This is good to know; I'm glad it wasn't symptomatic of a problem with the code for the GUI itself. It would be good to know if the outgoing connection is causing problems, or just the incoming connection - the latter is much less important. For now I will add a preference setting to disable the "server", and if that still doesn't solve the problem I'll disable both directions. (I may drop by your lab and ask to test it next time I'm in Cambridge, because I'd really like to know what part of Linux is causing socket problems. Are you running a very restrictive host-based firewall by any chance?) On Mar 12, 2010, at 12:52, John Berrisford wrote:

Dear All

Thanks for the suggestions on how to solve my GUI freezing issues. It looks like it was a communication problem with coot that was causing my problems. Editing App.py as below solved my problem.

Adding a preference setting to do this would be useful.

Thanks again John

Message: 3 Date: Thu, 11 Mar 2010 09:48:29 -0500 From: Nathaniel Echols To: PHENIX user mailing list Subject: Re: [phenixbb] phenix gui freezes Message-ID: <[email protected]> Content-Type: text/plain; charset=us-ascii

I have one other thought - the GUI listens on a socket for incoming commands from Coot (this isn't used very much at present). Apparently this caused problems on Linux with the old GUI, which also used Python sockets. If something goes wrong here, it could certainly take down the entire program.

To fix this, edit the file $PHENIX/phenix/wxGUI2/App.py, and comment out this line (in 1.6):

self.start_xmlrpc_server()

(if you're new to python, a comment starts with '#'.)

I will add a preferences setting to do this. I can also try slowing down the GUI updates while a process is running (using detached processes should also take care of this).

-- John Berrisford

Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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