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jinja2 cannot be found when running ommprotol through mmsetup #11

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JeanDidier opened this issue Mar 24, 2019 · 9 comments
Open

jinja2 cannot be found when running ommprotol through mmsetup #11

JeanDidier opened this issue Mar 24, 2019 · 9 comments
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@JeanDidier
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JeanDidier commented Mar 24, 2019 •
edited by jaimergp
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Hi again, sorry to bug off...

When running MDs with openMM on a small peptide (pdb code 1ze7), I have the following problem:

Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results
in singular transformations; automatically expanding.
left=1, right=1
  + 'left=%s, right=%s') % (left, right))
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 165, in statusCB
    self.finished()
  File "/Applications/Chimera.app/Contents/Resources/share/chimera/SubprocessMonitor.py", line 201, in finished
    self._after(self._aborted)
  File "/Users/jeandi/tangram/lib/python2.7/site-packages/mmsetup/core.py", line 92, in _after_cb
    raise chimera.UserError(msg)
UserError: OMMProtocol calculation failed! Reason: ImportError: No module named jinja2

Thanks a lot!
@jaimergp
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Is that the only molecule failing? I had success with 1RFO (first submodel only). Try to run that to discard any problems with the system (although it looks more of an installation issue).

@JeanDidier
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JeanDidier commented Mar 24, 2019 via email

@jaimergp
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Can you run these commands and send the output, please?

conda activate ~/tangram
conda list

@JeanDidier
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JeanDidier commented Mar 24, 2019 via email

@jaimergp
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jinja2 is listed. What is the result of which ommprotocol? I am worried that you might a past installation hanging on $PATH and the GUI is calling that one instead of the one provided in the new Tangram environment.

@JeanDidier
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JeanDidier commented Mar 24, 2019 via email

@jaimergp
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Hmmm, that should be the value.

Let's see if Chimera has something to do... Open Tangram and then the IDLE. Execute these commands:

from distutils.spawn import find_executable
find_executable('ommprotocol')

@JeanDidier
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JeanDidier commented Mar 24, 2019 via email

@jaimergp jaimergp added the osx label Mar 25, 2019
@JeanDidier
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OK, the jinja2 apparently is not properly installing on macOs. I am not sure why.

@jaimergp jaimergp changed the title MD on MacOS jinja2 cannot be found when running ommprotol through mmsetup Mar 26, 2019
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