[Chimera-users] Swapaa from Java Runtime.exec

ProtEUS proteus.support at gmail.com
Tue Jun 10 10:25:28 PDT 2008

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...

  ----- Original Message ----- 
  From: Eric Pettersen 
  To: ProtEUS 
  Cc: chimera-users at 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:


  You could use a series of commands like:

  open input.pdb
  swapaa TYR :15.a
  write output.pdb

  to do the swapaa.


                          Eric Pettersen

                          UCSF Computer Graphics Lab


  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 at cgl.ucsf.edu

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