Hi Rakesh, There is not Chimera command to run Segger, only a dialog. So you would have to use Python to run it and write out map files for each masked region if you wanted to script it. Segger uses several Chimera features such as Gaussian filtering, and watershed calculations that are in written in C++ and compiled against the Chimera Python. While you can get those to run in another Python if it has an identical version (e.g. 2.7.3), setting up the environment variables to find all the needed libraries is a difficult process. So I suggest using the Chimera Python. You can run Chimera scripts without the graphical interface by starting it from a shell "chimera --nogui myscript.py". The Segger Python functions are not documented so you would need to study the (complex and messy) code found in chimera/share/Segger or on Mac in Chimera.app/Contents/Resources/share/Segger Tom On Dec 18, 2013, at 5:54 PM, rakesh ramachandram wrote:

Hi,

I would like to know if I can run Segger in a script in an automated fashion and then obtain the individual segmented regions as separate density maps. Is there a way to run chimera scripts from command line directly without using the chimera's python interpreter but using the default python interpreter after importing its libraries.

Regards Rakesh