id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14954 Crash in garbage collection yakonfire@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000000017a567000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000177543000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000016f063000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ff60fac0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 59 in update File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 19 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py"", line 90 in copy File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 642 in _try File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 665 in _option File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 137 in __enter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 168 in _model_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 157 in block0 File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 787 in _positive_closure File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 159 in _model_list_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 136 in _as_term_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py"", line 89 in _atom_specifier_ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 497 in _invoke_rule File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 458 in _call File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 59 in wrapper File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py"", line 206 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 192 in _parse_unquoted File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 121 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py"", line 180 in defattr File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 81 in add_standard_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py"", line 34 in add_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 110 in assign_charges File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3468 in __call__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2929 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py"", line 184 in _run_commands File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py"", line 61 in run_command_script File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py"", line 51 in runscript File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, 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===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T114 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 2 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T114/T114_contacts_hbonds_rot.mp4 Changed 1591 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T114/T114_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.23, mean -4.14, maximum 10.47 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -10.42, mean -0.28, maximum 10.68 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T114/T114_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -33.89, mean -5.556, maximum 25.37 Map values for surface ""best_model.pdb_B SES surface"": minimum -28.27, mean -4.359, maximum 25.61 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T114/T114_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T114/T114_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T115 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/grako/ast.py"", line 63, in update for d in args: TypeError: NoneType takes no arguments 13 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T115/T115_contacts_hbonds_rot.mp4 Changed 1967 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T115/T115_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.97, mean -4.44, maximum 11.92 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.18, mean -0.12, maximum 14.03 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T115/T115_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -27.82, mean -5.541, maximum 26.28 Map values for surface ""best_model.pdb_B SES surface"": minimum -26.13, mean -3.721, maximum 22.6 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T115/T115_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T115/T115_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T116 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 2 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T116/T116_contacts_hbonds_rot.mp4 Changed 1963 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T116/T116_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.69, mean -4.04, maximum 11.91 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -18.26, mean -1.14, maximum 10.07 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T116/T116_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -25.18, mean -5.076, maximum 23.22 Map values for surface ""best_model.pdb_B SES surface"": minimum -24.51, mean -0.2534, maximum 23.12 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T116/T116_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T116/T116_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T117 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 7 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T117/T117_contacts_hbonds_rot.mp4 Changed 2188 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T117/T117_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.97, mean -5.18, maximum 11.74 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -11.49, mean -0.01, maximum 12.92 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T117/T117_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -24.83, mean -4.713, maximum 23.71 Map values for surface ""best_model.pdb_B SES surface"": minimum -26.96, mean -3.615, maximum 22.23 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T117/T117_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T117/T117_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T118 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 2 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T118/T118_contacts_hbonds_rot.mp4 Changed 2432 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T118/T118_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.25, mean -3.88, maximum 12.91 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.78, mean -1.43, maximum 12.45 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T118/T118_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -28.85, mean -5.105, maximum 24.32 Map values for surface ""best_model.pdb_B SES surface"": minimum -26.97, mean -2.082, maximum 26.52 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T118/T118_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T118/T118_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T119 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 2 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T119/T119_contacts_hbonds_rot.mp4 Changed 2455 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T119/T119_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -23.33, mean -4.23, maximum 12.18 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.27, mean -1.20, maximum 13.12 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T119/T119_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -25.72, mean -5.308, maximum 25.88 Map values for surface ""best_model.pdb_B SES surface"": minimum -27.73, mean -4.331, maximum 22.87 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T119/T119_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T119/T119_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T120 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 8 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T120/T120_contacts_hbonds_rot.mp4 Changed 2482 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T120/T120_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.23, mean -4.49, maximum 11.32 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.03, mean -2.50, maximum 13.02 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T120/T120_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -29.42, mean -5.278, maximum 21.3 Map values for surface ""best_model.pdb_B SES surface"": minimum -25.55, mean -3.796, maximum 25.68 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T120/T120_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T120/T120_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults T121 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T121/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 1 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T121/T121_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T121/T121_contacts_hbonds_rot.mp4 Changed 3082 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/T121/T121_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T121/T121_sphere_rot.mp4 Changed 0 atom styles Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/grako/ast.py"", line 59, in update def upairs(d): TypeError: NoneType takes no arguments ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W00106LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 9 days, 13 hours, 20 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX