Dear chimera power-users: I can use the gnuplot.py library from the python command line without issue. However, when I try to do the same in IDLE under chimera, I get a broken pipe error. Any suggestions? --John -------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com
Hi John, Where did you install gnuplot (the program, not the module)? The execution path (os.environ['PATH']) is considerably different in standalone Python than in Chimera's IDLE shell. I suspect that the gnuplot executable is not on IDLE's PATH (the Gnuplot module by default tries to run gnuplot simply as 'gnuplot'). If the problem is with PATH, your options include modifying os.environ['PATH'] before importing Gnuplot, or changing the Gnuplot module's options like so: import Gnuplot Gnuplot.GnuplotOpts.gnuplot_command = '/bin/mygnuplot' --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Feb 8, 2006, at 6:01 PM, John Robinson wrote:
Dear chimera power-users:
I can use the gnuplot.py library from the python command line without issue. However, when I try to do the same in IDLE under chimera, I get a broken pipe error.
Any suggestions?
--John
-------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi John, Does the gnuplot.py problem in Chimera generate a Python traceback? Could you send it? It sounds like gnuplot.py is trying to pipe data to an external program (I guess a gnuplot executable) and the program is not starting or is shutting down before all data is read. My guess is the gnuplot program simply is not starting -- maybe it is not in the search path, or an environment variable is not set when invoked from Chimera. Tom
Thanks Eric, It was the path. IDLE's default dir is '/'. Issuing the following made things work. Gnuplot.GnuplotOpts.gnuplot_command = '/usr/local/bin/gnuplot' Thanks again. On Feb 9, 2006, at 12:19 PM, Eric Pettersen wrote:
Hi John, Where did you install gnuplot (the program, not the module)? The execution path (os.environ['PATH']) is considerably different in standalone Python than in Chimera's IDLE shell. I suspect that the gnuplot executable is not on IDLE's PATH (the Gnuplot module by default tries to run gnuplot simply as 'gnuplot'). If the problem is with PATH, your options include modifying os.environ['PATH'] before importing Gnuplot, or changing the Gnuplot module's options like so:
import Gnuplot Gnuplot.GnuplotOpts.gnuplot_command = '/bin/mygnuplot'
--Eric
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On Feb 8, 2006, at 6:01 PM, John Robinson wrote:
Dear chimera power-users:
I can use the gnuplot.py library from the python command line without issue. However, when I try to do the same in IDLE under chimera, I get a broken pipe error.
Any suggestions?
--John
-------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com
participants (3)
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Eric Pettersen -
John Robinson -
Thomas Goddard