On Jun 10, 2008, at 10:25 AM, ProtEUS wrote:
Hello again!
I tried the way you explained me, but it doesn't seem to work.
I think I need more detail than "doesn't seem to work". Did you get an error message? Was the output wrong? What specifically happened?
I also tried to use the script mode with simple commands, but i am getting back error like:
cannot execute 'gzip'...
That's just a warning that files compressed with 'compress' (i.e. ending in '.Z') won't be openable in Chimera because no gzip executable could be found. You can ignore it assuming that none of the files you're using are compressed that way.
and a series of other errors of python.
The text of the script you used and the contents of the error messages would be helpful. --Eric
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
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