id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17518 Graphics hardware encountered an error and was reset chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.7.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff85f298940 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 556 in swap_buffers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, 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space 3.1G 4188 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""336ece9034c4fd65227f9fb379e1fb501877b2f9"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62c74108bcb0435c2153f963"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""657a4921d6ad146894c1b003"" }, ""deploymentId"" : 240000394 }, { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs Log from Fri Apr 4 09:11:39 2025UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs format session Log from Thu Mar 6 09:54:59 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/olgabednova/Downloads/model_02.pdb model_02.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for model_02.pdb #1 --- Chain | Description A | No description available B | No description available Non-standard residues in model_02.pdb #1 --- MG — (MG) > select /A 1668 atoms, 1707 bonds, 212 residues, 1 model selected > ui tool show ""Renumber Residues"" > renumber /A seqStart 1 0 residues renumbered > renumber /A seqStart 1 0 residues renumbered > select ~sel 1648 atoms, 1688 bonds, 219 residues, 1 model selected > ui tool show ""Renumber Residues"" > renumber /B seqStart 213 217 residues renumbered > renumber /B seqStart 213 0 residues renumbered > undo > select /A:1-212 1668 atoms, 1707 bonds, 212 residues, 1 model selected > select /A:1-212 1668 atoms, 1707 bonds, 212 residues, 1 model selected > select /B:1-217 42 atoms, 41 bonds, 5 residues, 1 model selected > select /B:1-217 42 atoms, 41 bonds, 5 residues, 1 model selected > select /A:1-212 1668 atoms, 1707 bonds, 212 residues, 1 model selected > select /B:1-217 42 atoms, 41 bonds, 5 residues, 1 model selected > select ~sel 3274 atoms, 3353 bonds, 426 residues, 1 model selected > select /A 1668 atoms, 1707 bonds, 212 residues, 1 model selected > select /B 1646 atoms, 1688 bonds, 217 residues, 1 model selected > ui tool show ""Change Chain IDs"" > changechains sel A Chain IDs of 217 residues changed > changechains sel A Chain IDs of 0 residues changed > select /A 3314 atoms, 3395 bonds, 429 residues, 1 model selected > select /B Nothing selected > select /A 3314 atoms, 3395 bonds, 429 residues, 1 model selected > ui tool show ""Dock Prep"" Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Summary of feedback from adding hydrogens to model_02.pdb #1 --- notes | No usable SEQRES records for model_02.pdb (#1) chain A; guessing termini instead No usable SEQRES records for model_02.pdb (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A ASP 1, /A GLN 213 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ASN 212, /A CYS 429 Chain-final residues that are not actual C termini: 384 hydrogen bonds 3250 hydrogens added Closest equivalent command: addcharge standardizeResidues none Using Amber 20 recommended default charges and atom types for standard residues Dock prep finished > save /Users/olgabednova/Desktop/rat_aNGF_Fab_prepared.pdb relModel #1 > open > /Users/olgabednova/Downloads/453316-rat_aNGF_mNGF_summary-2/cluster1_1.pdb Summary of feedback from opening /Users/olgabednova/Downloads/453316-rat_aNGF_mNGF_summary-2/cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME=""complex_45w.pdb0"" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_45.pdb Ignored bad PDB record found on line 5 REMARK =============================================================== 29 messages similar to the above omitted Chain information for cluster1_1.pdb #2 --- Chain | Description A | No description available B | No description available > hide #1 models > ui mousemode right zoom > ui mousemode right translate > select #2/B 2155 atoms, 2188 bonds, 1 pseudobond, 220 residues, 2 models selected > color pink > undo > ui tool show H-Bonds > hbonds twoColors true saltOnly true reveal true 54 hydrogen bonds found 31 strict hydrogen bonds found > hbonds twoColors true saltOnly true reveal true 54 hydrogen bonds found 31 strict hydrogen bonds found > ui tool show ViewDockX No suitable models found for ViewDockX > ui tool show Contacts > contacts resSeparation 5 ignoreHiddenModels true 3745 contacts > contacts resSeparation 5 ignoreHiddenModels true 3745 contacts > undo > hide > undo > hide #4 models > ui mousemode right zoom > surface #2-3 > select #2/A 4075 atoms, 4156 bonds, 2446 pseudobonds, 429 residues, 4 models selected > color (#!2 & sel) orange > hide (#!2 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!2 & sel-residues) > show (#!2 & sel-residues & backbone) target ab > select #2/B 2155 atoms, 2188 bonds, 1102 pseudobonds, 220 residues, 4 models selected > surface hidePatches (#!2 & sel) > volume style mesh No volumes specified > volume style surface No volumes specified > volume hide No volumes specified > hide sel surfaces > show sel cartoons > show sel atoms [Repeated 1 time(s)] > hide sel atoms > color sel bychain [Repeated 1 time(s)] > undo [Repeated 1 time(s)] > mlp sel Map values for surface ""cluster1_1.pdb_B SES surface"": minimum -26.86, mean -4.94, maximum 24.1 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""cluster1_1.pdb_B SES surface"": minimum -26.86, mean -4.94, maximum 24.1 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean 1.40, maximum 13.12 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean 1.39, maximum 13.12 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean 1.39, maximum 13.12 To also show corresponding color key, enter the above coulombic command and add key true > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset ""initial styles"" ""space-filling (chain colors)"" Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 12791 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > hide sel atoms > select #2/B 2152 atoms, 2185 bonds, 1102 pseudobonds, 220 residues, 4 models selected > hide sel atoms [Repeated 1 time(s)] > hide sel cartoons > hide sel surfaces [Repeated 1 time(s)] > show sel surfaces > select #1/A#1/A#2/A 10639 atoms, 10801 bonds, 2458 pseudobonds, 858 residues, 5 models selected > hide sel & #!2 atoms > style sel & #!2 sphere Changed 4075 atom styles > style sel & #!2 sphere Changed 4075 atom styles > show sel & #!2 surfaces > show sel & #!2 cartoons [Repeated 1 time(s)] > hide sel & #!2 cartoons > interfaces select & #!2 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & #!2 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #2/B 2152 atoms, 2185 bonds, 1102 pseudobonds, 220 residues, 4 models selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > color sel byhetero > coulombic sel Coulombic values for cluster1_1.pdb_B SES surface #2.3: minimum, -9.76, mean 1.39, maximum 13.12 To also show corresponding color key, enter the above coulombic command and add key true > select #1/A#1/A#2/A 10639 atoms, 10801 bonds, 2458 pseudobonds, 858 residues, 5 models selected > mlp sel & #!2 Map values for surface ""cluster1_1.pdb_A SES surface"": minimum -30.04, mean -6.604, maximum 23.23 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel & #!2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for cluster1_1.pdb_A SES surface #2.2: minimum, -9.77, mean 1.12, maximum 11.63 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel & #!2 Coulombic values for cluster1_1.pdb_A SES surface #2.2: minimum, -9.77, mean 1.12, maximum 11.63 To also show corresponding color key, enter the above coulombic command and add key true > hbonds sel & #!2 reveal true 382 hydrogen bonds found > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 4074 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hbonds sel & #!2 reveal true 382 hydrogen bonds found > ui tool show Clashes > clashes ignoreHiddenModels true 32 clashes > clashes ignoreHiddenModels true 32 clashes > show #4 models > hide #4 models > color (#!2 & sel) orange red > deselec Unknown command: deselec > deselect Unknown command: deselect > cancel selection Unknown command: cancel selection Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 0 maps. Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. Chains must have same sequence > select #2/A 4074 atoms, 4155 bonds, 2797 pseudobonds, 429 residues, 5 models selected Alignment identifier is 2/A > select #2/A:321-322 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:321-330 83 atoms, 82 bonds, 10 residues, 1 model selected > hide #5 models > show #5 models > hide #3 models > show #3 models > hide #5 models > show #5 models > hide #3 models > show #3 models > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select > #2/A:4-7,10-14,19-25,33-38,45-49,62-67,70-75,84-90,102-107,114-118,129-137,145-150,159-164,174-182,191-197,205-210,215-217,230-237,246-251,258-263,269-271,279-284,289-294,303-309,321-323,334-338,349-359,365-368,377-379,383-385,388-398,408-413,418-423 1913 atoms, 1913 bonds, 1356 pseudobonds, 197 residues, 4 models selected Drag select of 16 atoms, 3 residues, 15 bonds, 5 pseudobonds > ui mousemode right zoom > ui mousemode right translate > ui mousemode right rotate > ui mousemode right translate > select #2/A:80-82,122-127,183-188,273-275,299-301,369-371 232 atoms, 229 bonds, 10 pseudobonds, 24 residues, 3 models selected > ui tool show H-Bonds > hbonds twoColors true slopColor #41f300 saltOnly true reveal true 54 hydrogen bonds found 31 strict hydrogen bonds found > hbonds twoColors true slopColor #41f300 saltOnly true reveal true 54 hydrogen bonds found 31 strict hydrogen bonds found > undo Undo failed, probably because structures have been modified. > ui tool show H-Bonds > hbonds distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true reveal > true 75 hydrogen bonds found 31 strict hydrogen bonds found > hbonds distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true reveal > true 75 hydrogen bonds found 31 strict hydrogen bonds found > select #2/A:213 12 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:213-214 20 atoms, 19 bonds, 2 residues, 1 model selected > select #2/A:1 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:1-212 2058 atoms, 2097 bonds, 1228 pseudobonds, 212 residues, 4 models selected > ui tool show ""Model Loops"" > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #2/A:80-82,122-127,183-188,273-275,299-301,369-371 232 atoms, 229 bonds, 3 pseudobonds, 24 residues, 3 models selected > select #2/A:213 12 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:213-429 2016 atoms, 2058 bonds, 1093 pseudobonds, 217 residues, 4 models selected > ui tool show ""Change Chain IDs"" > ui tool show ""Renumber Residues"" > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #2/B 2152 atoms, 2185 bonds, 1125 pseudobonds, 220 residues, 5 models selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #1/A#1/A#2/A 10638 atoms, 10800 bonds, 2483 pseudobonds, 858 residues, 6 models selected > ui mousemode right zoom > hide #5 models > select add #5 10638 atoms, 10800 bonds, 2503 pseudobonds, 858 residues, 8 models selected > select subtract #5 10638 atoms, 10800 bonds, 2471 pseudobonds, 858 residues, 7 models selected > select add #3 10638 atoms, 10800 bonds, 2497 pseudobonds, 858 residues, 7 models selected > interfaces select & #!2 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > ui mousemode right translate > ui mousemode right rotate > ui mousemode right zoom > hide #2.1 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #2.1 models > hide #2.1 models > show #5 models > hide #5 models > show #4 models > hide #4 models > hide #3 models > show #3 models > hide #2.3 models > show #2.3 models > hide #2.3 models > show #2.3 models > hide #2.3 models > hide #2.2 models > show #2.2 models > hide #2.2 models > select subtract #2.2 6564 atoms, 6645 bonds, 40 pseudobonds, 429 residues, 4 models selected > interfaces #!2 & ~solvent 1 buried areas: A B 1389 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/B Alignment identifier is 2/B > toolshed show Downloading bundle ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl [Repeated 2 time(s)] > toolshed show Downloading bundle ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl [Repeated 1 time(s)] > instal isolde Unknown command: instal isolde > install isolde Unknown command: install isolde > toolshed install ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/toolshed.py"", line 312, in toolshed_install ts.install_bundle(bundles, logger, **kw) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 931, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/__init__.py"", line 216, in _install_bundle raise ValueError(""Non-existent wheel file"") ValueError: Non-existent wheel file ValueError: Non-existent wheel file File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/__init__.py"", line 216, in _install_bundle raise ValueError(""Non-existent wheel file"") See log for complete Python traceback. > toolshed install ChimeraX_ISOLDE-1.8-cp311-cp311-macosx_10_13_universal2.whl Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/toolshed.py"", line 312, in toolshed_install ts.install_bundle(bundles, logger, **kw) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py"", line 931, in install_bundle _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/__init__.py"", line 216, in _install_bundle raise ValueError(""Non-existent wheel file"") ValueError: Non-existent wheel file ValueError: Non-existent wheel file File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/__init__.py"", line 216, in _install_bundle raise ValueError(""Non-existent wheel file"") See log for complete Python traceback. > save /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF.pdb > open /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF.pdb Summary of feedback from opening /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF.pdb --- warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence records as basis for sequence. rat_aNGF_Fab_mNGF.pdb title: SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more info...] Chain information for rat_aNGF_Fab_mNGF.pdb --- Chain | Description 6.1/A 6.2/A | No description available 6.2/B | No description available > hide #!2 models > hide #!6.2 models > show #!6.2 models > hide #!6.2 models > hide #!6.1 models > show #!6.1 models > select add #6 13282 atoms, 12983 bonds, 9 pseudobonds, 1121 residues, 8 models selected > select subtract #6 492 atoms, 43 residues, 3 models selected > select add #6 13282 atoms, 12983 bonds, 9 pseudobonds, 1121 residues, 8 models selected > select subtract #6 492 atoms, 43 residues, 3 models selected > close #6 > show #!2 models > select subtract #2.3 243 atoms, 21 residues, 3 models selected > select add #2.3 2395 atoms, 241 residues, 2 models selected > select subtract #2.3 243 atoms, 21 residues, 3 models selected > select add #2.3 2395 atoms, 241 residues, 2 models selected > select subtract #2.3 243 atoms, 21 residues, 3 models selected > select subtract #2.2 1 model selected > select add #2.2 4074 atoms, 429 residues, 1 model selected > select subtract #2.2 1 model selected > select add #2.2 4074 atoms, 429 residues, 1 model selected > select subtract #2.2 1 model selected > show #2.3 models > select add #2.2 4074 atoms, 429 residues, 1 model selected > undo [Repeated 6 time(s)] > save /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs ——— End of log from Thu Mar 6 09:54:59 2025 ——— opened ChimeraX session > hide all > show sel target ab > interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 22 contacting residues > interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 22 contacting residues > show (#!2 & sel) target ab > color (#!2 & sel) lime > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > color (#!2 & sel) yellow > color (#!2 & sel) hot pink > ui tool show Clashes > save /Users/olgabednova/Desktop/rat_aNGF_Fab_mNGF_docked.cxs ——— End of log from Fri Apr 4 09:11:39 2025 ——— opened ChimeraX session > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #2/B 2152 atoms, 2185 bonds, 1125 pseudobonds, 220 residues, 5 models selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select all 12790 atoms, 12985 bonds, 3853 pseudobonds, 1078 residues, 6 models selected > interfaces select & #!2 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > deselect Unknown command: deselect > cancel Unknown command: cancel > stop > cancel Unknown command: cancel > end Unknown command: end > interfaces select #1/A & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 37 contacting residues > interfaces select #1/A & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 37 contacting residues > show #4 models > hide #4 models > interfaces #!2 & ~solvent 1 buried areas: A B 1389 > interfaces select #2/A & ::polymer_type>0 contacting #1/A & ::polymer_type>0 > areaCutoff 0 30 contacting residues > interfaces select #2/B & ::polymer_type>0 contacting #1/A & ::polymer_type>0 > areaCutoff 0 0 contacting residues > interfaces select #2/B#2/A & ::polymer_type>0 contacting #1/A#1/A & > ::polymer_type>0 areaCutoff 0 30 contacting residues > interfaces select #1/A#1/A & ::polymer_type>0 contacting #2/A#2/B & > ::polymer_type>0 areaCutoff 0 37 contacting residues > interfaces select #1/A#1/A & ::polymer_type>0 contacting #2/A#2/B & > ::polymer_type>0 areaCutoff 0 37 contacting residues > interfaces select #1/A#1/A & ::polymer_type>0 contacting #2/A#2/B & > ::polymer_type>0 areaCutoff 0 37 contacting residues > hide #3 models > show #3 models > list contacts Unknown command: list contacts > select #2/B 2152 atoms, 2185 bonds, 1125 pseudobonds, 220 residues, 5 models selected > interfaces select #2/B & ::polymer_type>0 contacting #1/A#1/A & > ::polymer_type>0 areaCutoff 0 0 contacting residues > interfaces select #2/B & ::polymer_type>0 contacting #1/A#1/A & > ::polymer_type>0 areaCutoff 0 0 contacting residues > show #5 models > hide #5 models > show #5 models > hide #5 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select #2/A 4074 atoms, 4155 bonds, 2464 pseudobonds, 429 residues, 5 models selected > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > list residues Unknown command: list residues > list Unknown command: list > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > ui tool show ""Selection Inspector"" > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > show #4 models > hide #4 models > show #4 models > hide #3 models > show #3 models > hide #3 models > show #3 models > select add #2 6226 atoms, 6340 bonds, 3834 pseudobonds, 649 residues, 6 models selected > select subtract #2 2 models selected > interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 22 contacting residues > interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 22 contacting residues > hide #3 models > show #3 models > hide #4 models > show #4 models > hide #3 models > show #3 models > hide #4 models > show #4 models > hide #4 models > color #4 #00efefff models > show #4 models > hide #4 target m > close #4 > interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 22 contacting residues > interfaces select #2/B & ::polymer_type>0 contacting #2/A & ::polymer_type>0 > areaCutoff 0 22 contacting residues > show #5 models > hide #5 models > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > interfaces select #2/A & ::polymer_type>0 contacting #2/B & ::polymer_type>0 > areaCutoff 0 21 contacting residues > myInterfaceResidues Unknown command: myInterfaceResidues > toolshed show > ui mousemode right select Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > hbonds sel reveal true 33 hydrogen bonds found > hide #3 models > show #3 models > ui mousemode right zoom > ui mousemode right translate > hide #!2 models > hide #3 models > show #!2 models > select add #2 6226 atoms, 6340 bonds, 67 pseudobonds, 649 residues, 5 models selected > select subtract #2 2 models selected > select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :0 ) & ((#2/A & ::polymer_type>0 ) : select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :0 ) & ((#2/A & ::polymer_type>0 ) : show #3 models > hide #3 models > ui tool show Contacts > contacts distanceOnly 4.0 intraModel false intraMol false ignoreHiddenModels > true color #977400 No distances > ui tool show H-Bonds > hbonds sel distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true > reveal true 14 hydrogen bonds found 5 strict hydrogen bonds found > hbonds sel distSlop 3.0 twoColors true slopColor #11ed00 saltOnly true > reveal true 14 hydrogen bonds found 5 strict hydrogen bonds found > show #3 models > color #3 #00e7e2ff models > color #3 #0108e7ff models > color #3 #00d8e3ff models > select #2/A:309 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/A:309-312 50 atoms, 50 bonds, 2 pseudobonds, 4 residues, 2 models selected > select > #2/A:4-7,10-14,19-25,33-38,45-49,62-67,70-75,84-90,102-107,114-118,129-137,145-150,159-164,174-182,191-197,205-210,215-217,230-237,246-251,258-263,269-271,279-284,289-294,303-309,321-323,334-338,349-359,365-368,377-379,383-385,388-398,408-413,418-423 1913 atoms, 1913 bonds, 11 pseudobonds, 197 residues, 2 models selected > select #2/A:308 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:308-314 71 atoms, 72 bonds, 2 pseudobonds, 7 residues, 2 models selected > select #2/A:238 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:238-245 86 atoms, 88 bonds, 8 residues, 1 model selected > select #2/A:308 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:308-316 95 atoms, 97 bonds, 2 pseudobonds, 9 residues, 2 models selected ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.7.3 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 529.140.2.0.0 OS Loader Version: 577.140.2~30 SMC Version (system): 2.43f11 Software: System Software Overview: System Version: macOS 13.7.1 (22H221) Kernel Version: Darwin 22.6.0 Time since boot: 16 days, 28 minutes Graphics/Displays: Intel Iris Plus Graphics 640: Chipset Model: Intel Iris Plus Graphics 640 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5926 Revision ID: 0x0006 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) 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: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 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2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Graphics duplicate all ChimeraX