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insilichem / tangram

:black_square_button::atom_symbol: A collection of molecular modelling tools for UCSF Chimera
http://tangram-suite.readthedocs.io
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jinja2 cannot be found when running ommprotol through mmsetup #11

Open JeanDidier opened 5 years ago

JeanDidier commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

1rfo same thing

Prof. Dr. Jean-Didier Maréchal Associate Professor

Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.inslichem.com

Le dim. 24 mars 2019 à 19:05, Jaime Rodríguez-Guerra < notifications@github.com> a écrit :

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).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/insilichem/tangram/issues/11#issuecomment-475984066, or mute the thread https://github.com/notifications/unsubscribe-auth/AP8jqMvvXQiwxDRTSGNkppHFE-67VzUlks5vZ75ggaJpZM4cFp0B .

jaimergp commented 5 years ago

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

conda activate ~/tangram
conda list
JeanDidier commented 5 years ago

Sure, this is: packages in environment at /Users/jeandi/tangram: #

Name Version Build Channel

ambermini 16.16.0 7 omnia asn1crypto 0.24.0 py27_1003 conda-forge babel 2.6.0 py_1 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.5 py_1 conda-forge backports_abc 0.5 py_1 conda-forge biopython 1.73 py27h1de35cc_0 conda-forge blas 1.1 openblas conda-forge blosc 1.15.1 h0a44026_1002 conda-forge bzip2 1.0.6 h1de35cc_1002 conda-forge ca-certificates 2018.11.29 ha4d7672_0 conda-forge cclib 1.6.1 py_0 conda-forge certifi 2018.11.29 py27_1000 conda-forge cffi 1.12.1 py27h342bebf_0 conda-forge cftime 1.0.3.4 py27h917ab60_1000 conda-forge chardet 3.0.4 py27_1003 conda-forge conda 4.6.4 py27_0 conda-forge cryptography 2.5 py27hdbc3d79_1 conda-forge curl 7.64.0 heae2a1f_0 conda-forge cycler 0.10.0 py_1 conda-forge docutils 0.14 py27_1001 conda-forge enum34 1.1.6 py27_1001 conda-forge fftw3f 3.3.4 2 omnia freetype 2.9.1 h597ad8a_1005 conda-forge functools32 3.2.3.2 py_3 conda-forge futures 3.2.0 py27_1000 conda-forge gaudiview 0.0.3 py27_0 insilichem/label/dev hdf4 4.2.13 hf3c6af0_1002 conda-forge hdf5 1.10.4 nompi_h5598ddc_1105 conda-forge idna 2.8 py27_1000 conda-forge imagesize 1.1.0 py_0 conda-forge ipaddress 1.0.22 py_1 conda-forge jinja2 2.10 py_1 conda-forge jpeg 9c h1de35cc_1001 conda-forge kiwisolver 1.0.1 py27h04f5b5a_1002 conda-forge krb5 1.16.3 h24a3359_1000 conda-forge libcurl 7.64.0 h76de61e_0 conda-forge libcxx 7.0.0 h2d50403_2 conda-forge libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 h0a44026_1005 conda-forge libgcc 4.8.5 1 conda-forge libgfortran 3.0.0 1001 conda-forge libnetcdf 4.6.2 h6b88ef6_1001 conda-forge libpng 1.6.36 ha441bb4_1000 conda-forge libssh2 1.8.0 hf30b1f0_1003 conda-forge libtangram 0.0.3 py27_0 insilichem/label/dev llvm-meta 7.0.0 0 conda-forge markupsafe 1.1.0 py27h1de35cc_1000 conda-forge matplotlib 2.2.3 py27_1 conda-forge matplotlib-base 2.2.3 py27hd64abcd_1 conda-forge mdtraj 1.9.1 py27_0 omnia nciplot git20170610 h60a02f8_2 insilichem ncurses 6.1 h0a44026_1002 conda-forge netcdf4 1.4.2 py27hd700958_1001 conda-forge nomkl 3.0 0 numexpr 2.6.9 py27h1702cab_1000 conda-forge numpy 1.15.4 py27_blas_openblashb06ca3d_0 [blas_openblas] conda-forge numpydoc 0.8.0 py_1 conda-forge ommprotocol 0.1.11 py27_0 insilichem openblas 0.3.3 ha44fe06_1 conda-forge openmm 7.3.0 py27_cuda92_rc_1 omnia openmoltools 0.8.3 py27_1 omnia openssl 1.0.2p h1de35cc_1002 conda-forge packaging 19.0 py_0 conda-forge pandas 0.24.1 py27h0a44026_0 conda-forge parmed 3.1.0 py27_0 omnia pdbfixer 1.5 py27_0 omnia periodictable 1.5.0 py_1 conda-forge pip 19.0.2 py27_0 conda-forge pmw 2.0.1 py27_1001 conda-forge prody 1.8.2 py27h6440ff4_0 insilichem propka 3.1.0 py27_0 insilichem pychimera 0.2.7 py27_0 insilichem pycosat 0.6.3 py27h1de35cc_1001 conda-forge pycparser 2.19 py_0 conda-forge pyopenssl 19.0.0 py27_0 conda-forge pyparsing 2.3.1 py_0 conda-forge pysocks 1.6.8 py27_1002 conda-forge pytables 3.4.4 py27h0af8b44_1004 conda-forge python 2.7.15 h61312e0_1006 conda-forge python-dateutil 2.8.0 py_0 conda-forge pytz 2018.9 py_0 conda-forge pyyaml 3.13 py27h1de35cc_1001 conda-forge rdkit 2015.09.1 py27_3 omnia readline 7.0 hcfe32e1_1001 conda-forge requests 2.21.0 py27_1000 conda-forge ruamel_yaml 0.15.71 py27h1de35cc_1000 conda-forge scipy 1.2.0 py27_blas_openblashb06ca3d_200 [blas_openblas] conda-forge setuptools 40.8.0 py27_0 conda-forge singledispatch 3.4.0.3 py27_1000 conda-forge six 1.12.0 py27_1000 conda-forge snowballstemmer 1.2.1 py_1 conda-forge sphinxcontrib-websupport 1.1.0 py_1 conda-forge sqlite 3.26.0 h1765d9f_1000 conda-forge subprocess32 3.2.6 py27_0 omnia tangram 0.0.7 py27_0 file:///Users/travis/miniconda/conda-bld tangram_bondorder 0.0.2 py27_0 insilichem/label/dev tangram_dummyatoms 0.0.2 py27_0 insilichem/label/dev tangram_mmsetup 0.0.2 py27_0 insilichem/label/dev tangram_nciplot 0.0.2 py27_0 insilichem/label/dev tangram_normalmodes 0.0.2 py27_0 insilichem/label/dev tangram_orbitraj 0.0.2 py27_0 insilichem/label/dev tangram_popmusicgui 0.0.2 py27_0 insilichem/label/dev tangram_propkagui 0.0.2 py27_0 insilichem/label/dev tangram_qmsetup 0.0.2 py27_0 insilichem/label/dev tangram_selection 0.0.2 py27_0 insilichem/label/dev tangram_snfg 0.0.2 py27_0 insilichem/label/dev tangram_subalign 0.0.2 py27_0 insilichem/label/dev tangram_vinarelaunch 0.0.2 py27_0 insilichem/label/dev tkintertable 1.1.2 py27_0 insilichem tornado 5.1.1 py27h1de35cc_1000 conda-forge tqdm 4.31.1 py_0 conda-forge typing 3.6.6 py27_1000 conda-forge urllib3 1.24.1 py27_1000 conda-forge wheel 0.33.0 py27_0 conda-forge yaml 0.1.7 h1de35cc_1001 conda-forge zlib 1.2.11 h1de35cc_1004 conda-forge

Prof. Dr. Jean-Didier Maréchal Associate Professor

Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.inslichem.com

Le dim. 24 mars 2019 à 19:09, Jaime Rodríguez-Guerra < notifications@github.com> a écrit :

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

conda activate ~/tangram conda list

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jaimergp commented 5 years ago

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 commented 5 years ago

Sure, this is the answer of which /Users/jeandi/tangram/bin/ommprotocol

Prof. Dr. Jean-Didier Maréchal Associate Professor

Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.inslichem.com

Le dim. 24 mars 2019 à 19:25, Jaime Rodríguez-Guerra < notifications@github.com> a écrit :

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.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/insilichem/tangram/issues/11#issuecomment-475985855, or mute the thread https://github.com/notifications/unsubscribe-auth/AP8jqIrEdAwCPS8A3iD4AU9HuMtO_QSTks5vZ8MXgaJpZM4cFp0B .

jaimergp commented 5 years ago

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 commented 5 years ago

here it comes '/Users/jeandi/tangram/bin/ommprotocol'

Prof. Dr. Jean-Didier Maréchal Associate Professor

Insilichem Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es personal webpage: http://gent.uab.cat/jdidier insilichem webpage: http://www.inslichem.com

Le dim. 24 mars 2019 à 19:44, Jaime Rodríguez-Guerra < notifications@github.com> a écrit :

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')

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JeanDidier commented 5 years ago

OK, the jinja2 apparently is not properly installing on macOs. I am not sure why.