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Opened 6 years ago
Closed 6 years ago
#2197 closed defect (fixed)
map-open func sometimes returns None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-07-02) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-07-02) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:quickstart > open /Users/umeyou/Downloads/chimerax_tutorial/6n2y.cif Summary of feedback from opening /Users/umeyou/Downloads/chimerax_tutorial/6n2y.cif --- notes | Fetching CCD ATP from http://ligand- expo.rcsb.org/reports/A/ATP/ATP.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD PO4 from http://ligand-expo.rcsb.org/reports/P/PO4/PO4.cif Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif 6n2y.cif title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y.cif #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y.cif #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > show target m > select /A:2-501 3827 atoms, 3888 bonds, 1 model selected Downloading bundle ChimeraX_ISOLDE-1.0b3.dev1-cp37-cp37m-macosx_10_9_x86_64.whl Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /Users/umeyou/Downloads/ChimeraX_ISOLDE-1.0b3.dev1-cp37-cp37m-macosx_10_9_x86_64.whl Collecting ChimeraX-Clipper>=0.9.6 (from ChimeraX-ISOLDE==1.0b3.dev1) Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.9.6/ChimeraX_Clipper-0.9.6-cp37-cp37m-macosx_10_9_x86_64.whl (36.2MB) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/lib/python3.7/site- packages (from ChimeraX-ISOLDE==1.0b3.dev1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in /private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/lib/python3.7/site- packages (from ChimeraX-ISOLDE==1.0b3.dev1) (0.91) Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE ERROR: Could not install packages due to an EnvironmentError: [Errno 30] Read- only file system: '/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages' Downloading bundle ChimeraX_ISOLDE-1.0b3.dev1-cp37-cp37m-macosx_10_9_x86_64.whl Successfully installed ChimeraX-Clipper-0.9.6 ChimeraX-ISOLDE-1.0b3.dev1 Installed ChimeraX-Clipper (0.9.6) Installed ChimeraX-ISOLDE (1.0b3.dev1) > select :ADP 27 atoms, 29 bonds, 1 model selected > style selAtoms stick Changed 27 atom styles > style selAtoms stick Changed 27 atom styles > select clear > select /B:140@NH2 1 atom, 1 model selected > select clear > select clear > select up Nothing selected > select up Nothing selected > select clear > select /B:248@CE1 1 atom, 1 model selected > select /B:140@NH2 1 atom, 1 model selected > select /B:141@O 1 atom, 1 model selected > select clear > select clear > select /b1/b2 1743 atoms, 1755 bonds, 1 model selected > select clear > select /B:2-501 3787 atoms, 3846 bonds, 1 model selected > select ~sel 31256 atoms, 31733 bonds, 13 pseudobonds, 3 models selected > style selAtoms stick Changed 31256 atom styles > select clear > select /B:2-501 3787 atoms, 3846 bonds, 1 model selected > style selAtoms stick Changed 3787 atom styles > select clear > select clear > hide selAtoms > show selAtoms ribbons > show selAtoms ribbons > preset "initial styles" "original look" Preset implemented in Python; no expansion to individual ChimeraX commands available. > hide > show ribbons > preset "initial styles" "original look" Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting simple > lighting soft > lighting full > lighting full > lighting soft > lighting simple > lighting full > lighting soft > lighting full > set bgColor black > lighting simple > lighting full > lighting soft > lighting simple > lighting full > lighting simple > lighting soft > lighting full > lighting simple > lighting full > set bgColor white > save /Users/umeyou/Desktop/image1.png supersample 3 Empty filename passed to function Empty filename passed to function > save image /Users/umeyou/image1.png width 1500 height 1680 > show selAtoms surfaces > color bfactor selAtoms 35043 atoms, 4722 residues, 22 surfaces, atom bfactor range 0 to 144 > mlp selAtoms Map values for surface "6n2y.cif_A SES surface": minimum -49.67, mean -9.103, maximum 22.97 Map values for surface "6n2y.cif_B SES surface": minimum -54.79, mean -9.429, maximum 23.24 Map values for surface "6n2y.cif_C SES surface": minimum -48.93, mean -9.469, maximum 24.15 Map values for surface "6n2y.cif_D SES surface": minimum -49.82, mean -8.614, maximum 25.56 Map values for surface "6n2y.cif_E SES surface": minimum -49, mean -8.976, maximum 23.87 Map values for surface "6n2y.cif_F SES surface": minimum -49.92, mean -8.684, maximum 22.56 Map values for surface "6n2y.cif_G SES surface": minimum -43.34, mean -8.507, maximum 22.41 Map values for surface "6n2y.cif_H SES surface": minimum -43.27, mean -8.606, maximum 23.31 Map values for surface "6n2y.cif_I SES surface": minimum -46.41, mean -8.739, maximum 25.32 Map values for surface "6n2y.cif_b2 SES surface": minimum -42.06, mean -10.19, maximum 22.08 Map values for surface "6n2y.cif_b1 SES surface": minimum -44.2, mean -11.65, maximum 22.09 Map values for surface "6n2y.cif_a SES surface": minimum -47.69, mean -5.122, maximum 23.05 Map values for surface "6n2y.cif_c0 SES surface": minimum -39.73, mean -4.977, maximum 22.62 Map values for surface "6n2y.cif_c1 SES surface": minimum -39.53, mean -4.684, maximum 21.9 Map values for surface "6n2y.cif_c2 SES surface": minimum -40.37, mean -4.997, maximum 22.64 Map values for surface "6n2y.cif_c3 SES surface": minimum -38.97, mean -4.955, maximum 22.04 Map values for surface "6n2y.cif_c4 SES surface": minimum -40.82, mean -5.091, maximum 21.96 Map values for surface "6n2y.cif_c5 SES surface": minimum -42.06, mean -5.229, maximum 22.34 Map values for surface "6n2y.cif_c6 SES surface": minimum -38.51, mean -5.224, maximum 22.54 Map values for surface "6n2y.cif_c7 SES surface": minimum -41.11, mean -4.995, maximum 21.92 Map values for surface "6n2y.cif_c8 SES surface": minimum -40.72, mean -5.006, maximum 22.67 Map values for surface "6n2y.cif_c9 SES surface": minimum -39.75, mean -4.963, maximum 22.49 > color bfactor selAtoms 35043 atoms, 4722 residues, 22 surfaces, atom bfactor range 0 to 144 > mlp selAtoms Map values for surface "6n2y.cif_A SES surface": minimum -49.67, mean -9.103, maximum 22.97 Map values for surface "6n2y.cif_B SES surface": minimum -54.79, mean -9.429, maximum 23.24 Map values for surface "6n2y.cif_C SES surface": minimum -48.93, mean -9.469, maximum 24.15 Map values for surface "6n2y.cif_D SES surface": minimum -49.82, mean -8.614, maximum 25.56 Map values for surface "6n2y.cif_E SES surface": minimum -49, mean -8.976, maximum 23.87 Map values for surface "6n2y.cif_F SES surface": minimum -49.92, mean -8.684, maximum 22.56 Map values for surface "6n2y.cif_G SES surface": minimum -43.34, mean -8.507, maximum 22.41 Map values for surface "6n2y.cif_H SES surface": minimum -43.27, mean -8.606, maximum 23.31 Map values for surface "6n2y.cif_I SES surface": minimum -46.41, mean -8.739, maximum 25.32 Map values for surface "6n2y.cif_b2 SES surface": minimum -42.06, mean -10.19, maximum 22.08 Map values for surface "6n2y.cif_b1 SES surface": minimum -44.2, mean -11.65, maximum 22.09 Map values for surface "6n2y.cif_a SES surface": minimum -47.69, mean -5.122, maximum 23.05 Map values for surface "6n2y.cif_c0 SES surface": minimum -39.73, mean -4.977, maximum 22.62 Map values for surface "6n2y.cif_c1 SES surface": minimum -39.53, mean -4.684, maximum 21.9 Map values for surface "6n2y.cif_c2 SES surface": minimum -40.37, mean -4.997, maximum 22.64 Map values for surface "6n2y.cif_c3 SES surface": minimum -38.97, mean -4.955, maximum 22.04 Map values for surface "6n2y.cif_c4 SES surface": minimum -40.82, mean -5.091, maximum 21.96 Map values for surface "6n2y.cif_c5 SES surface": minimum -42.06, mean -5.229, maximum 22.34 Map values for surface "6n2y.cif_c6 SES surface": minimum -38.51, mean -5.224, maximum 22.54 Map values for surface "6n2y.cif_c7 SES surface": minimum -41.11, mean -4.995, maximum 21.92 Map values for surface "6n2y.cif_c8 SES surface": minimum -40.72, mean -5.006, maximum 22.67 Map values for surface "6n2y.cif_c9 SES surface": minimum -39.75, mean -4.963, maximum 22.49 > hide selAtoms > hide selAtoms > show selAtoms > hide selAtoms > mlp selAtoms Map values for surface "6n2y.cif_A SES surface": minimum -49.67, mean -9.103, maximum 22.97 Map values for surface "6n2y.cif_B SES surface": minimum -54.79, mean -9.429, maximum 23.24 Map values for surface "6n2y.cif_C SES surface": minimum -48.93, mean -9.469, maximum 24.15 Map values for surface "6n2y.cif_D SES surface": minimum -49.82, mean -8.614, maximum 25.56 Map values for surface "6n2y.cif_E SES surface": minimum -49, mean -8.976, maximum 23.87 Map values for surface "6n2y.cif_F SES surface": minimum -49.92, mean -8.684, maximum 22.56 Map values for surface "6n2y.cif_G SES surface": minimum -43.34, mean -8.507, maximum 22.41 Map values for surface "6n2y.cif_H SES surface": minimum -43.27, mean -8.606, maximum 23.31 Map values for surface "6n2y.cif_I SES surface": minimum -46.41, mean -8.739, maximum 25.32 Map values for surface "6n2y.cif_b2 SES surface": minimum -42.06, mean -10.19, maximum 22.08 Map values for surface "6n2y.cif_b1 SES surface": minimum -44.2, mean -11.65, maximum 22.09 Map values for surface "6n2y.cif_a SES surface": minimum -47.69, mean -5.122, maximum 23.05 Map values for surface "6n2y.cif_c0 SES surface": minimum -39.73, mean -4.977, maximum 22.62 Map values for surface "6n2y.cif_c1 SES surface": minimum -39.53, mean -4.684, maximum 21.9 Map values for surface "6n2y.cif_c2 SES surface": minimum -40.37, mean -4.997, maximum 22.64 Map values for surface "6n2y.cif_c3 SES surface": minimum -38.97, mean -4.955, maximum 22.04 Map values for surface "6n2y.cif_c4 SES surface": minimum -40.82, mean -5.091, maximum 21.96 Map values for surface "6n2y.cif_c5 SES surface": minimum -42.06, mean -5.229, maximum 22.34 Map values for surface "6n2y.cif_c6 SES surface": minimum -38.51, mean -5.224, maximum 22.54 Map values for surface "6n2y.cif_c7 SES surface": minimum -41.11, mean -4.995, maximum 21.92 Map values for surface "6n2y.cif_c8 SES surface": minimum -40.72, mean -5.006, maximum 22.67 Map values for surface "6n2y.cif_c9 SES surface": minimum -39.75, mean -4.963, maximum 22.49 > color selAtoms bychain > color bypolymer > select /A/B/C 11476 atoms, 11659 bonds, 9 pseudobonds, 2 models selected > color sel orange > select clear > set bgColor black > open /Users/umeyou/Downloads/chimerax_tutorial/6n2z.cif 6n2z.cif title: Bacillus PS3 ATP synthase class 2 [more info...] Chain information for 6n2z.cif #2 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | Bacillus PS3 ATP synthase subunit δ a | Bacillus PS3 ATP synthase subunit a b1 | Bacillus PS3 ATP synthase subunit b b2 | Bacillus PS3 ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2z.cif #2 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open /Users/umeyou/Downloads/chimerax_tutorial/6n30.cif 6n30.cif title: Bacillus PS3 ATP synthase class 3 [more info...] Chain information for 6n30.cif #3 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | Bacillus PS3 ATP synthase subunit δ a | Bacillus PS3 ATP synthase subunit a b1 | Bacillus PS3 ATP synthase subunit b b2 | Bacillus PS3 ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n30.cif #3 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > lighting simple > lighting full > show selAtoms > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > morph #1,2 Computed 21 frame morph #4 > coordset #4 1,21 > hide #!3 models > show #!3 models > hide #!3 models > lighting simple > style selAtoms sphere Changed 139673 atom styles > select clear > select ~sel 139673 atoms, 141821 bonds, 43 pseudobonds, 11 models selected > style selAtoms sphere Changed 139673 atom styles Expected a keyword > select clear Expected a keyword Expected a keyword > hide #!4 models > show #!1 models > show #!2 models > show #!3 models Expected a keyword Expected a keyword > close #4 Expected a keyword > hide #!1 models > hide #!2 models > hide #!3 models > show #!1 models > show #!2 models > show #!3 models Expected a keyword > close #3 > close > open /Users/umeyou/Downloads/chimerax_tutorial/6n2y.cif 6n2y.cif title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y.cif #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y.cif #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open /Users/umeyou/Downloads/chimerax_tutorial/6n2y.cif 6n2y.cif title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y.cif #2 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y.cif #2 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open /Users/umeyou/Downloads/chimerax_tutorial/6n30.cif 6n30.cif title: Bacillus PS3 ATP synthase class 3 [more info...] Chain information for 6n30.cif #3 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | Bacillus PS3 ATP synthase subunit δ a | Bacillus PS3 ATP synthase subunit a b1 | Bacillus PS3 ATP synthase subunit b b2 | Bacillus PS3 ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n30.cif #3 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion Expected a keyword Expected a keyword Expected a keyword > morph #1,2,3 Computed 41 frame morph #4 > coordset #4 1,41 > lighting simple > close > open /Users/umeyou/Downloads/chimerax_tutorial/6n2y.cif 6n2y.cif title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y.cif #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y.cif #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open /Users/umeyou/Downloads/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2646, in run result = ci.function(session, **kw_args) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open /Users/umeyou/Downloads/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2646, in run result = ci.function(session, **kw_args) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open 9333 fromDatabase emdb Summary of feedback from opening 9333 fetched from emdb --- note | Fetching compressed map 9333 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-9333/map/emd_9333.map.gz Traceback (most recent call last): File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2646, in run result = ci.function(session, **kw_args) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 44, in open db_models, status = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 150, in _fetch_from_database _handle_unexpected_keyword_error(e, 4) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 148, in _fetch_from_database ignore_cache=ignore_cache, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py", line 434, in fetch_from_database models, status = df.fetch(session, id, format=format, ignore_cache=ignore_cache, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py", line 497, in fetch return fetch(session, database_id, ignore_cache=ignore_cache, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/emdb_fetch.py", line 48, in fetch_emdb models, status = io.open_data(session, filename, format = 'ccp4', name = emdb_id, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open /Users/umeyou/Downloads/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2646, in run result = ci.function(session, **kw_args) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "/private/var/folders/0w/lp86bt490_l59jj1p_xpb9wh0000gn/T/AppTranslocation/AD49DDD1-93AD-4A46-A8E2-3D86E1E6F8E7/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.9.22 OpenGL renderer: Intel(R) Iris(TM) Graphics 550 OpenGL vendor: Intel Inc.
Change History (5)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → map-open func sometimes returns None |
comment:2 by , 6 years ago
| Reporter: | changed from to |
|---|
comment:3 by , 6 years ago
comment:4 by , 6 years ago
From #2199:
Greetings,
For whatever reason, *.map files are loading with no problems in chimerax - as they always did with chimera - today -
Thank you,
Matt
comment:5 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
The density map file format registration got messed up by toolshed installing ISOLDE at the beginning of this session. It ended up using an incorrect open_file() method in the map bundle. I removed that incorrect open_file() function.
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Reported by Matt Sachs