matplotlib inline problem

[freedom00y]

I tried to use the pychimera in the notebook. I tried to plot something inline using the command “%matplotlib inline”. When I run some code related with plots in “pychimera notebook”, it will show errors. But when I run the same code in “jupiter notebook”, it run successfully. I’d like to know how to solve this problem.

Here is my code and error message:

Code

from pychimera import enable_chimera, enable_chimera_inline, chimera_view enable_chimera() enable_chimera_inline() import chimera import numpy as np import matplotlib.pyplot as plt %matplotlib inline

a = np.arange(10) plt.hist(a) plt.show()

Error message

---

AttributeError Traceback (most recent call last)

in () 10 a = np.arange(10) 11 plt.hist(a) ---> 12 plt.show() /Users/zhouhuiya/anaconda3/envs/pychimera/lib/python2.7/site-packages/ipykernel/pylab/backend_inline.pyc in show(close, block) 37 display( 38 figure_manager.canvas.figure, ---> 39 metadata=_fetch_figure_metadata(figure_manager.canvas.figure) 40 ) 41 finally: /Users/zhouhuiya/anaconda3/envs/pychimera/lib/python2.7/site-packages/ipykernel/pylab/backend_inline.pyc in _fetch_figure_metadata(fig) 172 """Get some metadata to help with displaying a figure.""" 173 # determine if a background is needed for legibility --> 174 if _is_transparent(fig.get_facecolor()): 175 # the background is transparent 176 ticksLight = _is_light([label.get_color() /Users/zhouhuiya/anaconda3/envs/pychimera/lib/python2.7/site-packages/ipykernel/pylab/backend_inline.pyc in _is_transparent(color) 193 def _is_transparent(color): 194 """Determine transparency from alpha.""" --> 195 rgba = colors.to_rgba(color) 196 return rgba[3] < .5 AttributeError: 'module' object has no attribute 'to_rgba' **Here is my conda list:** # Name Version Build Channel appnope 0.1.0 py27hb466136_0 attrs 19.1.0 py27_1 backports 1.0 py_2 backports.functools_lru_cache 1.5 py_2 backports.shutil_get_terminal_size 1.0.0 py27_2 backports_abc 0.5 py27h6972548_0 blas 1.0 openblas bleach 3.1.0 py27_0 certifi 2019.11.28 py27_0 configparser 3.7.4 py27_0 cycler 0.10.0 py27hfc73c78_0 dbus 1.13.6 h90a0687_0 decorator 4.4.0 py27_1 defusedxml 0.6.0 py_0 entrypoints 0.3 py27_0 enum34 1.1.6 py27_1 expat 2.2.6 h0a44026_0 freetype 2.9.1 hb4e5f40_0 functools32 3.2.3.2 py27_1 futures 3.3.0 py27_0 gettext 0.19.8.1 h15daf44_3 glib 2.56.2 hd9629dc_0 icu 58.2 h4b95b61_1 ipaddress 1.0.22 py27_0 ipykernel 4.10.0 py27_0 ipython 5.8.0 py27_0 ipython_genutils 0.2.0 py27h8b9a179_0 ipywidgets 7.5.1 py_0 jinja2 2.10.1 py27_0 jpeg 9b he5867d9_2 jsonschema 3.0.2 py27_0 jupyter 1.0.0 py27_7 jupyter_client 5.3.1 py_0 jupyter_console 5.2.0 py27_1 jupyter_core 4.5.0 py_0 kiwisolver 1.1.0 py27h0a44026_0 libcxx 4.0.1 hcfea43d_1 libcxxabi 4.0.1 hcfea43d_1 libedit 3.1.20181209 hb402a30_0 libffi 3.2.1 h475c297_4 libgfortran 3.0.1 h93005f0_2 libiconv 1.15 hdd342a3_7 libopenblas 0.3.6 hdc02c5d_1 libpng 1.6.37 ha441bb4_0 libsodium 1.0.16 h3efe00b_0 markupsafe 1.1.1 py27h1de35cc_0 matplotlib 2.2.4 pypi_0 pypi mistune 0.8.4 py27h1de35cc_0 nbconvert 5.5.0 py_0 nbformat 4.4.0 py27hddc86d0_0 ncurses 6.1 h0a44026_1 nglview 1.1.7 py_0 bioconda nomkl 3.0 0 notebook 5.7.8 py27_0 numpy 1.16.4 py27h926163e_0 numpy-base 1.16.4 py27ha711998_0 pandoc 2.2.3.2 0 pandocfilters 1.4.2 py27_1 pathlib2 2.3.4 py27_0 pcre 8.43 h0a44026_0 pexpect 4.7.0 py27_0 pickleshare 0.7.5 py27_0 pip 19.2.2 py27_0 prometheus_client 0.7.1 py_0 prompt_toolkit 1.0.15 py27h4a7b9c2_0 ptyprocess 0.6.0 py27_0 pychimera 0.2.7 py27_0 insilichem pygments 2.4.2 py_0 pyparsing 2.4.2 py_0 pyqt 5.9.2 py27h655552a_2 pyrsistent 0.14.11 py27h1de35cc_0 python 2.7.16 h97142e2_4 python-dateutil 2.8.0 py27_0 pytz 2019.2 py_0 pyzmq 18.1.0 py27h0a44026_0 qt 5.9.7 h468cd18_1 qtconsole 4.5.3 py_0 readline 7.0 h1de35cc_5 scandir 1.10.0 py27h1de35cc_0 send2trash 1.5.0 py27_0 setuptools 41.0.1 py27_0 simplegeneric 0.8.1 py27_2 singledispatch 3.4.0.3 py27he22c18d_0 sip 4.19.8 py27h0a44026_0 six 1.12.0 py27_0 sqlite 3.29.0 ha441bb4_0 subprocess32 3.5.4 py27h1de35cc_0 terminado 0.8.2 py27_0 testpath 0.4.2 py27_0 tk 8.6.8 ha441bb4_0 tornado 5.1.1 py27h1de35cc_0 traitlets 4.3.2 py27hcf08151_0 wcwidth 0.1.7 py27h817c265_0 webencodings 0.5.1 py27_1 wheel 0.33.4 py27_0 widgetsnbextension 3.5.1 py27_0 zeromq 4.3.1 h0a44026_3 zlib 1.2.11 h1de35cc_3 **Python version:** Python 2.7.16 :: Anaconda, Inc.

[jaimergp]

I suspect this has to do with the version of matplotlib Chimera itself ships, which will get loaded before the one in your conda env.

This is not an easy problem to solve, but the quickest (and dirtiest) way to do it is to remove matplotlib from UCSF Chimera. Since this will affect the extension inside Chimera, I would recommend having a separate installation (maybe the headless one?) that you can modify without fear. You can point to that separate installation for pychimera using the CHIMERADIR environment variable.

To uninstall libraries already present in Chimera, you need to install pip first in Chimera, and then use that one to remove whatever you need. Let me know if you need help in this step.

[freedom00y]

So can I use the matplotlib package in Chimera?

[jaimergp]

In principle, yes. Try to follow the instructions above and let me know if it works for you!

A second alternative would be:

1. Use pychimera notebook to generate all the numeric data you want to plot, but do not import matplotlib yet. Save the data to disk (via pickle, numpy.save, pandas.Dataframe.to_csv, etc). Get rid of all chimera objects so you can use the data without pychimera!
2. In a separate instance, run jupyter notebook and load the data. You will be able to plot it with matplotlib just fine.