id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19768 Crash in swap_buffers when status line exposed Mac Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x00000001f905ec40 (most recent call first): File ""/Applications/ChimeraX-1.11.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-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, PIL._imaging, 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, PIL._imagingmath, chimerax.mlp._mlp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 63) 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[ { ""treatmentId"" : ""1cabf156-a0a4-4874-8eb1-0ff7c514ddbf"", ""experimentId"" : ""687ad3eb2c0a4d3b710c5dcd"", ""deploymentId"" : 400000011 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/GP-1-cut.cxs format session > view name session-start opened ChimeraX session > select #1 :20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > color bfactor sel 24 atoms, 3 residues, atom bfactor range 97 to 98.7 > select add #1 3562 atoms, 3640 bonds, 1 pseudobond, 490 residues, 4 models selected > color bfactor sel 3562 atoms, 490 residues, atom bfactor range 0 to 98.9 > select subtract #1 Nothing selected > select #1 :20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > save /Users/kouei/Desktop/image52.png supersample 3 > close session > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/J-2-cut.cxs format session > view name session-start opened ChimeraX session > color bfactor 3558 atoms, 490 residues, atom bfactor range 0 to 98.9 > select #1 :20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > save /Users/kouei/Desktop/image53.png supersample 3 > close session > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/GP-2-cut.cxs format session > view name session-start opened ChimeraX session > color bfactor 3519 atoms, 489 residues, 1 surfaces, atom bfactor range 0 to 98.9 > select #1 :20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > save /Users/kouei/Desktop/image54.png supersample 3 > close session > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/J-3-cut.cxs format session > view name session-start opened ChimeraX session > color bfactor 3360 atoms, 464 residues, atom bfactor range 0 to 98.4 > select #1 :140,215,274 24 atoms, 22 bonds, 3 residues, 1 model selected > save /Users/kouei/Desktop/image55.png supersample 3 > mlp sel Map values for surface ""fold_j3_signalcut_model_0.cif_A SES surface"": minimum -30.06, mean -6.987, maximum 21.46 To also show corresponding color key, enter the above mlp command and add key true > select add #1 3360 atoms, 3442 bonds, 1 pseudobond, 464 residues, 5 models selected > mlp sel Map values for surface ""fold_j3_signalcut_model_0.cif_A SES surface"": minimum -30.06, mean -6.987, maximum 21.46 To also show corresponding color key, enter the above mlp command and add key true > select subtract #1 1 model selected > select #1 :140,215,274 24 atoms, 22 bonds, 3 residues, 1 model selected > close session > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/fold_gp_1_signalcut_model_0.cif > /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/fold_gp_2_signalcut_model_0.cif > /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/fold_j1_signalcut_model_0.cif > /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/fold_j2_signalcut_model_0.cif > /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/fold_j3_signalcut_model_0.cif Chain information for fold_gp_1_signalcut_model_0.cif #1 --- Chain | Description A | . Chain information for fold_gp_2_signalcut_model_0.cif #2 --- Chain | Description A | . Chain information for fold_j1_signalcut_model_0.cif #3 --- Chain | Description A | . Chain information for fold_j2_signalcut_model_0.cif #4 --- Chain | Description A | . Chain information for fold_j3_signalcut_model_0.cif #5 --- Chain | Description A | . Computing secondary structure > mmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_gp_1_signalcut_model_0.cif, chain A (#1), sequence alignment score = 2170.8 RMSD between 327 pruned atom pairs is 0.275 angstroms; (across all 487 pairs: 8.106) > mmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j1_signalcut_model_0.cif, chain A (#3), sequence alignment score = 531.8 RMSD between 4 pruned atom pairs is 0.514 angstroms; (across all 334 pairs: 19.942) > mmaker #4 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j2_signalcut_model_0.cif, chain A (#4), sequence alignment score = 2129.9 RMSD between 323 pruned atom pairs is 0.256 angstroms; (across all 487 pairs: 12.630) > mmaker #5 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j3_signalcut_model_0.cif, chain A (#5), sequence alignment score = 568.6 RMSD between 72 pruned atom pairs is 0.597 angstroms; (across all 335 pairs: 25.274) > hide #1 models > hide #3 models > hide #4 models > hide #5 models > mlp #2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > select #2 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > show #1 models > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > hide #1 models > show #1 models > hide #!2 models > hide #1 models > show #!2 models > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > select add #2 3517 atoms, 3596 bonds, 487 residues, 2 models selected > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > select subtract #2 1 model selected > select #2 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > set bgColor white > set bgColor black > save /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/5strains.cxs > show #1 models > hide #!2 models > select add #2 3517 atoms, 3596 bonds, 487 residues, 2 models selected > select add #1 7077 atoms, 7236 bonds, 975 residues, 3 models selected > select subtract #2 3560 atoms, 3640 bonds, 488 residues, 2 models selected > mlp sel Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -28.97, mean -7.263, maximum 24.92 To also show corresponding color key, enter the above mlp command and add key true > select #2 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > select #2 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > select #1 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > select add #1 3560 atoms, 3640 bonds, 488 residues, 2 models selected > select subtract #1 1 model selected > hide #!1 models > show #4 models > mlp #4 Map values for surface ""fold_j2_signalcut_model_0.cif_A SES surface"": minimum -29.06, mean -7.334, maximum 23.95 To also show corresponding color key, enter the above mlp command and add key true > select #1 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > select #4 : 20,105,140 24 atoms, 22 bonds, 3 residues, 1 model selected > show #3 models > hide #!4 models > select add #4 3556 atoms, 3636 bonds, 488 residues, 2 models selected > mlp #3 Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -28.93, mean -6.652, maximum 22.08 To also show corresponding color key, enter the above mlp command and add key true > select #3 : 140,212,271 24 atoms, 22 bonds, 3 residues, 1 model selected > select add #3 3385 atoms, 3470 bonds, 471 residues, 2 models selected > select subtract #3 1 model selected > hide #!3 models > show #5 models > mlp #5 Map values for surface ""fold_j3_signalcut_model_0.cif_A SES surface"": minimum -29.92, mean -6.99, maximum 21.26 To also show corresponding color key, enter the above mlp command and add key true > select #5 : 140,215,274 24 atoms, 22 bonds, 3 residues, 1 model selected > hide #!5 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > view > show #!1 models > show #!3 models > hide #!2 models > hide #!3 models > view > hide #!1 models > show #!2 models > view > ui mousemode right distance > sequence chain #5/A Alignment identifier is 5/A > ui mousemode #2 : 468 to 438 > mousemode #2 : 468 to 438 Expected a keyword > ui mousemode #2 : 468 438 > mousemode #2 : 468 438 Expected a keyword > distance #2/A:468@CE2 #2/A:468@CZ Distance between fold_gp_2_signalcut_model_0.cif #2/A PHE 468 CE2 and CZ: 1.407Å > distance #2/A:438@CZ #2/A:468@CZ Distance between fold_gp_2_signalcut_model_0.cif #2/A TYR 438 CZ and PHE 468 CZ: 11.381Å > distance #2/A:465@CZ3 #2/A:438@CZ Distance between fold_gp_2_signalcut_model_0.cif #2/A TRP 465 CZ3 and TYR 438 CZ: 6.446Å > distance #2/A:465@CH2 #2/A:438@CZ Distance between fold_gp_2_signalcut_model_0.cif #2/A TRP 465 CH2 and TYR 438 CZ: 5.405Å > view > distance #2/A:465@CZ3 #2/A:438@CE1 Distance between fold_gp_2_signalcut_model_0.cif #2/A TRP 465 CZ3 and TYR 438 CE1: 7.489Å > distance #2/A:465@CE3 #2/A:467@CG1 Distance between fold_gp_2_signalcut_model_0.cif #2/A TRP 465 CE3 and VAL 467 CG1: 8.815Å > distance #2/A:465@CE3 #2/A:438@CG Distance between fold_gp_2_signalcut_model_0.cif #2/A TRP 465 CE3 and TYR 438 CG: 6.201Å > coulombic #!2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_gp_2_signalcut_model_0.cif_A SES surface #2.1: minimum, -10.97, mean -0.67, maximum 10.78 To also show corresponding color key, enter the above coulombic command and add key true > rainbow #!2 > color #!2 bypolymer > color #!2 bychain > color #!2 byhetero > color bfactor #!2 3517 atoms, 487 residues, 1 surfaces, atom bfactor range 21.7 to 98.9 > hide #!2 surfaces > show #!2 surfaces > color bfactor #!2 3517 atoms, 487 residues, 1 surfaces, atom bfactor range 21.7 to 98.9 > color bfactor #!2 3517 atoms, 487 residues, 1 surfaces, atom bfactor range 21.7 to 98.9 > mlp #!2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 surfaces > mlp #!2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 surfaces > show #!2 atoms > ui mousemode right ""delete markers"" > select add #5 3358 atoms, 3442 bonds, 462 residues, 2 models selected > select subtract #5 1 model selected > select add #6 7 pseudobonds, 2 models selected > close #6 > mlp #!2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 surfaces > mlp #!2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > ui mousemode right distance > distance #2/A:468@CZ #2/A:438@CE1 Distance between fold_gp_2_signalcut_model_0.cif #2/A PHE 468 CZ and TYR 438 CE1: 10.969Å > distance #2/A:438@CE1 #2/A:465@CZ3 Distance between fold_gp_2_signalcut_model_0.cif #2/A TYR 438 CE1 and TRP 465 CZ3: 7.489Å > hide #!2 surfaces > select add #6 2 pseudobonds, 2 models selected > hide #!2 models > close #2 > hide #6 models > close #6 > close session > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/GP-2-cut.cxs format session > view name session-start opened ChimeraX session > mlp Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > mlp Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > ui mousemode right distance > distance #!1/A:465@CZ3 #!1/A:438@CZ Distance between fold_gp_2_signalcut_model_0.cif #!1/A TRP 465 CZ3 and TYR 438 CZ: 6.446Å > hide #!1 models > select add #2 2 pseudobonds, 2 models selected > close #1 > close > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/5strains.cxs format session > view name session-start opened ChimeraX session > ui mousemode right ""play map series"" > ui mousemode right ""map eraser"" > select add #6 24 atoms, 22 bonds, 3 residues, 2 models selected > select add #2 3517 atoms, 3596 bonds, 487 residues, 2 models selected > select subtract #2 2 models selected > hide #!2 models > close > open /Users/kouei/Library/CloudStorage/GoogleDrive- > daxiazihy@keio.jp/共有ドライブ/宮本研微生物班/研究データ/論文用データ/PHBH- > GP2/AlphaFold3_Signal6.0_signalcut/20250121/5strains.cxs format session > view name session-start opened ChimeraX session > select add #1 3584 atoms, 3662 bonds, 491 residues, 2 models selected > show #1 models > select subtract #1 24 atoms, 22 bonds, 3 residues, 1 model selected > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > select add #1 3584 atoms, 3662 bonds, 491 residues, 2 models selected > select add #2 7077 atoms, 7236 bonds, 975 residues, 2 models selected > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -28.97, mean -7.263, maximum 24.92 To also show corresponding color key, enter the above mlp command and add key true > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A Alignment identifier is 2/A > select subtract #1 3517 atoms, 3596 bonds, 487 residues, 3 models selected > select subtract #2 1 model selected > mmaker #1 : 470 to #2 : 469 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_gp_1_signalcut_model_0.cif, chain A (#1), sequence alignment score = 0.5 Fewer than 3 residues aligned; cannot match fold_gp_2_signalcut_model_0.cif, chain A with fold_gp_1_signalcut_model_0.cif, chain A > mmaker #1 : 438-488 to #2 : 437-487 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_gp_1_signalcut_model_0.cif, chain A (#1), sequence alignment score = 263.7 RMSD between 51 pruned atom pairs is 0.107 angstroms; (across all 51 pairs: 0.107) > view > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > color bfactor #!1 3560 atoms, 488 residues, 1 surfaces, atom bfactor range 18.6 to 98.9 > show #!2 models > color bfactor #!1-2 7077 atoms, 975 residues, 2 surfaces, atom bfactor range 18.6 to 98.9 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > view > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > mlp #!1-2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -27.95, mean -7.255, maximum 25 To also show corresponding color key, enter the above mlp command and add key true > color bfactor #!1-2 7077 atoms, 975 residues, 2 surfaces, atom bfactor range 18.6 to 98.9 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > mlp #!1-2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -27.95, mean -7.255, maximum 25 To also show corresponding color key, enter the above mlp command and add key true > view orient > color bfactor #!1-2 7077 atoms, 975 residues, 2 surfaces, atom bfactor range 18.6 to 98.9 > mlp #!1-2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -27.95, mean -7.255, maximum 25 To also show corresponding color key, enter the above mlp command and add key true > hide #!1 models > show #!1 models > show #3 models > mmaker #3 : 438-488 to #2 : 437-487 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j1_signalcut_model_0.cif, chain A (#3), sequence alignment score = 123.3 RMSD between 31 pruned atom pairs is 0.297 angstroms; (across all 34 pairs: 1.703) > mlp #3#!1-2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -29.02, mean -6.647, maximum 21.51 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -27.95, mean -7.255, maximum 25 To also show corresponding color key, enter the above mlp command and add key true > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > sequence chain #2/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > sequence chain #3/A Alignment identifier is 3/A > sequence chain #4/A Alignment identifier is 4/A > sequence chain #5/A Alignment identifier is 5/A > mmaker #3 : 422-451 to #2 : 437-487 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j1_signalcut_model_0.cif, chain A (#3), sequence alignment score = 106.7 RMSD between 29 pruned atom pairs is 0.292 angstroms; (across all 30 pairs: 0.656) > mmaker #4 : 438-488 to #2 : 437-487 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j2_signalcut_model_0.cif, chain A (#4), sequence alignment score = 243.3 RMSD between 51 pruned atom pairs is 0.240 angstroms; (across all 51 pairs: 0.240) > hide #!3 models > show #4 models > mlp #4#!1-2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_j2_signalcut_model_0.cif_A SES surface"": minimum -28.64, mean -7.335, maximum 23.55 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -27.95, mean -7.255, maximum 25 To also show corresponding color key, enter the above mlp command and add key true > select add #4 3556 atoms, 3636 bonds, 488 residues, 1 model selected > mlp sel Map values for surface ""fold_j2_signalcut_model_0.cif_A SES surface"": minimum -28.64, mean -7.335, maximum 23.55 To also show corresponding color key, enter the above mlp command and add key true > select subtract #4 1 model selected > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > color bfactor #!2,4 7073 atoms, 975 residues, 2 surfaces, atom bfactor range 19.5 to 98.9 > show #!1 models > color bfactor #!1-2,4 10633 atoms, 1463 residues, 3 surfaces, atom bfactor range 18.6 to 98.9 > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > mlp #!2,4 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 Map values for surface ""fold_j2_signalcut_model_0.cif_A SES surface"": minimum -28.64, mean -7.335, maximum 23.55 To also show corresponding color key, enter the above mlp command and add key true > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > mlp #!1,4 Map values for surface ""fold_j2_signalcut_model_0.cif_A SES surface"": minimum -28.64, mean -7.335, maximum 23.55 Map values for surface ""fold_gp_1_signalcut_model_0.cif_A SES surface"": minimum -27.95, mean -7.255, maximum 25 To also show corresponding color key, enter the above mlp command and add key true > show #!2 models > view > hide #!1 models > hide #!2 models > hide #!4 models > show #!3 models > show #5 models > mlp #5#!3 Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -28.46, mean -6.648, maximum 21.6 Map values for surface ""fold_j3_signalcut_model_0.cif_A SES surface"": minimum -29.92, mean -6.99, maximum 21.26 To also show corresponding color key, enter the above mlp command and add key true > mmaker #5 : 412-462 to #2 : 437-487 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_gp_2_signalcut_model_0.cif, chain A (#2) with fold_j3_signalcut_model_0.cif, chain A (#5), sequence alignment score = 199.9 RMSD between 48 pruned atom pairs is 0.326 angstroms; (across all 51 pairs: 1.314) > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > interfaces #!3 & ~solvent 0 buried areas: > hide #!3 models > show #!2 models > interfaces #!2 & ~solvent 0 buried areas: > select add #2 3517 atoms, 3596 bonds, 487 residues, 1 model selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select subtract #2 1 model selected > ui mousemode right ""tape measure"" > view orient > select #2/A:274@ND2 1 atom, 1 residue, 1 model selected > select #2/A:137@CA 1 atom, 1 residue, 1 model selected > select add #2/A:274@ND2 2 atoms, 2 residues, 2 models selected > ui mousemode right ""tape measure"" > segmentations mouseModes true > ui mousemode shift wheel 'resize segmentation cursor' > ui mousemode right 'create segmentations' > ui mousemode shift right 'erase segmentations' > ui mousemode shift middle 'move segmentation cursor' > select #2/A:137@CA 1 atom, 1 residue, 1 model selected > select add #2/A:274@ND2 2 atoms, 2 residues, 2 models selected > ui mousemode right distance > select add #2 3517 atoms, 3596 bonds, 487 residues, 2 models selected > select subtract #2 1 model selected > select #2/A:137@CA 1 atom, 1 residue, 1 model selected > select add #2/A:274@ND2 2 atoms, 2 residues, 2 models selected > ui mousemode right distance > hide sel surfaces > select add #2 3517 atoms, 3596 bonds, 487 residues, 2 models selected > hide sel surfaces > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > ui mousemode right distance > select subtract #2 1 model selected > select #2/A:137@CA 1 atom, 1 residue, 1 model selected > select #2/A:274@ND2 1 atom, 1 residue, 1 model selected > select add #2/A:137@CA 2 atoms, 2 residues, 2 models selected > distance Missing or invalid ""objects"" argument: empty atom specifier > ui mousemode right distance > hide #!2 models > hide #2.1 models > show #2.1 models > hide #!2 models > show #!2 models > select add #2 3517 atoms, 3596 bonds, 487 residues, 2 models selected > select subtract #2 1 model selected > select add #2.1 3517 atoms, 487 residues, 1 model selected > close #2.1 > select add #2 3517 atoms, 3596 bonds, 487 residues, 1 model selected > mlp sel Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > select subtract #2.1 1 model selected > select #2/A:106@CD2 1 atom, 1 residue, 1 model selected > select #2/A:156@OG 1 atom, 1 residue, 1 model selected > distance #2/A:106@CD2 #2/A:156@OG Distance between fold_gp_2_signalcut_model_0.cif #2/A TYR 106 CD2 and SER 156 OG: 10.486Å > select #2/A:137@CA 1 atom, 1 residue, 1 model selected > select #2/A:283@CA 1 atom, 1 residue, 1 model selected > select #2/A:282@O 1 atom, 1 residue, 1 model selected > distance #2/A:137@CA #2/A:282@O Distance between fold_gp_2_signalcut_model_0.cif #2/A GLY 137 CA and SER 282 O: 33.320Å > select #2/A:157@CB 1 atom, 1 residue, 1 model selected > select #2/A:161@CE1 1 atom, 1 residue, 1 model selected > select #2/A:283@CB 1 atom, 1 residue, 1 model selected > distance #2/A:161@CE1 #2/A:283@CB Distance between fold_gp_2_signalcut_model_0.cif #2/A TYR 161 CE1 and LEU 283 CB: 18.328Å > close #6 > distance #2/A:137@CA #2/A:157@O Distance between fold_gp_2_signalcut_model_0.cif #2/A GLY 137 CA and SER 157 O: 13.652Å > select add #2 3517 atoms, 3596 bonds, 1 pseudobond, 487 residues, 3 models selected > select subtract #2 1 model selected > select add #6 1 pseudobond, 2 models selected > close #6 > distance #2/A:283@CB #2/A:161@CE1 Distance between fold_gp_2_signalcut_model_0.cif #2/A LEU 283 CB and TYR 161 CE1: 18.328Å > distance #2/A:161@CE1 #2/A:283@CD2 Distance between fold_gp_2_signalcut_model_0.cif #2/A TYR 161 CE1 and LEU 283 CD2: 18.371Å > distance #2/A:157@O #2/A:283@CA Distance between fold_gp_2_signalcut_model_0.cif #2/A SER 157 O and LEU 283 CA: 20.938Å > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > color bfactor #!2 3517 atoms, 487 residues, 1 surfaces, atom bfactor range 21.7 to 98.9 > mlp #!2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > show #!1 models > hide #!2 models > hide #2.1 models > view > select #1/A:157@CB 1 atom, 1 residue, 1 model selected > select #1/A:283@CA 1 atom, 1 residue, 1 model selected > select #1/A:157@CB 1 atom, 1 residue, 1 model selected > select add #1/A:283@CA 2 atoms, 2 residues, 2 models selected > distance #1/A:157@CB #1/A:283@CA Distance between fold_gp_1_signalcut_model_0.cif #1/A SER 157 CB and LEU 283 CA: 21.621Å > select #1/A:161@CE1 1 atom, 1 residue, 1 model selected > distance #1/A:157@O #1/A:283@CB Distance between fold_gp_1_signalcut_model_0.cif #1/A SER 157 O and LEU 283 CB: 20.168Å > hide #!1 models > show #!4 models > view > select #4/A:157@CB 1 atom, 1 residue, 1 model selected > select #4/A:283@CB 1 atom, 1 residue, 1 model selected > select #4/A:157@CB 1 atom, 1 residue, 1 model selected > select add #4/A:284@N 2 atoms, 2 residues, 2 models selected > distance #4/A:157@CB #4/A:284@N Distance between fold_j2_signalcut_model_0.cif #4/A SER 157 CB and ALA 284 N: 21.189Å > select #4/A:161@CE1 1 atom, 1 residue, 1 model selected > select add #4/A:284@N 2 atoms, 2 residues, 2 models selected > distance #4/A:284@N #4/A:161@CE1 Distance between fold_j2_signalcut_model_0.cif #4/A ALA 284 N and TYR 161 CE1: 18.630Å > select #4/A:161@CE1 1 atom, 1 residue, 1 model selected > select #4/A:284@N 1 atom, 1 residue, 1 model selected > select add #4/A:161@CE1 2 atoms, 2 residues, 2 models selected > select #4/A:161@OH 1 atom, 1 residue, 1 model selected > select #4/A:283@CD2 1 atom, 1 residue, 1 model selected > distance #4/A:284@N #4/A:161@OH Distance between fold_j2_signalcut_model_0.cif #4/A ALA 284 N and TYR 161 OH: 16.996Å > select #4/A:161@CE1 1 atom, 1 residue, 1 model selected > distance #4/A:283@CB #4/A:284@N Distance between fold_j2_signalcut_model_0.cif #4/A LEU 283 CB and ALA 284 N: 3.272Å > select #4/A:283@CB 1 atom, 1 residue, 1 model selected > distance #4/A:161@CE1 #4/A:283@CB Distance between fold_j2_signalcut_model_0.cif #4/A TYR 161 CE1 and LEU 283 CB: 18.481Å > distance #4/A:287@ND2 #4/A:60@CE Distance between fold_j2_signalcut_model_0.cif #4/A ASN 287 ND2 and MET 60 CE: 7.999Å > distance #4/A:236@NE2 #4/A:107@CG2 Distance between fold_j2_signalcut_model_0.cif #4/A GLN 236 NE2 and THR 107 CG2: 8.538Å > hide #!4 models > show #!5 models > distance #5/A:287@OH #5/A:173@CZ3 Distance between fold_j3_signalcut_model_0.cif #5/A TYR 287 OH and TRP 173 CZ3: 15.036Å > distance #5/A:287@OH #5/A:172@CB Distance between fold_j3_signalcut_model_0.cif #5/A TYR 287 OH and ARG 172 CB: 14.231Å > hide #!5 models > show #!3 models > sequence chain #4/A Alignment identifier is 4/A > select > #4/A:20-32,50-53,56-59,67-82,89-94,110-122,127-129,169-178,190-192,199-201,218-221,239-249,252-258,306-320,438-443 884 atoms, 884 bonds, 118 residues, 1 model selected > select #3 : 20 8 atoms, 7 bonds, 1 residue, 1 model selected > color bfactor sel 8 atoms, 1 residues, 1 surfaces, atom bfactor range 80.8 to 91.5 > color bfactor sel 8 atoms, 1 residues, 1 surfaces, atom bfactor range 80.8 to 91.5 > sequence chain #3/A Alignment identifier is 3/A > select #3 : 140 6 atoms, 5 bonds, 1 residue, 1 model selected > color bfactor sel 6 atoms, 1 residues, 1 surfaces, atom bfactor range 91.1 to 95.3 > select add #3 3385 atoms, 3470 bonds, 471 residues, 2 models selected > mlp sel Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -28.46, mean -6.648, maximum 21.6 To also show corresponding color key, enter the above mlp command and add key true > view > distance #3/A:172@CB #3/A:284@OH Distance between fold_j1_signalcut_model_0.cif #3/A THR 172 CB and TYR 284 OH: 14.607Å > select #3 : 140 6 atoms, 5 bonds, 1 residue, 1 model selected > style sel stick Changed 6 atom styles > style sel stick Changed 6 atom styles > color bfactor sel 6 atoms, 1 residues, 1 surfaces, atom bfactor range 91.1 to 95.3 > mlp sel Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -28.46, mean -6.648, maximum 21.6 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -28.46, mean -6.648, maximum 21.6 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""fold_j1_signalcut_model_0.cif_A SES surface"": minimum -28.46, mean -6.648, maximum 21.6 To also show corresponding color key, enter the above mlp command and add key true > color bfactor sel 6 atoms, 1 residues, 1 surfaces, atom bfactor range 91.1 to 95.3 > hide sel surfaces > show #!2 models > hide #!3 models > mlp #!2 Map values for surface ""fold_gp_2_signalcut_model_0.cif_A SES surface"": minimum -31.3, mean -7.297, maximum 24.15 To also show corresponding color key, enter the above mlp command and add key true > view ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac13,1 Model Number: Z14J000HDJ/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 4日 6時間 20分 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: EV3240X: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Graphics duplicate all ChimeraX