Hi Fabrice, I do not think Chimera could run using Jython because Chimera uses dozens of compiled C/Python modules. You can communicate with Chimera via a pipe. One approach is to start Chimera with a popen() system call and send commands to Chimera's stdin using the ReadStdin capability: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/readstdin... It is also possible to talk to an already running instance of Chimera using the "chimera --send <file>" shell command. This is used to have a web browser helper application directly send files to Chimera. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.htm... The implementation uses a socket that Chimera is listening on but it is somewhat tricky to find the right port number. It is saved on the local machine in a file as a security measure to prevent network connections. The details of that implementation are in your Chimera distribution chimera/share/send_to_chimera.py Scooter Morris in our lab has written code to communicate with Chimera from a Java application called Cytoscape. He might be able to provide more advice. Tom Fabrice Jossinet wrote:

Dear developers,

I would like to launch Chimera from my Java program. I would like to send messages to Chimera to highlight in its own display selections I do in my Java program's display. I already did that with PyMOL using a pipe communication.

So, several questions: - is it possible to start Chimera from a classical python distribution (not the embedded python of Chimera)? One of my ideas is to start Chimera from Jython, a Java implementation of Python - is it possible to communicate with Chimera using a pipe ? - and the most general question: is it possible to communicate with Chimera from the outside?

Thank you for your answers

Fabrice