Hello again! I tried the way you explained me, but it doesn't seem to work. I also tried to use the script mode with simple commands, but i am getting back error like: cannot execute 'gzip'... and a series of other errors of python. Could you please help me with this situation? Thank you so much in advance... Andreas. ----- Original Message ----- From: Eric Pettersen To: ProtEUS Cc: chimera-users@cgl.ucsf.edu Sent: Tuesday, June 10, 2008 1:31 AM Subject: Re: [Chimera-users] Swapaa from Java Runtime.exec If you run Chimera in nogui mode (i.e. with the command-line flag "--nogui") with no script file argument then standard input would be interpreted as Chimera commands. Alternatively, you could supply a script file (Chimera commands or Python) as an argument. This is basically described here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui You could use a series of commands like: open input.pdb swapaa TYR :15.a write output.pdb to do the swapaa. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 9, 2008, at 1:14 PM, ProtEUS wrote: Hello all! I am sorry if this is a dump question, but is it possible for swapaa to run fromJava server with Runtime.exec()? Thank you very much!! Andreas, Greece. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users