[Chimera-users] questions about modeller and task panel

Smith, Susan Margaret Ellen smsmit7 at emory.edu
Sun Feb 17 14:43:14 PST 2013


Hello,
I am trying to use Chimera as an interface to a local installation of Modeller on my Mac.

I have two questions:
1) When I open the task panel, I can see the current tasks and the completed tasks (nice visual cuing), but I do not see any way to kill a job.  How can I select a job and how can I stop it?

2) When I run the tutorial example for Modeller, I get the following message, which seems like it is telling me that something is wrong (although the job appears to still be running in the task panel).  I have re-installed the Modeller package, but I don't know what 'environment variable' was not set ... It seems like the program doesn't know where to put the output, although I specified a path for the temporary output.  Can you help with this?

Thanks,
Susan

Target seq: oprd_human
Template structures:
        4DKL (#0)Run locally, the Modeller binary location: /Library/modeller-9.11/bin/mod9.11_mac10v4
Now, modeller is running locally...
MODELLER process output
-----------------------
FATAL ERROR: MODINSTALL9v11 environment variable not set: incomplete MODELLER installation
-----------------------
MODELLER process errors
-----------------------
-----------------------
Traceback (most recent call last):
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/tasks.py", line 179, in runStatusCB
    task.statusCBList[0]()
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 166, in statusCB
    self.finished()
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 201, in finished
    self._after(self._aborted)
  File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 635, in _collectResultsCB
    OKModels = self._showingOKmodels(self.pathTemp)
  File "/Applications/Chimera.app/Contents/Resources/share/MultAlignViewer/ModellerBase.py", line 646, in _showingOKmodels
    modelsInfoFile = osOpen(os.path.join(outputPath, "ok_models.dat"))
  File "/Applications/Chimera.app/Contents/Resources/share/OpenSave/__init__.py", line 324, in osOpen
    raise UserError(val)
UserError: [Errno 2] No such file or directory: '/Users/dlambe/Desktop/ok_models.dat'

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