id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2581 color comparison: numpy stupidity Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-11-15) Description Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-11-15) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b3.dev7-cp37-cp37m-macosx_10_9_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/tic20/Library/Caches/ChimeraX/0.91/installers/ChimeraX_ISOLDE-1.0b3.dev7-cp37-cp37m-macosx_10_9_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /Applications/ChimeraX_Daily.app/Contents/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0b3.dev7) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in /Applications/ChimeraX_Daily.app/Contents/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0b3.dev7) (0.91) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.11 in /Users/tic20/Library/Application Support/ChimeraX/0.91/site-packages (from ChimeraX-ISOLDE==1.0b3.dev7) (0.9.11) Installing collected packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b3.dev6 Uninstalling ChimeraX-ISOLDE-1.0b3.dev6: Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev6 Successfully installed ChimeraX-ISOLDE-1.0b3.dev7 Lock 4506110736 acquired on /Users/tic20/Library/Caches/ChimeraX/0.91/toolshed/bundle_info.cache.lock Lock 4506110736 released on /Users/tic20/Library/Caches/ChimeraX/0.91/toolshed/bundle_info.cache.lock WARNING: You are using pip version 19.2.3, however version 19.3.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. > open 3io0 format mmCIF fromDatabase pdb 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 #1 --- Chain | Description A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > close > open 3io0 structureFactors true Summary of feedback from opening 3io0 fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma, pdbx_anom_difference, pdbx_anom_difference_sigma, intensity_meas, intensity_sigma, pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma Automatically choosing ""intensity_meas, intensity_sigma"". notes | Fetching compressed 3io0 structure factors from http://files.rcsb.org/download/3io0-sf.cif Resolution: 3.003 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... 3io0 title: Crystal structure of EtuB from Clostridium kluyveri [more info...] Chain information for 3io0 --- Chain | Description 1.3/A | EtuB protein 3io0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > addh Summary of feedback from adding hydrogens to 3io0 #1.3 --- notes | Termini for 3io0 (#1.3) chain A determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A PRO 76 Chain-final residues that are actual C termini: /A PHE 304 Chain-final residues that are not actual C termini: Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 62, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 167, in hbond_add_hydrogens _prep_add(session, structures, unknowns_info, template, **prot_schemes) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/addh/cmd.py"", line 423, in _prep_add complete_terminal_carboxylate(session, rc) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/addh/util.py"", line 27, in complete_terminal_carboxylate if c.color == element_colors(c.element.number): ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/addh/util.py"", line 27, in complete_terminal_carboxylate if c.color == element_colors(c.element.number): See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.10.12 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. }}} " defect closed normal Structure Editing fixed all ChimeraX