hainm
commented
1 year ago hi, does nv.demo() show anything at all?
Closed xperrylinn closed 5 months ago
hainm
commented
1 year ago hi, does nv.demo() show anything at all?
xperrylinn
commented
1 year ago Hi @hainm, I can confirm nv.demo() appears to work fine.
This suggests the issue might be related to my topology and trajectory files, but I'm not sure how to confirm this.
hainm
commented
1 year ago @xperrylinn it might because the default representation does not work well for your system. try to mda_view.add_line(...) or anything else to check? or you might need to center your system (nglview/ngl does it but you might need to explicitly provide the atom selection (mda_view.center(...))
xperrylinn
commented
1 year ago Hi @hainm, apologies for the late reply. I've tried both add_line and center and still, all I see is a blank screen. Here a links to the files I'm using topology.pdb and trajectory.dcd.
hainm
commented
1 year ago hi @xperrylinn
it's fine with my test
xperrylinn
commented
1 year ago Thank you, @hainm! I will try to reproduce using your package versions and let you now how it goes.
xperrylinn
commented
1 year ago Hi @hainm, it looks like I'm still running into the same issue.
It looks like your code is not emitting the same logging warning message that I have. I did a search in my IDE to see where this was coming from and it's coming from /Users/xperrylinn/miniconda3/envs/atomate2-openmm/lib/python3.8/site-packages/simtk/openmm.
Did you install all of the imported dependencies from conda-forge or PyPI? Do you also mind sharing an export of your environment, so I can see your all of the package versions?
hainm
commented
1 year ago I did not install openmm, so I did not get the warning like you did.
By the way, I am using python 3.9 (yours is 3.8).
Do you also mind sharing an export of your environment, so I can see your all of the package versions?
I am sorry I can't share this since it has some private products.
xperrylinn
commented
1 year ago Roger. I'll try building a fresh environment with Python 3.9.
Here's my conda export:
name: atomate2-openmm
channels:
- conda-forge
- defaults
dependencies:
- aioitertools=0.11.0=pyhd8ed1ab_0
- ambertools=22.4=py38h6498154_0
- anyio=3.6.2=pyhd8ed1ab_0
- appnope=0.1.3=pyhd8ed1ab_0
- argon2-cffi=21.3.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py38hef030d1_3
- arpack=3.7.0=hefb7bc6_2
- asttokens=2.2.1=pyhd8ed1ab_0
- astunparse=1.6.3=pyhd8ed1ab_0
- atk-1.0=2.38.0=h1d18e73_1
- atomate2=0.0.10=pyhd8ed1ab_0
- attrs=22.2.0=pyh71513ae_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=pyhd8ed1ab_3
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- bcrypt=3.2.2=py38hef030d1_1
- beautifulsoup4=4.12.2=pyha770c72_0
- biopython=1.81=py38hef030d1_0
- bleach=6.0.0=pyhd8ed1ab_0
- blosc=1.21.2=hebb52c4_0
- boost=1.78.0=py38he49a349_4
- boost-cpp=1.78.0=hf5ba120_3
- boto3=1.26.116=pyhd8ed1ab_0
- botocore=1.29.116=pyhd8ed1ab_0
- brotli=1.0.9=hb7f2c08_8
- brotli-bin=1.0.9=hb7f2c08_8
- brotlipy=0.7.0=py38hef030d1_1005
- bzip2=1.0.8=h0d85af4_4
- c-ares=1.18.1=h0d85af4_0
- c-blosc2=2.8.0=had5f71b_1
- ca-certificates=2023.5.7=h8857fd0_0
- cached-property=1.5.2=hd8ed1ab_1
- cached_property=1.5.2=pyha770c72_1
- cachetools=5.3.0=pyhd8ed1ab_0
- cairo=1.16.0=h297c08e_1015
- certifi=2023.5.7=pyhd8ed1ab_0
- cffi=1.15.1=py38hb368cf1_3
- cftime=1.6.2=py38hbd87e4b_1
- charset-normalizer=3.1.0=pyhd8ed1ab_0
- click=8.1.3=unix_pyhd8ed1ab_2
- colorama=0.4.6=pyhd8ed1ab_0
- comm=0.1.3=pyhd8ed1ab_0
- commonmark=0.9.1=py_0
- contourpy=1.0.7=py38h98b9b1b_0
- cryptography=40.0.2=py38h4257468_0
- curl=8.0.1=h1fead75_0
- custodian=2023.3.10=pyhd8ed1ab_0
- cycler=0.11.0=pyhd8ed1ab_0
- cython=0.29.34=py38h4cd09af_0
- dataclasses=0.8=pyhc8e2a94_3
- debugpy=1.6.7=py38h4cd09af_0
- decorator=5.1.1=pyhd8ed1ab_0
- defusedxml=0.7.1=pyhd8ed1ab_0
- dnspython=2.3.0=pyhd8ed1ab_0
- emmet-core=0.52.0=pyhd8ed1ab_0
- entrypoints=0.4=pyhd8ed1ab_0
- erdantic=0.5.0=pyhd8ed1ab_0
- exceptiongroup=1.1.1=pyhd8ed1ab_0
- executing=1.2.0=pyhd8ed1ab_0
- expat=2.5.0=hf0c8a7f_1
- fastapi=0.95.1=pyhd8ed1ab_0
- fasteners=0.17.3=pyhd8ed1ab_0
- fftw=3.3.10=nompi_h4fa670e_107
- flask=2.2.3=pyhd8ed1ab_0
- flit-core=3.8.0=pyhd8ed1ab_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.14.2=h5bb23bf_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.39.3=py38hef030d1_0
- freetype=2.12.1=h3f81eb7_1
- fribidi=1.0.10=hbcb3906_0
- future=0.18.3=pyhd8ed1ab_0
- gdk-pixbuf=2.42.10=hff535ac_2
- gettext=0.21.1=h8a4c099_0
- giflib=5.2.1=hb7f2c08_3
- gmp=6.2.1=h2e338ed_0
- gmpy2=2.1.2=py38h919de47_1
- graphite2=1.3.13=h2e338ed_1001
- graphviz=7.1.0=hc51f7b9_0
- greenlet=2.0.2=py38h4cd09af_0
- griddataformats=1.0.1=pyhd8ed1ab_0
- gsd=2.8.1=py38h073b4c8_0
- gtk2=2.24.33=h7c1209e_2
- gts=0.7.6=hccb3bdf_2
- h5py=3.8.0=nompi_py38hd2287a7_101
- harfbuzz=6.0.0=hc28939c_1
- hdf4=4.2.15=h9804679_6
- hdf5=1.14.0=nompi_hbf0aa07_103
- icu=72.1=h7336db1_0
- idna=3.4=pyhd8ed1ab_0
- importlib-metadata=6.5.0=pyha770c72_0
- importlib-resources=5.12.0=pyhd8ed1ab_0
- importlib_metadata=6.5.0=hd8ed1ab_0
- importlib_resources=5.12.0=pyhd8ed1ab_0
- iniconfig=2.0.0=pyhd8ed1ab_0
- ipykernel=6.22.0=pyh736e0ef_0
- ipython=8.12.0=pyhd1c38e8_0
- ipython_genutils=0.2.0=py_1
- itsdangerous=2.1.2=pyhd8ed1ab_0
- jedi=0.18.2=pyhd8ed1ab_0
- jinja2=3.1.2=pyhd8ed1ab_1
- jmespath=1.0.1=pyhd8ed1ab_0
- jobflow=0.1.11=pyhd8ed1ab_0
- joblib=1.2.0=pyhd8ed1ab_0
- jsonschema=4.17.3=pyhd8ed1ab_0
- jupyter_client=8.2.0=pyhd8ed1ab_0
- jupyter_core=5.3.0=py38h50d1736_0
- jupyter_events=0.6.3=pyhd8ed1ab_0
- jupyter_server=2.5.0=pyhd8ed1ab_0
- jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
- jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
- khronos-opencl-icd-loader=2023.04.17=hb7f2c08_0
- kiwisolver=1.4.4=py38h98b9b1b_1
- krb5=1.20.1=h049b76e_0
- latexcodec=2.0.1=pyh9f0ad1d_0
- lcms2=2.15=h2dcdeff_1
- lerc=4.0.0=hb486fe8_0
- libaec=1.0.6=hf0c8a7f_1
- libblas=3.9.0=16_osx64_openblas
- libbrotlicommon=1.0.9=hb7f2c08_8
- libbrotlidec=1.0.9=hb7f2c08_8
- libbrotlienc=1.0.9=hb7f2c08_8
- libcblas=3.9.0=16_osx64_openblas
- libcurl=8.0.1=h1fead75_0
- libcxx=16.0.1=h71dddab_0
- libdeflate=1.18=hac1461d_0
- libedit=3.1.20191231=h0678c8f_2
- libev=4.33=haf1e3a3_1
- libexpat=2.5.0=hf0c8a7f_1
- libffi=3.4.2=h0d85af4_5
- libgd=2.3.3=h3d994df_6
- libgfortran=5.0.0=11_3_0_h97931a8_31
- libgfortran5=12.2.0=he409387_31
- libglib=2.76.1=h4c723e1_0
- libiconv=1.17=hac89ed1_0
- libjpeg-turbo=2.1.5.1=hb7f2c08_0
- liblapack=3.9.0=16_osx64_openblas
- libnetcdf=4.9.1=nompi_hb6dca1b_103
- libnghttp2=1.52.0=he2ab024_0
- libopenblas=0.3.21=openmp_h429af6e_3
- libpng=1.6.39=ha978bb4_0
- librsvg=2.56.0=h123f2dd_0
- libsodium=1.0.18=hbcb3906_1
- libsqlite=3.40.0=ha978bb4_0
- libssh2=1.10.0=h47af595_3
- libtiff=4.5.0=hedf67fa_6
- libtool=2.4.7=hf0c8a7f_0
- libwebp=1.3.0=ha9aa8fa_0
- libwebp-base=1.3.0=hb7f2c08_0
- libxcb=1.13=h0d85af4_1004
- libxml2=2.10.4=h554bb67_0
- libzip=1.9.2=h6db710c_1
- libzlib=1.2.13=hfd90126_4
- llvm-openmp=16.0.1=h61d9ccf_0
- lz4-c=1.9.4=hf0c8a7f_0
- maggma=0.50.3=pyhd8ed1ab_0
- markupsafe=2.1.2=py38hef030d1_0
- matplotlib-base=3.7.1=py38hcb346ec_0
- matplotlib-inline=0.1.6=pyhd8ed1ab_0
- mdanalysis=2.2.0=py38h2b30649_0
- mdtraj=1.9.7=py38hb25ac7b_4
- mistune=2.0.5=pyhd8ed1ab_0
- mmtf-python=1.1.3=pyhd8ed1ab_0
- mongogrant=0.3.3=pyhd8ed1ab_0
- mongomock=4.0.0=pyhd8ed1ab_0
- monty=2023.4.10=pyhd8ed1ab_0
- mp-api=0.30.10=pyhd8ed1ab_0
- mpc=1.3.1=h81bd1dd_0
- mpfr=4.2.0=h4f9bd69_0
- mpmath=1.3.0=pyhd8ed1ab_0
- mrcfile=1.4.3=pyhd8ed1ab_0
- msgpack-python=1.0.5=py38h98b9b1b_0
- munkres=1.1.4=pyh9f0ad1d_0
- nbclassic=0.5.5=pyh8b2e9e2_0
- nbclient=0.7.3=pyhd8ed1ab_0
- nbconvert-core=7.3.1=pyhd8ed1ab_0
- nbformat=5.8.0=pyhd8ed1ab_0
- ncurses=6.3=h96cf925_1
- nest-asyncio=1.5.6=pyhd8ed1ab_0
- netcdf-fortran=4.6.0=nompi_hf174cb6_104
- netcdf4=1.6.3=nompi_py38ha7327cc_101
- networkx=3.1=pyhd8ed1ab_0
- nglview=3.0.6=pyhba93850_0
- notebook=6.5.4=pyha770c72_0
- notebook-shim=0.2.2=pyhd8ed1ab_0
- numexpr=2.8.4=py38hdaefe69_0
- numpy=1.24.2=py38h5a2dcdf_0
- ocl_icd_wrapper_apple=1.0.0=hbcb3906_0
- openbabel=3.1.1=py38heac13bf_5
- openff-amber-ff-ports=0.0.3=pyh6c4a22f_0
- openff-forcefields=2023.04.1=pyh1a96a4e_0
- openff-interchange=0.2.3=pyhd8ed1ab_1
- openff-interchange-base=0.2.3=pyhd8ed1ab_1
- openff-toolkit=0.12.1=pyhd8ed1ab_2
- openff-toolkit-base=0.12.1=pyhd8ed1ab_2
- openff-units=0.2.0=pyh1a96a4e_0
- openff-utilities=0.1.8=pyh1a96a4e_0
- openjpeg=2.5.0=h13ac156_2
- openmm=8.0.0=py38h190fa25_0_khronos
- openssl=3.1.1=h8a1eda9_1
- orjson=3.8.10=py38hf03b6bc_0
- packaging=23.1=pyhd8ed1ab_0
- packmol=20.010=h508aa58_0
- palettable=3.3.3=pyhd8ed1ab_0
- pandas=2.0.0=py38hec72209_0
- pandocfilters=1.5.0=pyhd8ed1ab_0
- panedr=0.7.1=pyhd8ed1ab_0
- pango=1.50.14=hbd9bf65_0
- paramiko=3.1.0=pyhd8ed1ab_0
- parmed=3.4.4=py38h4cd09af_0
- parso=0.8.3=pyhd8ed1ab_0
- patsy=0.5.3=pyhd8ed1ab_0
- pbr=5.11.1=pyhd8ed1ab_0
- pcre2=10.40=h1c4e4bc_0
- perl=5.32.1=2_h0d85af4_perl5
- pexpect=4.8.0=pyh1a96a4e_2
- pickleshare=0.7.5=py_1003
- pillow=9.5.0=py38h3c5639a_0
- pint=0.20.1=pyhd8ed1ab_0
- pip=23.1=pyhd8ed1ab_0
- pixman=0.40.0=hbcb3906_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
- platformdirs=3.2.0=pyhd8ed1ab_0
- plotly=5.14.1=pyhd8ed1ab_0
- pluggy=1.0.0=pyhd8ed1ab_5
- pooch=1.7.0=pyha770c72_3
- prometheus_client=0.16.0=pyhd8ed1ab_0
- prompt-toolkit=3.0.38=pyha770c72_0
- prompt_toolkit=3.0.38=hd8ed1ab_0
- psutil=5.9.5=py38hef030d1_0
- pthread-stubs=0.4=hc929b4f_1001
- ptyprocess=0.7.0=pyhd3deb0d_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- py-cpuinfo=9.0.0=pyhd8ed1ab_0
- pybtex=0.24.0=pyhd8ed1ab_2
- pycairo=1.23.0=py38ha545138_0
- pycparser=2.21=pyhd8ed1ab_0
- pydantic=1.10.7=py38hef030d1_0
- pydash=7.0.1=pyh1a96a4e_0
- pyedr=0.7.1=pyhd8ed1ab_0
- pygments=2.15.1=pyhd8ed1ab_0
- pygraphviz=1.10=py38he99214c_3
- pymongo=4.3.3=py38h4cd09af_0
- pynacl=1.5.0=py38hef030d1_2
- pynng=0.7.1=py38h96a0964_0
- pyopenssl=23.1.1=pyhd8ed1ab_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- pyrsistent=0.19.3=py38hef030d1_0
- pysocks=1.7.1=pyha2e5f31_6
- pytables=3.8.0=py38hb4e847d_1
- pytest=7.3.1=pyhd8ed1ab_0
- python=3.8.16=hf9b03c3_1_cpython
- python-constraint=1.4.0=py_0
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-fastjsonschema=2.16.3=pyhd8ed1ab_0
- python-json-logger=2.0.7=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd8ed1ab_0
- python_abi=3.8=3_cp38
- pytng=0.3.0=py38hadfd06d_0
- pytz=2023.3=pyhd8ed1ab_0
- pyyaml=6.0=py38hef030d1_5
- pyzmq=24.0.1=py38h0b711fd_0
- rdkit=2022.09.5=py38h76e2731_0
- readline=8.2=h9e318b2_1
- reportlab=3.6.12=py38hfce4c1c_2
- requests=2.28.2=pyhd8ed1ab_1
- rfc3339-validator=0.1.4=pyhd8ed1ab_0
- rfc3986-validator=0.1.1=pyh9f0ad1d_0
- rich=12.6.0=pyhd8ed1ab_0
- ruamel.yaml=0.17.21=py38hef030d1_3
- ruamel.yaml.clib=0.2.7=py38hef030d1_1
- s3transfer=0.6.0=pyhd8ed1ab_0
- scikit-learn=1.2.2=py38h1081964_1
- scipy=1.10.1=py38h1a492ef_0
- seaborn=0.12.2=hd8ed1ab_0
- seaborn-base=0.12.2=pyhd8ed1ab_0
- send2trash=1.8.0=pyhd8ed1ab_0
- sentinels=1.0.0=py_1
- sentry-sdk=1.20.0=pyhd8ed1ab_0
- setuptools=67.6.1=pyhd8ed1ab_0
- shellingham=1.5.1=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- smirnoff99frosst=1.1.0=pyh44b312d_0
- snappy=1.1.10=h225ccf5_0
- sniffio=1.3.0=pyhd8ed1ab_0
- solvation_analysis=0.3.3=pyhd8ed1ab_0
- soupsieve=2.3.2.post1=pyhd8ed1ab_0
- spglib=2.0.2=py38hbd87e4b_0
- sqlalchemy=2.0.9=py38hef030d1_0
- sshtunnel=0.4.0=pyhd8ed1ab_1
- stack_data=0.6.2=pyhd8ed1ab_0
- starlette=0.26.1=pyhd8ed1ab_0
- statsmodels=0.13.5=py38hbd87e4b_2
- sympy=1.11.1=pypyh9d50eac_103
- tabulate=0.9.0=pyhd8ed1ab_1
- tenacity=8.2.2=pyhd8ed1ab_0
- terminado=0.17.1=pyhd1c38e8_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tidynamics=1.0.0=py_0
- tinycss2=1.2.1=pyhd8ed1ab_0
- tk=8.6.12=h5dbffcc_0
- tomli=2.0.1=pyhd8ed1ab_0
- tornado=6.3=py38hef030d1_0
- tqdm=4.65.0=pyhd8ed1ab_1
- traitlets=5.9.0=pyhd8ed1ab_0
- typer=0.7.0=pyhd8ed1ab_0
- typing-extensions=4.5.0=hd8ed1ab_0
- typing_extensions=4.5.0=pyha770c72_0
- uncertainties=3.1.7=pyhd8ed1ab_0
- unicodedata2=15.0.0=py38hef030d1_0
- urllib3=1.26.15=pyhd8ed1ab_0
- wcwidth=0.2.6=pyhd8ed1ab_0
- webencodings=0.5.1=py_1
- websocket-client=1.5.1=pyhd8ed1ab_0
- werkzeug=2.2.3=pyhd8ed1ab_0
- wheel=0.40.0=pyhd8ed1ab_0
- xmltodict=0.13.0=pyhd8ed1ab_0
- xorg-kbproto=1.0.7=h35c211d_1002
- xorg-libice=1.0.10=h0d85af4_0
- xorg-libsm=1.2.3=h0d85af4_1000
- xorg-libx11=1.8.4=hb7f2c08_0
- xorg-libxau=1.0.9=h35c211d_0
- xorg-libxdmcp=1.1.3=h35c211d_0
- xorg-libxext=1.3.4=hb7f2c08_2
- xorg-libxt=1.2.1=h0d85af4_2
- xorg-xextproto=7.3.0=hb7f2c08_1003
- xorg-xproto=7.0.31=h35c211d_1007
- xz=5.2.6=h775f41a_0
- yaml=0.2.5=h0d85af4_2
- zeromq=4.3.4=he49afe7_1
- zipp=3.15.0=pyhd8ed1ab_0
- zlib=1.2.13=hfd90126_4
- zlib-ng=2.0.7=hb7f2c08_0
- zstd=1.5.2=hbc0c0cd_6
- pip:
- amberlite==22.0
- amberutils==21.0
- arrow==1.2.3
- chardet==5.1.0
- coverage==7.2.6
- fqdn==1.5.1
- ipywidgets==8.0.0
- isoduration==20.11.0
- jsonpointer==2.3
- jupyterlab-widgets==3.0.7
- mmpbsa-py==16.0
- packmol-memgen==1.2.3rc0
- pdb4amber==22.0
- pydot==1.4.2
- pymatgen==2023.3.23
- pymatgen-io-openmm==0.0.1
- pytest-cov==4.1.0
- pytraj==2.0.6
- sander==22.0
- uri-template==1.2.0
- webcolors==1.13
- widgetsnbextension==4.0.7I got the same result with Python 3.9.16.
name: debug_nglview
channels:
- conda-forge
- anaconda
- defaults
dependencies:
- argon2-cffi=21.3.0=pyhd3eb1b0_0
- argon2-cffi-bindings=21.2.0=py39hca72f7f_0
- attrs=21.4.0=pyhd3eb1b0_0
- backcall=0.2.0=pyhd3eb1b0_0
- beautifulsoup4=4.11.1=py39hecd8cb5_0
- biopython=1.81=py39ha30fb19_0
- bleach=4.1.0=pyhd3eb1b0_0
- brotli=1.0.9=hb7f2c08_8
- brotli-bin=1.0.9=hb7f2c08_8
- bzip2=1.0.8=h0d85af4_4
- c-ares=1.19.1=h0dc2134_0
- ca-certificates=2023.5.7=h8857fd0_0
- certifi=2023.5.7=pyhd8ed1ab_0
- cffi=1.15.0=py39hc55c11b_1
- cftime=1.6.2=py39h7cc1f47_1
- colorama=0.4.6=pyhd8ed1ab_0
- curl=8.1.1=h6c40b1e_1
- cycler=0.11.0=pyhd8ed1ab_0
- decorator=5.1.1=pyhd3eb1b0_0
- defusedxml=0.7.1=pyhd3eb1b0_0
- entrypoints=0.4=py39hecd8cb5_0
- fonttools=4.40.0=py39hdc70f33_0
- freetype=2.10.4=h4cff582_1
- giflib=5.2.1=hb7f2c08_3
- griddataformats=1.0.1=pyhd8ed1ab_0
- gsd=3.0.1=py39h57e1da4_0
- h5py=2.10.0=nompi_py39h1bb8402_106
- hdf4=4.2.15=hefd3b78_3
- hdf5=1.10.6=nompi_haae91d6_101
- icu=58.2=h0a44026_3
- ipython_genutils=0.2.0=pyhd3eb1b0_1
- ipywidgets=8.0.0=pyhd8ed1ab_0
- jinja2=3.0.3=pyhd3eb1b0_0
- joblib=1.2.0=pyhd8ed1ab_0
- jpeg=9e=hca72f7f_0
- jsonschema=4.4.0=py39hecd8cb5_0
- jupyter=1.0.0=py39hecd8cb5_7
- jupyter_client=7.2.2=py39hecd8cb5_0
- jupyter_console=6.4.3=pyhd3eb1b0_0
- jupyter_core=4.10.0=py39hecd8cb5_0
- jupyterlab_pygments=0.1.2=py_0
- jupyterlab_widgets=3.0.7=pyhd8ed1ab_1
- kiwisolver=1.4.4=py39h92daf61_1
- krb5=1.20.1=h049b76e_0
- lcms2=2.15=h29502cd_0
- lerc=3.0=he9d5cce_0
- libblas=3.9.0=8_openblas
- libbrotlicommon=1.0.9=hb7f2c08_8
- libbrotlidec=1.0.9=hb7f2c08_8
- libbrotlienc=1.0.9=hb7f2c08_8
- libcblas=3.9.0=8_openblas
- libcurl=8.1.1=hf20ceda_1
- libcxx=14.0.6=h9765a3e_0
- libdeflate=1.17=hac1461d_0
- libedit=3.1.20191231=h0678c8f_2
- libev=4.33=haf1e3a3_1
- libffi=3.4.4=hecd8cb5_0
- libgfortran=4.0.0=7_5_0_h1a10cd1_23
- libgfortran4=7.5.0=h1a10cd1_23
- liblapack=3.9.0=8_openblas
- libnetcdf=4.8.1=nompi_hb4d10b0_100
- libnghttp2=1.52.0=h9beae6a_1
- libopenblas=0.3.12=openmp_h63d9170_1
- libpng=1.6.37=ha441bb4_0
- libsodium=1.0.18=h1de35cc_0
- libssh2=1.10.0=h04015c4_2
- libtiff=4.5.0=hcec6c5f_2
- libwebp=1.2.4=hf6ce154_1
- libwebp-base=1.2.4=h6c40b1e_1
- libzip=1.8.0=h29ab7a1_1
- llvm-openmp=16.0.6=hff08bdf_0
- lz4-c=1.9.4=hf0c8a7f_0
- markupsafe=2.1.1=py39hca72f7f_0
- matplotlib-base=3.5.3=py39h03b9044_0
- mdanalysis=2.2.0=py39hf72b562_0
- mistune=0.8.4=py39h9ed2024_1000
- mmtf-python=1.1.3=pyhd8ed1ab_0
- mrcfile=1.4.3=pyhd8ed1ab_0
- msgpack-python=1.0.5=py39h92daf61_0
- munkres=1.1.4=pyh9f0ad1d_0
- nbclient=0.5.13=py39hecd8cb5_0
- nbconvert=6.4.4=py39hecd8cb5_0
- nbformat=5.3.0=py39hecd8cb5_0
- ncurses=6.4=hcec6c5f_0
- netcdf4=1.6.2=py39hd243f81_0
- networkx=3.1=pyhd8ed1ab_0
- nglview=3.0.6=pyhba93850_0
- notebook=6.4.11=py39hecd8cb5_0
- openssl=3.1.1=h8a1eda9_1
- pandas=2.0.0=py39hecff1ad_0
- pandocfilters=1.5.0=pyhd3eb1b0_0
- parso=0.8.3=pyhd3eb1b0_0
- patsy=0.5.3=pyhd8ed1ab_0
- pexpect=4.8.0=pyhd3eb1b0_3
- pickleshare=0.7.5=pyhd3eb1b0_1003
- pip=23.1.2=py39hecd8cb5_0
- prometheus_client=0.13.1=pyhd3eb1b0_0
- prompt_toolkit=3.0.20=hd3eb1b0_0
- ptyprocess=0.7.0=pyhd3eb1b0_2
- pure_eval=0.2.2=pyhd3eb1b0_0
- pycparser=2.21=pyhd3eb1b0_0
- pyqt=5.9.2=py39h23ab428_6
- pyrsistent=0.18.0=py39hca72f7f_0
- python=3.9.16=h5ee71fb_3
- python-dateutil=2.8.2=pyhd3eb1b0_0
- python-fastjsonschema=2.15.1=pyhd3eb1b0_0
- python-tzdata=2023.3=pyhd8ed1ab_0
- python_abi=3.9=2_cp39
- pytz=2023.3=pyhd8ed1ab_0
- qt=5.9.7=h468cd18_1
- qtconsole=5.3.0=pyhd3eb1b0_0
- qtpy=2.0.1=pyhd3eb1b0_0
- readline=8.2=hca72f7f_0
- scikit-learn=1.2.2=py39h151e6e4_1
- seaborn=0.12.2=hd8ed1ab_0
- seaborn-base=0.12.2=pyhd8ed1ab_0
- send2trash=1.8.0=pyhd3eb1b0_1
- setuptools=67.8.0=py39hecd8cb5_0
- sip=4.19.13=py39h23ab428_0
- six=1.16.0=pyhd3eb1b0_1
- soupsieve=2.3.1=pyhd3eb1b0_0
- sqlite=3.41.2=h6c40b1e_0
- stack_data=0.2.0=pyhd3eb1b0_0
- statsmodels=0.14.0=py39h57e1da4_1
- terminado=0.13.1=py39hecd8cb5_0
- testpath=0.6.0=py39hecd8cb5_0
- threadpoolctl=3.1.0=pyh8a188c0_0
- tidynamics=1.0.0=py_0
- tk=8.6.12=h5d9f67b_0
- tqdm=4.65.0=pyhd8ed1ab_1
- typing_extensions=4.1.1=pyh06a4308_0
- tzdata=2023c=h04d1e81_0
- unicodedata2=15.0.0=py39ha30fb19_0
- webencodings=0.5.1=py39hecd8cb5_1
- wheel=0.38.4=py39hecd8cb5_0
- widgetsnbextension=4.0.7=pyhd8ed1ab_0
- xz=5.4.2=h6c40b1e_0
- zeromq=4.3.4=h23ab428_0
- zlib=1.2.13=h4dc903c_0
- zstd=1.5.5=hc035e20_0
- pip:
- appnope==0.1.3
- asttokens==2.2.1
- comm==0.1.3
- contourpy==1.1.0
- debugpy==1.6.7
- executing==1.2.0
- fasteners==0.18
- importlib-metadata==6.7.0
- ipykernel==6.23.3
- ipython==8.14.0
- jedi==0.18.2
- jupyter-client==8.3.0
- jupyter-core==5.3.1
- matplotlib==3.7.1
- matplotlib-inline==0.1.6
- nest-asyncio==1.5.6
- numpy==1.25.0
- packaging==23.1
- pillow==9.5.0
- platformdirs==3.8.0
- prompt-toolkit==3.0.38
- psutil==5.9.5
- pygments==2.15.1
- pyparsing==3.1.0
- pyzmq==25.1.0
- scipy==1.10.1
- stack-data==0.6.2
- tornado==6.3.2
- traitlets==5.9.0
- typing-extensions==4.6.3
- wcwidth==0.2.6
- zipp==3.15.0um sorry, I don't really know how to debug this issue. By the way, I was using Macbook.
Howdy! I've created an MDAnalysis Universe instance and passed its atoms attribute (count of 740) to nglview.show_mdanalysis, but the rendered image has no atoms/molecules. Example code screen captured below. What's the best approach to debugging here?
Additional context: