id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20362 Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 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 0x00000001f1947080 (most recent call first): File ""/Applications/ChimeraX-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 122 in make_current File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 555 in make_current File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 584 in use_shared_context File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 146 in render File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 115 in _redraw File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 169 in update_graphics_now File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 153 in resizeEvent File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 61 in event File ""/Applications/ChimeraX-1.11.1.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-1.11.1.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-1.11.1.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, 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""rollouts"" : [ { ""rolloutId"" : ""67181b10c68c361a728c7cfa"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : [ ""65a855f5f087695cfac03d1f"" ], ""deploymentId"" : 240000272 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/osperand/Downloads/Q9E005_1_2153_8qgu.1.B.cif > /Users/osperand/Downloads/AF-0000000365765852-model_v1.cif Summary of feedback from opening /Users/osperand/Downloads/AF-0000000365765852-model_v1.cif --- warning | Atom H is not in the residue template for ILE /A:1 Q9E005_1_2153_8qgu.1.B.cif title: Model for UniProtKB entries Q9E005 [more info...] Chain information for Q9E005_1_2153_8qgu.1.B.cif #1 --- Chain | Description A B | . Color Q9E005_1_2153_8qgu.1.B.cif by residue attribute QMEANDisCo_score Alignment identifier is 1 Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Alignment identifier is 2 Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Chain information for AF-0000000365765852-model_v1.cif #2 --- Chain | Description | UniProt A | RNA-directed RNA polymerase L | L_ANDV Color AF-0000000365765852-model_v1.cif by residue attribute pLDDT_score Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain A to target with 0 mismatches Associated Q9E005_1_2153_8qgu.1.B.cif chain B to target with 0 mismatches Associated AF-0000000365765852-model_v1.cif chain A to target with 0 mismatches Computing secondary structure > matchmaker #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 AF-0000000365765852-model_v1.cif, chain A (#2) with Q9E005_1_2153_8qgu.1.B.cif, chain B (#1), sequence alignment score = 3493.1 RMSD between 335 pruned atom pairs is 1.216 angstroms; (across all 724 pairs: 4.159) > lighting soft > help indeep > indeep predict #1 device cpu clusterPockets true pocketMap ligandability > pocketThreshold 0.95 openPocketMaps true > save /Users/osperand/.local/share/ChimeraX/indeep- > runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif.pdb > format pdb models #1 selectedOnly true Running InDeep externally: /Users/osperand/.local/share/ChimeraX/indeep-runtime/bin/indeep-python /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/scripts/predict_maps.py --exp /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/results/experiments/HPO.exp --pdb /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif.pdb --out- prefix /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/Q9E005_1_2153_8qgu.1.B.cif/Q9E005_1_2153_8qgu.1.B.cif --device cpu --cluster-pockets --pocket-map ligandability --pocket-threshold 0.95 --pocket-min-voxels 20 --pocket-contact-radius 4.0 Missing Python environment at /Users/osperand/.local/share/ChimeraX/indeep- runtime/.venv/bin/python Run /Users/osperand/.local/share/ChimeraX/indeep- runtime/setup_linux_chimerax_env.sh first. InDeep prediction failed. Check the ChimeraX log for stderr from the external process. > indeep predict #2 device cpu clusterPockets true pocketMap ligandability > pocketThreshold 0.95 openPocketMaps true > save /Users/osperand/.local/share/ChimeraX/indeep- > runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif.pdb > format pdb models #2 selectedOnly true Running InDeep externally: /Users/osperand/.local/share/ChimeraX/indeep-runtime/bin/indeep-python /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/scripts/predict_maps.py --exp /Users/osperand/.local/share/ChimeraX/indeep- runtime/InDeep/results/experiments/HPO.exp --pdb /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif.pdb --out-prefix /Users/osperand/.local/share/ChimeraX/indeep- runtime/runs/AF-0000000365765852-model_v1.cif/AF-0000000365765852-model_v1.cif --device cpu --cluster-pockets --pocket-map ligandability --pocket-threshold 0.95 --pocket-min-voxels 20 --pocket-contact-radius 4.0 Missing Python environment at /Users/osperand/.local/share/ChimeraX/indeep- runtime/.venv/bin/python Run /Users/osperand/.local/share/ChimeraX/indeep- runtime/setup_linux_chimerax_env.sh first. InDeep prediction failed. Check the ChimeraX log for stderr from the external process. > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif Summary of feedback from opening /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif --- warning | No mmCIF models found. > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif Summary of feedback from opening /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif --- warning | No mmCIF models found. > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517-s_model_0.cif bd43-517-s_model_0.cif title: . [more info...] Chain information for bd43-517-s_model_0.cif #3 --- Chain | Description B | . Q | . Color bd43-517-s_model_0.cif by residue attribute pLDDT_score > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517-s2_model_0.cif bd43-517-s2_model_0.cif title: . [more info...] Chain information for bd43-517-s2_model_0.cif #4 --- Chain | Description B | . Q | . Color bd43-517-s2_model_0.cif by residue attribute pLDDT_score Computing secondary structure > close #1-2 > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd517-43_model_0.cif bd517-43_model_0.cif title: . [more info...] Chain information for bd517-43_model_0.cif #1 --- Chain | Description B | . Q | . Color bd517-43_model_0.cif by residue attribute pLDDT_score Computing secondary structure > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/summary/bd43-517_model_0.cif bd43-517_model_0.cif title: . [more info...] Chain information for bd43-517_model_0.cif #2 --- Chain | Description B | . Q | . Color bd43-517_model_0.cif by residue attribute pLDDT_score Computing secondary structure > matchmaker #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 bd43-517_model_0.cif, chain Q (#2) with bd517-43_model_0.cif, chain Q (#1), sequence alignment score = 1443.1 RMSD between 191 pruned atom pairs is 0.331 angstroms; (across all 276 pairs: 8.213) > matchmaker #2 to #1 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 bd517-43_model_0.cif, chain Q (#1) with bd43-517_model_0.cif, chain Q (#2), sequence alignment score = 1443.1 RMSD between 191 pruned atom pairs is 0.331 angstroms; (across all 276 pairs: 8.213) > matchmaker #3 to #1 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 bd517-43_model_0.cif, chain Q (#1) with bd43-517-s_model_0.cif, chain Q (#3), sequence alignment score = 1432.3 RMSD between 205 pruned atom pairs is 0.713 angstroms; (across all 276 pairs: 6.793) > matchmaker #4 to #1 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 bd517-43_model_0.cif, chain Q (#1) with bd43-517-s2_model_0.cif, chain Q (#4), sequence alignment score = 1417.9 RMSD between 206 pruned atom pairs is 0.624 angstroms; (across all 276 pairs: 5.255) > show atoms > hide #2 models > hide #1 models > hide #3 models > show #2 models > select #2/B:6@CA 1 atom, 1 residue, 1 model selected > view sel > ui tool show ""Side View"" > select clear > hide #4 models > show #1 models > show #3 models > hide #2 models > show #2 models > show #4 models > hide #3 models > hide #1 models > show #3 models > hide #4 models > hide #2-3 cartoons > show #2-3 cartoons > hide #2-3 cartoons > show #2-3 cartoons > hide #2-3 cartoons > hide #2 models > color #3 bychain > color #3 byhetero > show #3 cartoons > style #3 ball Changed 2346 atom styles > show #2 models > show #2-3 cartoons > hide #3 models > show #1 models > show #3 models > show #4 models > hide cartoons > style ball Changed 9434 atom styles > hide #3 models > hide #4 models > style #1-2 stick Changed 4742 atom styles > show #3 models > hide #3 models > hide #2 models > show #3 models > style #1,3 stick Changed 4716 atom styles > hide #3 models > show #4 models > style #1,4 stick Changed 4716 atom styles > show #3 models > hide #4 models > show #4 models > hide #3 models > show #2 models > hide #1 models > show #3 models > hide #3 models > hide #4 models > show #3 models > show #4 models > show #1 models > hide #1 models > hide #4 models > show #4 models > hide #3 models > hide #4 models > show #3 models > show #1 models > hide #2 models > hide #1 models > show #4 models > show #2 models > hide #2 models > hide #4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/Q #4/Q #1/Q #2/Q Alignment identifier is 1 > select #3/Q:146 #4/Q:146 #1/Q:146 #2/Q:146 24 atoms, 20 bonds, 4 residues, 4 models selected > select #3/Q:146-158 #4/Q:146-158 #1/Q:146-158 #2/Q:146-158 400 atoms, 408 bonds, 52 residues, 4 models selected . [ID: 1] region 4 chains [146-158] RMSD: 0.554 > select #3/Q:196-197 #4/Q:196-197 #1/Q:196-197 #2/Q:196-197 88 atoms, 84 bonds, 8 residues, 4 models selected > select #3/Q:149-196 #4/Q:149-196 #1/Q:149-196 #2/Q:149-196 1500 atoms, 1520 bonds, 192 residues, 4 models selected . [ID: 1] region 4 chains [149-196] RMSD: 0.442 > select #3/Q:115 #4/Q:115 #1/Q:115 #2/Q:115 56 atoms, 60 bonds, 4 residues, 4 models selected > select #3/Q:115-129 #4/Q:115-129 #1/Q:115-129 #2/Q:115-129 524 atoms, 544 bonds, 60 residues, 4 models selected . [ID: 1] region 4 chains [115-129] RMSD: 0.766 > select #3/B:6@CA 1 atom, 1 residue, 1 model selected > select #3/B:4@CB 1 atom, 1 residue, 1 model selected > select clear > select #3/Q:115-129 #4/Q:115-129 #1/Q:115-129 #2/Q:115-129 524 atoms, 544 bonds, 60 residues, 4 models selected > select > #3/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 > #4/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 > #1/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 > #2/Q:59-63,106-114,118-125,128-132,136-139,144-146,159-161,188-193,199-203,208-212,239-245,251-258 2204 atoms, 2208 bonds, 272 residues, 4 models selected > select clear > show #4 models > hide #4 models > show #1 models > hide #3 models > show #4 models > hide #1 models > hide #4 models > show #3 models > show #4 models > hide #4 models > rock > select #3/B:7@O 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 83 atoms, 84 bonds, 10 residues, 1 model selected > select up 136 atoms, 139 bonds, 16 residues, 1 model selected > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > select clear > stop > open > /Users/osperand/Downloads/fold_2025_12_02_11_29/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #5 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #5 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#5), sequence alignment score = 1422.7 RMSD between 186 pruned atom pairs is 0.478 angstroms; (across all 276 pairs: 9.241) > hide #5 models > show #5 models > select add #5 2342 atoms, 2387 bonds, 292 residues, 1 model selected > show sel atoms > hide sel cartoons > select clear > hide #!3 models > show #!3 models > hide #!3 models > select add #5 2342 atoms, 2387 bonds, 292 residues, 1 model selected > color sel bychain > color sel byhetero > select clear > show #!3 models > hide #5 models > show #5 models > hide #5 models > open > /Users/osperand/Downloads/bd43-517-s-s2/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #6 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #6 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#6), sequence alignment score = 1401.1 RMSD between 195 pruned atom pairs is 0.656 angstroms; (across all 276 pairs: 10.056) > show #6#!3 atoms > hide #6#!3 cartoons > hide #6 models > show #6 models > hide #6 models > show #6 models > open > /Users/osperand/Downloads/bd43-517-s-s2/fold_2025_12_02_11_29_model_1.cif Chain information for fold_2025_12_02_11_29_model_1.cif #7 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #7 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_1.cif, chain A (#7), sequence alignment score = 1411.9 RMSD between 192 pruned atom pairs is 0.675 angstroms; (across all 276 pairs: 10.634) > show #6-7#!3 atoms > hide #6-7#!3 cartoons > close #7 > hide #!3 models > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #7 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #7 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#7), sequence alignment score = 1420.9 RMSD between 182 pruned atom pairs is 0.643 angstroms; (across all 276 pairs: 13.990) > color #6-7 bychain > hide #6-7 cartoons > hide #6 models > hide #7 models > show #7 models > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_1.cif Chain information for fold_2025_12_02_11_29_model_1.cif #8 --- Chain | Description A | . B | . Computing secondary structure > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #9 --- Chain | Description A | . B | . Computing secondary structure > hide #9 models > hide #8 models > close #8-9 > show #7 target m > view #7 clip false No displayed objects specified. > hide #7 models > show #7 models > close #7 > show #4 models > hide #4 models > show #!3 models > show #5 models > hide #5 models > show #6 models > select add #6 2343 atoms, 2387 bonds, 292 residues, 1 model selected > color sel byhetero > select clear > hide #6 models > open > /Users/osperand/Downloads/bd43-517-s-s3/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #7 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #7 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#7), sequence alignment score = 1420.9 RMSD between 182 pruned atom pairs is 0.643 angstroms; (across all 276 pairs: 13.990) > show #7#!3 atoms > color #7#!3 bychain > color #7#!3 byhetero > hide #7#!3 cartoons > hide #!3 models > show #!3 models > hide #7 models > show #7 models > hide #!3 models > show #4 models > show #!3 models > hide #7 models > hide #4 models > show #7 models > hide #!3 models > ui tool show H-Bonds > hbonds reveal true 9600 hydrogen bonds found > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #7/B:9@CA 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #7/B:10@N 11 atoms, 8 bonds, 3 residues, 1 model selected > select add #7/B:10@C 12 atoms, 8 bonds, 3 residues, 1 model selected > select up 21 atoms, 20 bonds, 3 residues, 1 model selected > show #4 models > hide #8 models > hide #7 models > ui tool show H-Bonds > hbonds reveal true 9600 hydrogen bonds found > show #8 models > show #5 models > hide #4 models > show #4 models > hide #5 models > open > /Users/osperand/Downloads/bd43-517-s-s4/fold_2025_12_02_11_29_model_0.cif Chain information for fold_2025_12_02_11_29_model_0.cif #9 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #9 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#9), sequence alignment score = 1399.3 RMSD between 175 pruned atom pairs is 0.605 angstroms; (across all 276 pairs: 9.666) > show #4,9 atoms > color #4,9 bychain > color #4,9 byhetero > hide #4,9 cartoons > hide #8 models > hide #4 models > show #!3 models > hide #!3 models > hide #9 models > show #!3 models > show #9 models > hide #!3 models > open ""/Users/osperand/Downloads/fold_2025_12_02_11_29 > (4)/fold_2025_12_02_11_29_model_0.cif"" Chain information for fold_2025_12_02_11_29_model_0.cif #10 --- Chain | Description A | . B | . Computing secondary structure > matchmaker #10 to #1 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 bd517-43_model_0.cif, chain Q (#1) with fold_2025_12_02_11_29_model_0.cif, chain A (#10), sequence alignment score = 1422.7 RMSD between 179 pruned atom pairs is 0.632 angstroms; (across all 276 pairs: 10.382) > show #9-10 atoms > hide #9 models > hide #10 cartoons ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/osperand/Dropbox/work/Research/AntiPPIBiotics/02_Donnees/Nettoyees/peptides/bd43-517-s-s7/bd43-517-s-s7_model_0.cif Chain information for bd43-517-s-s7_model_0.cif #1 --- Chain | Description A | . B | . Computing secondary structure OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Ultra 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: Mac15,14 Model Number: Z1CE000FKFN/A Chip: Apple M3 Ultra Total Number of Cores: 28 (20 Performance and 8 Efficiency) Memory: 96 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3 (25D125) Kernel Version: Darwin 25.3.0 Time since boot: 35 jours, 1 heure et 53 minutes Graphics/Displays: Apple M3 Ultra: Chipset Model: Apple M3 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Studio Display XDR: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 120.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Studio Display XDR: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 120.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 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: 1.11.1 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-InDeep: 0.1.1 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: 2.7.12 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-SDFFrames: 0.1.1 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: 7.13.1 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: 4.26.0 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: 3.3.2 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 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: 4.1.0 roman-numerals-py: 4.1.0 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: 2.8.3 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: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 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 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 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