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