jinja2 cannot be found when running ommprotol through mmsetup
JeanDidier opened this issue · 9 comments
JeanDidier commented
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
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
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).
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jaimergp commented
Can you run these commands and send the output, please?
conda activate ~/tangram
conda list
JeanDidier commented
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
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
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.
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jaimergp commented
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
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
OK, the jinja2 apparently is not properly installing on macOs. I am not sure why.