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.

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