save files.

I open a terminal and cd to the /opt/pycharm-community-4.5.4/bin folder and type ./pycharm to run the app.

When trying to save a file a dialog appears with title of "Clear Read-Only Status"; I then select 'Using file system' and click ok, but the dialog won't close and the terminal prints an error message of  WARN: Can't set writable attribute of '/home/sam/Documents/Knowledge.py' to false.

I 'can' however run Pycharm as root and can save files, but this should not be the way to use Pycharm.

Please show me how to use Pycharm without being root so I may edit and save files.

Thank you,

Sam