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nglviewer / nglview

Jupyter widget to interactively view molecular structures and trajectories
http://nglviewer.org/nglview/latest/
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Nglview not showing #1082

Closed samuelmurail closed 5 months ago

samuelmurail commented 7 months ago

Hello,

I have issue with nglview widget not showing with show_pdbid or show_file as the demo works well:

Screenshot from 2023-11-13 13-35-07

Cheers, Samuel

hainm commented 7 months ago

@samuelmurail Hi, is this is lab or notebook?

samuelmurail commented 7 months ago

@hainm Hi, this is notebook but I just test it with jupyter-lab and I have the same issue.

Here a list of the conda package I use that might be related to the issue:

ipykernel                 6.26.0             pyhf8b6a83_0    conda-forge
ipympl                    0.9.3              pyhd8ed1ab_0    conda-forge
ipython                   8.16.1             pyh0d859eb_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.1.1              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0             pyhd8ed1ab_10    conda-forge
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.5.0              pyhd8ed1ab_0    conda-forge
jupyter_console           6.6.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.5.0           py310hff52083_0    conda-forge
jupyter_events            0.8.0              pyhd8ed1ab_0    conda-forge
jupyter_server            2.9.1              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.8              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.25.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.9              pyhd8ed1ab_0    conda-forge
nglview                   3.0.8              pyh1da8cd4_0    conda-forge
nodejs                    20.8.1               h1990674_0    conda-forge
notebook                  7.0.6              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numpy                     1.26.0          py310hb13e2d6_0    conda-forge
python                    3.10.13         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    4_cp310    conda-forge
samuelmurail commented 7 months ago

I create a minimal conda env :

mamba create -n tmp nglview jupyter -c conda-forge
 Package                               Version  Build                Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                           0.1  conda_forge          conda-forge/linux-64     Cached
  + _openmp_mutex                           4.5  2_gnu                conda-forge/linux-64     Cached
  + anyio                                 4.0.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + argon2-cffi                          23.1.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + argon2-cffi-bindings                 21.2.0  py312h98912ed_4      conda-forge/linux-64       35kB
  + arrow                                 1.3.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + asttokens                             2.4.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + async-lru                             2.0.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + attrs                                23.1.0  pyh71513ae_1         conda-forge/noarch       Cached
  + babel                                2.13.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + backports                               1.0  pyhd8ed1ab_3         conda-forge/noarch       Cached
  + backports.functools_lru_cache         1.6.5  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + beautifulsoup4                       4.12.2  pyha770c72_0         conda-forge/noarch       Cached
  + bleach                                6.1.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + brotli-python                         1.1.0  py312h30efb56_1      conda-forge/linux-64      351kB
  + bzip2                                 1.0.8  hd590300_5           conda-forge/linux-64     Cached
  + ca-certificates                   2023.7.22  hbcca054_0           conda-forge/linux-64     Cached
  + cached-property                       1.5.2  hd8ed1ab_1           conda-forge/noarch       Cached
  + cached_property                       1.5.2  pyha770c72_1         conda-forge/noarch       Cached
  + certifi                           2023.7.22  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + cffi                                 1.16.0  py312hf06ca03_0      conda-forge/linux-64      295kB
  + charset-normalizer                    3.3.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + comm                                  0.1.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + debugpy                               1.8.0  py312h30efb56_1      conda-forge/linux-64        3MB
  + decorator                             5.1.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + defusedxml                            0.7.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + entrypoints                             0.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + exceptiongroup                        1.1.3  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + executing                             2.0.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + fqdn                                  1.5.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + gmp                                   6.3.0  h59595ed_0           conda-forge/linux-64      563kB
  + idna                                    3.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + importlib-metadata                    6.8.0  pyha770c72_0         conda-forge/noarch       Cached
  + importlib_metadata                    6.8.0  hd8ed1ab_0           conda-forge/noarch       Cached
  + importlib_resources                   6.1.1  pyhd8ed1ab_0         conda-forge/noarch         30kB
  + ipykernel                            6.26.0  pyhf8b6a83_0         conda-forge/noarch       Cached
  + ipython                              8.17.2  pyh41d4057_0         conda-forge/noarch       Cached
  + ipywidgets                            8.1.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + isoduration                         20.11.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jedi                                 0.19.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jinja2                                3.1.2  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + json5                                0.9.14  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jsonpointer                             2.4  py312h7900ff3_3      conda-forge/linux-64       18kB
  + jsonschema                           4.19.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jsonschema-specifications          2023.7.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jsonschema-with-format-nongpl        4.19.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jupyter                               1.0.0  pyhd8ed1ab_10        conda-forge/noarch       Cached
  + jupyter-lsp                           2.2.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jupyter_client                        8.6.0  pyhd8ed1ab_0         conda-forge/noarch        106kB
  + jupyter_console                       6.6.3  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jupyter_core                          5.5.0  py312h7900ff3_0      conda-forge/linux-64       92kB
  + jupyter_events                        0.9.0  pyhd8ed1ab_0         conda-forge/noarch         21kB
  + jupyter_server                       2.10.0  pyhd8ed1ab_0         conda-forge/noarch        317kB
  + jupyter_server_terminals              0.4.4  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + jupyterlab                            4.0.8  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jupyterlab_pygments                   0.2.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + jupyterlab_server                    2.25.1  pyhd8ed1ab_0         conda-forge/noarch         49kB
  + jupyterlab_widgets                    3.0.9  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + ld_impl_linux-64                       2.40  h41732ed_0           conda-forge/linux-64     Cached
  + libblas                               3.9.0  19_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas                              3.9.0  19_linux64_openblas  conda-forge/linux-64     Cached
  + libexpat                              2.5.0  hcb278e6_1           conda-forge/linux-64     Cached
  + libffi                                3.4.2  h7f98852_5           conda-forge/linux-64     Cached
  + libgcc-ng                            13.2.0  h807b86a_3           conda-forge/linux-64     Cached
  + libgfortran-ng                       13.2.0  h69a702a_3           conda-forge/linux-64     Cached
  + libgfortran5                         13.2.0  ha4646dd_3           conda-forge/linux-64     Cached
  + libgomp                              13.2.0  h807b86a_3           conda-forge/linux-64     Cached
  + liblapack                             3.9.0  19_linux64_openblas  conda-forge/linux-64     Cached
  + libnsl                                2.0.1  hd590300_0           conda-forge/linux-64     Cached
  + libopenblas                          0.3.24  pthreads_h413a1c8_0  conda-forge/linux-64     Cached
  + libsodium                            1.0.18  h36c2ea0_1           conda-forge/linux-64     Cached
  + libsqlite                            3.44.0  h2797004_0           conda-forge/linux-64     Cached
  + libstdcxx-ng                         13.2.0  h7e041cc_3           conda-forge/linux-64     Cached
  + libuuid                              2.38.1  h0b41bf4_0           conda-forge/linux-64     Cached
  + libzlib                              1.2.13  hd590300_5           conda-forge/linux-64     Cached
  + markupsafe                            2.1.3  py312h98912ed_1      conda-forge/linux-64       27kB
  + matplotlib-inline                     0.1.6  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + mistune                               3.0.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + nbclient                              0.8.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + nbconvert                            7.11.0  pyhd8ed1ab_0         conda-forge/noarch          8kB
  + nbconvert-core                       7.11.0  pyhd8ed1ab_0         conda-forge/noarch        188kB
  + nbconvert-pandoc                     7.11.0  pyhd8ed1ab_0         conda-forge/noarch          7kB
  + nbformat                              5.9.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + ncurses                                 6.4  h59595ed_2           conda-forge/linux-64     Cached
  + nest-asyncio                          1.5.8  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + nglview                               3.0.8  pyh1da8cd4_0         conda-forge/noarch       Cached
  + notebook                              7.0.6  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + notebook-shim                         0.2.3  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + numpy                                1.26.0  py312heda63a1_0      conda-forge/linux-64     Cached
  + openssl                               3.1.4  hd590300_0           conda-forge/linux-64     Cached
  + overrides                             7.4.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + packaging                              23.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pandoc                                3.1.3  h32600fe_0           conda-forge/linux-64     Cached
  + pandocfilters                         1.5.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + parso                                 0.8.3  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pexpect                               4.8.0  pyh1a96a4e_2         conda-forge/noarch       Cached
  + pickleshare                           0.7.5  py_1003              conda-forge/noarch       Cached
  + pip                                  23.3.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pkgutil-resolve-name                 1.3.10  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + platformdirs                          4.0.0  pyhd8ed1ab_0         conda-forge/noarch         20kB
  + prometheus_client                    0.18.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + prompt-toolkit                       3.0.40  pyha770c72_0         conda-forge/noarch       Cached
  + prompt_toolkit                       3.0.40  hd8ed1ab_0           conda-forge/noarch       Cached
  + psutil                                5.9.5  py312h98912ed_1      conda-forge/linux-64      481kB
  + ptyprocess                            0.7.0  pyhd3deb0d_0         conda-forge/noarch       Cached
  + pure_eval                             0.2.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pycparser                              2.21  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pygments                             2.16.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pysocks                               1.7.1  pyha2e5f31_6         conda-forge/noarch       Cached
  + python                               3.12.0  hab00c5b_0_cpython   conda-forge/linux-64     Cached
  + python-dateutil                       2.8.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + python-fastjsonschema                2.18.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + python-json-logger                    2.0.7  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + python_abi                             3.12  4_cp312              conda-forge/linux-64     Cached
  + pytz                           2023.3.post1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + pyyaml                                6.0.1  py312h98912ed_1      conda-forge/linux-64      197kB
  + pyzmq                                25.1.1  py312h886d080_2      conda-forge/linux-64      529kB
  + qtconsole-base                        5.5.0  pyha770c72_0         conda-forge/noarch        100kB
  + qtpy                                  2.4.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + readline                                8.2  h8228510_1           conda-forge/linux-64     Cached
  + referencing                          0.30.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + requests                             2.31.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + rfc3339-validator                     0.1.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + rfc3986-validator                     0.1.1  pyh9f0ad1d_0         conda-forge/noarch       Cached
  + rpds-py                              0.12.0  py312h4b3b743_0      conda-forge/linux-64      985kB
  + send2trash                            1.8.2  pyh41d4057_0         conda-forge/noarch       Cached
  + setuptools                           68.2.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + six                                  1.16.0  pyh6c4a22f_0         conda-forge/noarch       Cached
  + sniffio                               1.3.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + soupsieve                               2.5  pyhd8ed1ab_1         conda-forge/noarch       Cached
  + stack_data                            0.6.2  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + terminado                            0.18.0  pyh0d859eb_0         conda-forge/noarch         22kB
  + tinycss2                              1.2.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + tk                                   8.6.13  noxft_h4845f30_101   conda-forge/linux-64     Cached
  + tomli                                 2.0.1  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + tornado                               6.3.3  py312h98912ed_1      conda-forge/linux-64      830kB
  + traitlets                            5.13.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + types-python-dateutil             2.8.19.14  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + typing-extensions                     4.8.0  hd8ed1ab_0           conda-forge/noarch       Cached
  + typing_extensions                     4.8.0  pyha770c72_0         conda-forge/noarch       Cached
  + typing_utils                          0.1.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + tzdata                                2023c  h71feb2d_0           conda-forge/noarch       Cached
  + uri-template                          1.3.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + urllib3                               2.1.0  pyhd8ed1ab_0         conda-forge/noarch         85kB
  + wcwidth                               0.2.9  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + webcolors                              1.13  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + webencodings                          0.5.1  pyhd8ed1ab_2         conda-forge/noarch       Cached
  + websocket-client                      1.6.4  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + wheel                                0.41.3  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + widgetsnbextension                    4.0.9  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + xz                                    5.2.6  h166bdaf_0           conda-forge/linux-64     Cached
  + yaml                                  0.2.5  h7f98852_2           conda-forge/linux-64     Cached
  + zeromq                                4.3.5  h59595ed_0           conda-forge/linux-64     Cached
  + zipp                                 3.17.0  pyhd8ed1ab_0         conda-forge/noarch       Cached
  + zlib                                 1.2.13  hd590300_5           conda-forge/linux-64     Cached

I still have the same issue with firefox and chromium-browser, I am running ubuntu 22.04. I hope that could help.

Cheers, Samuel

hainm commented 7 months ago

@samuelmurail I could reproduce the issue. Let me investigate.

hainm commented 7 months ago

if I download the 3pqr.pdb to local disk

nv.show_file('./3pqr.pdb') does NOT work
nv.show_structure_file('./3pqr.pdb') work

um

hainm commented 7 months ago
image

um, does the CIF format has change that NGL (nglview uses it) doesn't know how to parse it?

samuelmurail commented 7 months ago

Yes I confirm that using show_structure_file() fix the issue.

Cheers, Samuel

hainm commented 7 months ago
hainm commented 5 months ago

nglview.show_file should work properly in 3.1.0 now. If not, please file a new case. Thanks.