id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1942 matplotlib traceback drawing interfaces diagram Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-05-15) Description Traceback from using ""interfaces"" command, perhaps related to using small overall window to make screenshot figures and causing problems for matplotlib to draw the diagram. When I'd tried with an even smaller window and more chains (all of 5cd4) I didn't even get a diagram. Besides small window, salient commands are probably: open 5cd4 delete /a-l interfaces selAtoms Log: UCSF ChimeraX version: 0.9 (2019-05-15) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5cd4 5cd4 title: The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back [more info...] Chain information for 5cd4 #1 --- Chain | Description A M | CRISPR system Cascade subunit CasE B C D E F G N O P Q R S | CRISPR system Cascade subunit CasC H T | CRISPR system Cascade subunit CasD I U | CRISPR system Cascade subunit CasA J K V W | CRISPR system Cascade subunit CasB L X | crRNA Non-standard residues in 5cd4 #1 --- 23G — guanosine-5'-phosphate-2',3'-cyclic phosphate ZN — zinc ion 5cd4 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > sym #1 assembly 1 > view > close #2 > show #!1 models > select /a-l 27069 atoms, 27696 bonds, 27 pseudobonds, 3 models selected > delete sel > view > nucleotides ladder > ribbon nucleic > color /o red > interfaces selAtoms 21 buried areas: S T 2156, R S 1930, Q R 1895, Q P 1886, P O 1878, O N 1807, M X 1503, U T 1376, T X 1324, S X 1287, O X 1219, R X 1158, Q X 1134, P X 1116, N M 1040, N X 636, U S 620, W V 536, U W 535, R W 493, O V 427 /Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/networkx/drawing/nx_pylab.py:611: MatplotlibDeprecationWarning: isinstance(..., numbers.Number) if cb.is_numlike(alpha): /Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/axes/_base.py:1551: RuntimeWarning: divide by zero encountered in double_scalars Xsize = ysize / data_ratio Traceback (most recent call last): File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/backends/backend_qt5.py"", line 519, in _draw_idle self.draw() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/backends/backend_agg.py"", line 402, in draw self.figure.draw(self.renderer) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/artist.py"", line 50, in draw_wrapper return draw(artist, renderer, *args, **kwargs) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/figure.py"", line 1649, in draw renderer, self, artists, self.suppressComposite) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/image.py"", line 138, in _draw_list_compositing_images a.draw(renderer) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/artist.py"", line 50, in draw_wrapper return draw(artist, renderer, *args, **kwargs) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/axes/_base.py"", line 2575, in draw self.apply_aspect() File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/axes/_base.py"", line 1592, in apply_aspect self.set_xbound((x0, x1)) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/axes/_base.py"", line 3097, in set_xbound self.set_xlim(lower, upper, auto=None) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/axes/_base.py"", line 3227, in set_xlim left = self._validate_converted_limits(left, self.convert_xunits) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/matplotlib/axes/_base.py"", line 3139, in _validate_converted_limits raise ValueError(""Axis limits cannot be NaN or Inf"") ValueError: Axis limits cannot be NaN or Inf OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102 OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics can't reproduce all ChimeraX