Yuhan-Fei commented 2 years ago

I opened the jupyer-notebook by using "pychimera notebook" successfully. However, I got the "ValueError: missing default material" when I used both two command below: ####################################### import chimera print chimera.MaterialColor(1, 1, 1)

import DockPrep ####################################### Is there anyway to solve this problem? Thanks!

jaimergp commented 2 years ago

This is usually a problem with libraries being loaded. I'll need some more info:

conda info --all
conda activate <your pychimera environment> followed by conda list

Yuhan-Fei commented 2 years ago

After I enter the pychimera environment, and input "conda list" in the terminal. I got the list as follow: #

Name Version Build Channel

_libgcc_mutex 0.1 main _openmp_mutex 4.5 1_gnu backports 1.0 pyhd3eb1b0_2 backports-functools-lru-cache 1.6.4 pypi_0 pypi backports.shutil_get_terminal_size 1.0.0 pyhd3eb1b0_3 backports_abc 0.5 py_1 blas 1.0 mkl bleach 1.4.2 py27_0 bioconda ca-certificates 2021.5.30 ha878542_0 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge configparser 4.0.2 py27_0 dbus 1.13.18 hb2f20db_0 decorator 4.4.2 pyhd3eb1b0_0 defusedxml 0.7.1 pyhd3eb1b0_0 entrypoints 0.3 py27_0 enum34 1.1.6 py27_1 expat 2.4.1 h2531618_2 fontconfig 2.13.0 h0c61d53_4 conda-forge freetype 2.8.1 hfa320df_1 conda-forge functools32 3.2.3.2 py27_1 futures 3.3.0 py27_0 gettext 0.19.8.1 h0b5b191_1005 conda-forge glib 2.55.0 0 conda-forge gst-plugins-base 1.12.5 h3865690_1000 conda-forge gstreamer 1.12.5 h61a6719_0 conda-forge html5lib 1.1 pyhd3eb1b0_0 icu 58.2 he6710b0_3 intel-openmp 2021.3.0 h06a4308_3350 ipaddress 1.0.23 py_0 ipykernel 4.10.0 py27_0 ipython 5.8.0 py27_0 ipython_genutils 0.2.0 pyhd3eb1b0_1 ipywidgets 7.6.0 pyhd3eb1b0_1 jinja2 2.11.3 pyhd3eb1b0_0 jpeg 9d h7f8727e_0 jsonschema 2.6.0 py27_0 jupyter 1.0.0 py27_7 jupyter_client 5.3.4 py27_0 jupyter_console 5.2.0 py27_1 jupyter_core 4.6.1 py27_0 libffi 3.3 he6710b0_2 libgcc-ng 9.3.0 h5101ec6_17 libgfortran-ng 7.5.0 ha8ba4b0_17 libgfortran4 7.5.0 ha8ba4b0_17 libgomp 9.3.0 h5101ec6_17 libiconv 1.15 h516909a_1006 conda-forge libpng 1.6.37 hbc83047_0 libsodium 1.0.18 h7b6447c_0 libstdcxx-ng 9.3.0 hd4cf53a_17 libuuid 1.0.3 h1bed415_2 libxcb 1.14 h7b6447c_0 libxml2 2.9.12 h03d6c58_0 markupsafe 1.1.1 py27h7b6447c_0 mistune 0.8.4 py27h7b6447c_0 mkl 2021.3.0 h06a4308_520 nbconvert 5.6.1 py27_0 nbformat 4.4.0 py27_0 ncurses 6.2 he6710b0_1 nglview 1.1.7 py_0 bioconda notebook 5.7.10 py27_0 numpy 1.14.2 py27hdbf6ddf_0 openssl 1.0.2u h516909a_0 conda-forge pandoc 2.12 h06a4308_0 pandocfilters 1.4.2 py27_1 pathlib2 2.3.5 py27_0 pcre 8.39 0 conda-forge pexpect 4.8.0 pyhd3eb1b0_3 pickleshare 0.7.5 py27_0 pip 19.3.1 py27_0 prometheus_client 0.11.0 pyhd3eb1b0_0 prompt_toolkit 1.0.15 py27_0 ptyprocess 0.7.0 pyhd3eb1b0_2 pychimera 0.2.1 py27h9188f34_0 insilichem pygments 2.5.2 py_0 pyqt 5.9.2 py27h751905a_0 python 2.7.18 ha1903f6_2 python-dateutil 2.8.2 pyhd3eb1b0_0 python_abi 2.7 1_cp27mu conda-forge pyzmq 18.1.0 py27he6710b0_0 qt 5.9.4 h4e5bff0_0 qtconsole 4.7.7 py_0 qtpy 1.10.0 pyhd3eb1b0_0 readline 8.1 h27cfd23_0 scandir 1.10.0 pyh5d7bf9c_3 send2trash 1.5.0 pyhd3eb1b0_1 setuptools 44.0.0 py27_0 simplegeneric 0.8.1 py27_2 singledispatch 3.7.0 pyhd3eb1b0_1001 sip 4.19.8 py27hf484d3e_0 six 1.16.0 pyhd3eb1b0_0 sqlite 3.36.0 hc218d9a_0 terminado 0.8.3 py27_0 testpath 0.4.4 pyhd3eb1b0_0 tk 8.6.10 hbc83047_0 tornado 5.1.1 py27h7b6447c_0 traitlets 4.3.3 py27_0 wcwidth 0.2.5 pyhd3eb1b0_0 webencodings 0.5.1 py27_1 wheel 0.37.0 pyhd3eb1b0_1 widgetsnbextension 3.5.1 py27_0 xz 5.2.5 h7b6447c_0 zeromq 4.3.4 h2531618_0 zlib 1.2.11 h7b6447c_3

insilichem / pychimera

ValueError: missing default material #18

Name Version Build Channel