id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17790 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.5.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x00000002a7e97000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a6e8b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a4e73000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001f0fca080 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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{ ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""62fe74515312cd4599bd3c80"", ""factorPackIds"" : { ""MYRIAD_BOOSTS"" : ""62fe74805312cd4599bd3c81"" }, ""deploymentId"" : 240000006 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Registration file '/Users/ak/Library/Application Support/ChimeraX/registration' has expired note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/ak/Downloads/fold_wp_220577189_1_atp_1x_mg_2x > 2/fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif"" Summary of feedback from opening /Users/ak/Downloads/fold_wp_220577189_1_atp_1x_mg_2x 2/fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif --- notes | Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif Chain information for fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif #1 --- Chain | Description A | . Computing secondary structure > ui tool show Contacts > contacts intraMol false ignoreHiddenModels true color #ff2600 78 contacts > select protein 3894 atoms, 3967 bonds, 486 residues, 1 model selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_wp_220577189_1_atp_1x_mg_2x_model_0.cif_A SES surface #1.2: minimum, -17.42, mean -1.68, maximum 9.15 To also show corresponding color key, enter the above coulombic command and add key true > select add #1 3927 atoms, 4000 bonds, 78 pseudobonds, 489 residues, 3 models selected > select subtract #1 1 model selected > lighting soft > close #1 > open /Users/ak/Downloads/mohawk_0502_fixed- > bsheets_ccID_isolde_real_space_refined_022.pdb format pdb Chain information for mohawk_0502_fixed- bsheets_ccID_isolde_real_space_refined_022.pdb #1 --- Chain | Description Q T c d f | No description available V W Z | No description available X Y | No description available > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 92403 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 > lighting soft > color bychain > select add /X:299 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true color #ff2600 59 contacts > select add /Y:310 40 atoms, 40 bonds, 2 residues, 1 model selected > show sel atoms > view orient > select subtract /X:299@CE2 39 atoms, 37 bonds, 2 residues, 1 model selected > select add /X:299@CE2 40 atoms, 37 bonds, 2 residues, 1 model selected > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true color #ff2600 83 contacts > select add #1 92643 atoms, 93968 bonds, 83 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > open ""/Users/ak/Downloads/cryosparc_P755_J51_006_volume_map_flipped (1).mrc"" > format mrc Opened cryosparc_P755_J51_006_volume_map_flipped (1).mrc as #2, grid size 300,300,300, pixel 1.3, shown at level 0.031, step 2, values float32 > close #2 > select add /Z:299 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true color #ff2600 15 contacts > select add /Y:667 40 atoms, 40 bonds, 2 residues, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true color #ff2600 15 contacts > open /Users/ak/Downloads/cryosparc_P69_J76_004_volume_map_sharp.mrc Opened cryosparc_P69_J76_004_volume_map_sharp.mrc as #2, grid size 800,800,800, pixel 0.65, shown at step 1, values float32 > volume #2 region 0,0,0,799,799,799 step 4 > volume #2 step 2 > ui tool show ""Hide Dust"" > surface dust #2 size 3.9 > surface dust #2 size 4.09 > surface dust #2 size 4.67 > surface dust #2 size 4.75 > surface dust #2 size 14.16 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb (#1) to map cryosparc_P69_J76_004_volume_map_sharp.mrc (#2) using 92643 atoms average map value = 0.03889, steps = 256 shifted from previous position = 14.2 rotated from previous position = 13.1 degrees atoms outside contour = 32736, contour level = 0.012731 Position of mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb (#1) relative to cryosparc_P69_J76_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99045848 -0.00227239 0.13779270 -31.69279510 0.02723002 0.98337865 -0.17951308 42.57371435 -0.13509447 0.18155235 0.97405761 9.43191854 Axis 0.79609040 0.60167170 0.06504800 Axis point 0.00000000 -17.94595110 235.47683584 Rotation angle (degrees) 13.10722620 Shift along axis 0.99859690 > volume flip #2 Opened cryosparc_P69_J76_004_volume_map_sharp.mrc z flip as #3, grid size 800,800,800, pixel 0.65, shown at step 1, values float32 > ui tool show ""Hide Dust"" > surface dust #3 size 3.9 > surface dust #3 size 4.1 > surface dust #3 size 15.07 > close #2 > fitmap #1 inMap #3 Fit molecule mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb (#1) to map cryosparc_P69_J76_004_volume_map_sharp.mrc z flip (#3) using 92643 atoms average map value = 0.07151, steps = 236 shifted from previous position = 14.2 rotated from previous position = 13.1 degrees atoms outside contour = 1851, contour level = 0.012731 Position of mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb (#1) relative to cryosparc_P69_J76_004_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99999996 -0.00028340 -0.00006686 0.07437942 0.00028337 0.99999983 -0.00051374 0.07442764 0.00006701 0.00051372 0.99999987 -0.15564442 Axis 0.86997172 -0.11334700 0.47989756 Axis point 0.00000000 285.80387684 140.71460724 Rotation angle (degrees) 0.03383382 Shift along axis -0.01842154 > volume #3 style mesh > volume #3 level 0.0682 > hide #!3 models > show #!3 models > volume #3 style surface > volume #3 level 0.0912 > volume #3 level 0.125 > volume #3 level 0.1043 > volume #3 level 0.08218 > ui tool show ""Side View"" > volume #3 style mesh > volume #3 level 0.06639 > volume #3 style surface > volume #3 style mesh > volume #3 level 0.01499 > volume #3 style surface > volume #3 style mesh > ui tool show ""Side View"" > view sel > ui tool show ""Side View"" > view sel > volume #3 style surface > volume #3 style mesh > view sel > select add #1 92643 atoms, 93968 bonds, 15 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > volume #3 level 0.05647 > view orient > volume #3 style surface > volume #3 level 0.08218 > volume #3 level 0.08939 > volume #3 style mesh > volume #3 level 0.03618 > volume #3 level 0.05106 > volume #3 level 0.05602 > volume #3 level 0.0691 > volume #3 level 0.06459 Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 > select /V-W,Z:288 60 atoms, 60 bonds, 3 residues, 1 model selected > select /V-W,Z:288 60 atoms, 60 bonds, 3 residues, 1 model selected > select add #1 92643 atoms, 93968 bonds, 15 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > select /V-W,Z:288 60 atoms, 60 bonds, 3 residues, 1 model selected > select /V-W,Z:288 60 atoms, 60 bonds, 3 residues, 1 model selected > select /V-W,Z:288-289 132 atoms, 132 bonds, 6 residues, 1 model selected > select /V-W,Z:288-289 132 atoms, 132 bonds, 6 residues, 1 model selected > select /V-W,Z:288-290 204 atoms, 204 bonds, 9 residues, 1 model selected > select /V-W,Z:284 36 atoms, 33 bonds, 3 residues, 1 model selected > select /V-W,Z:284-289 315 atoms, 321 bonds, 18 residues, 1 model selected > select add #1 92643 atoms, 93968 bonds, 15 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > hide #!3 models > select > /V-W,Z:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-416,420-426,452-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,695-697,731-740,770-774,778-780,808-813,842-845,885-890,904-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044 13155 atoms, 13230 bonds, 765 residues, 1 model selected > select /V-W,Z:3 39 atoms, 36 bonds, 3 residues, 1 model selected > select /V-W,Z:3-292 14190 atoms, 14397 bonds, 870 residues, 1 model selected > select /V-W,Z:298 21 atoms, 18 bonds, 3 residues, 1 model selected > select /V-W,Z:298-300 114 atoms, 114 bonds, 9 residues, 1 model selected > select /V-W,Z:297 36 atoms, 33 bonds, 3 residues, 1 model selected > select /V-W,Z:297-301 210 atoms, 213 bonds, 15 residues, 1 model selected > select /V-W,Z:301 60 atoms, 60 bonds, 3 residues, 1 model selected > select /V-W,Z:300-301 93 atoms, 93 bonds, 6 residues, 1 model selected > select /V-W,Z:300 33 atoms, 30 bonds, 3 residues, 1 model selected > select /V-W,Z:293-300 360 atoms, 363 bonds, 24 residues, 1 model selected > select /V-W,Z:294 72 atoms, 69 bonds, 3 residues, 1 model selected > select /V-W,Z:294-299 264 atoms, 264 bonds, 18 residues, 1 model selected > select /V-W,Z:295 33 atoms, 30 bonds, 3 residues, 1 model selected > select /V-W,Z:295-300 225 atoms, 225 bonds, 18 residues, 1 model selected > select /V-W,Z:297 36 atoms, 33 bonds, 3 residues, 1 model selected > select /V-W,Z:297 36 atoms, 33 bonds, 3 residues, 1 model selected > show sel atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true color #ff2600 10 contacts > hide #!1 models > select add #1 92643 atoms, 93968 bonds, 10 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > open /Users/ak/Downloads/rzago_apo-tet_rsr19_mg- > added_real_space_refined_021.cif format mmcif Summary of feedback from opening /Users/ak/Downloads/rzago_apo-tet_rsr19_mg- added_real_space_refined_021.cif --- warnings | Atom H1 is not in the residue template for LYS /C:161 Atom H1 is not in the residue template for LYS /A:161 Missing or incomplete sequence information. Inferred polymer connectivity. note | Fetching CCD AGS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/AGS/AGS.cif Chain information for rzago_apo-tet_rsr19_mg-added_real_space_refined_021.cif #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available Computing secondary structure > view orient > color #2 bychain > show #!1 models > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,3.5852,0,1,0,-53.978,0,0,1,-63.769 > hide #!1 models Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 2/A Alignment identifier is 2/B > select #1/V-W,Z:287 #2/C:287 96 atoms, 100 bonds, 4 residues, 2 models selected > select #1/V-W,Z:287-288 #2/C:287-288 176 atoms, 184 bonds, 8 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [285-286] RMSD: 173.329 > select add #2 50524 atoms, 51178 bonds, 3114 residues, 2 models selected > select subtract #2 132 atoms, 138 bonds, 6 residues, 1 model selected > select add #1 92643 atoms, 93968 bonds, 10 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > select add #1 92643 atoms, 93968 bonds, 10 pseudobonds, 5643 residues, 2 models selected > select subtract #1 Nothing selected > rainbow #2 > select #1/V-W,Z:430 #2/C:430 60 atoms, 56 bonds, 4 residues, 2 models selected > select #1/V-W,Z:430-431 #2/C:430-431 120 atoms, 116 bonds, 8 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [428-429] RMSD: 179.231 > view matrix models #2,1,0,0,-3.412,0,1,0,-40.267,0,0,1,-81.673 > select #1/V-W,Z:426-427 #2/C:426-427 124 atoms, 120 bonds, 8 residues, 2 models selected > select #1/V-W,Z:426-429 #2/C:426-429 256 atoms, 252 bonds, 16 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [424-427] RMSD: 179.326 > select add #1 92707 atoms, 94031 bonds, 10 pseudobonds, 5647 residues, 3 models selected > select subtract #1 64 atoms, 63 bonds, 4 residues, 1 model selected > select add #2 50392 atoms, 51040 bonds, 3108 residues, 1 model selected > select subtract #2 Nothing selected > color #2 bychain > select #1/V-W,Z:430 #2/C:430 60 atoms, 56 bonds, 4 residues, 2 models selected > select #1/V-W,Z:430-431 #2/C:430-431 120 atoms, 116 bonds, 8 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [428-429] RMSD: 182.955 > view matrix models #2,1,0,0,-13.298,0,1,0,-25.764,0,0,1,-90.718 > select #1/V-W,Z:426 #2/C:426 68 atoms, 64 bonds, 4 residues, 2 models selected > select #1/V-W,Z:426 #2/C:426 68 atoms, 64 bonds, 4 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [424] RMSD: 178.957 > select > #1/V-W,Z:4-9,11-19,21-29,42-59,85-98,151-161,166-168,176-178,181-191,198-200,203-210,224-230,234-236,252-254,258-260,271-284,309-322,373-381,389-391,396-408,429-436,461-463,466-483,492-494,510-515,549-551,554-559,569-571,591-593,601-603,610-620,626-633,641-659,708-710,716-723,741-756,764-768,783-796,798-801,827-838,847-851,857-868,896-900,926-944,963-976,1050-1063,1076-1095,1102-1106 > #2/C:4-9,11-19,21-29,42-59,85-98,151-161,166-168,176-178,181-191,198-200,203-210,224-230,234-236,252-254,258-260,271-284,309-322,373-381,389-391,396-408,429-436,461-463,466-483,492-494,510-515,549-551,554-559,569-571,591-593,601-603,610-620,626-633,641-659,708-710,716-723,741-756,764-768,783-796,798-801,827-838,847-851,857-868,896-900,926-944,963-976,1050-1063,1076-1095,1102-1106 27608 atoms, 27668 bonds, 1656 residues, 2 models selected > select #1/V-W,Z:423 #2/C:423 76 atoms, 72 bonds, 4 residues, 2 models selected > select #1/V-W,Z:423 #2/C:423 76 atoms, 72 bonds, 4 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [421] RMSD: 174.657 > select > #1/V-W,Z:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044 > #2/C:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044 18508 atoms, 18616 bonds, 1080 residues, 2 models selected > select #1/V-W,Z:427-428 #2/C:427-428 112 atoms, 108 bonds, 8 residues, 2 models selected > select #1/V-W,Z:427-428 #2/C:427-428 112 atoms, 108 bonds, 8 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [425-426] RMSD: 181.637 > select #1/V-W,Z:427 #2/C:427 56 atoms, 52 bonds, 4 residues, 2 models selected > select #1/V-W,Z:427-460 #2/C:427-460 2197 atoms, 2229 bonds, 136 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [425-458] RMSD: 192.731 > select #1/V-W,Z:449 #2/C:449 84 atoms, 84 bonds, 4 residues, 2 models selected > select #1/V-W,Z:427-449 #2/C:427-449 1493 atoms, 1513 bonds, 92 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [425-447] RMSD: 190.943 > select > #1/V-W,Z:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044 > #2/C:31-34,64-68,105-111,114-121,139-142,145-148,170-173,213-216,219-223,243-247,263-267,290-294,301-305,331-336,339-345,358-360,414-417,420-426,449-459,486-492,495-500,516-529,532-545,563-568,573-581,585-590,595-600,604-606,662-664,667-671,675-677,695-697,731-740,770-774,778-780,808-814,842-846,885-893,901-909,918-921,952-957,981-988,1010-1014,1017-1020,1038-1044 18508 atoms, 18616 bonds, 1080 residues, 2 models selected > select #1/V-W,Z:449 #2/C:449 84 atoms, 84 bonds, 4 residues, 2 models selected > select #1/V-W,Z:449 #2/C:449 84 atoms, 84 bonds, 4 residues, 2 models selected 2 [ID: 2] region chains C,V,W,Z [447] RMSD: 196.345 > show sel & #2 atoms > ui tool show Contacts > contacts sel intraMol false ignoreHiddenModels true color #ff2600 No contacts > select add #1 92664 atoms, 93989 bonds, 10 pseudobonds, 5644 residues, 3 models selected > select subtract #1 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #2 50392 atoms, 51040 bonds, 3108 residues, 1 model selected > select subtract #2 Nothing selected > select subtract #4 Nothing selected > select add #4 Nothing selected > select subtract #4 Nothing selected > select add #4 Nothing selected > select subtract #4 Nothing selected > close #4 > rainbow #2 > open /Users/ak/Downloads/5xq2.cif 5xq2.cif title: Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 5A6 on the guide strand [more info...] Chain information for 5xq2.cif #4 --- Chain | Description | UniProt A B | TtAgo (D546N) | Q746M7_THET2 1-685 C D | DNA (5'-D(*AP*GP*T)-3') | E X | DNA (5'-D(P*TP*GP*AP*AP*GP*AP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') | F Y | DNA (5'-D(*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') | Non-standard residues in 5xq2.cif #4 --- MG — magnesium ion > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 11721 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 > ui tool show Matchmaker > matchmaker #!4 to #1 Computing secondary structure 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 mohawk_0502_fixed-bsheets_ccID_isolde_real_space_refined_022.pdb, chain W (#1) with 5xq2.cif, chain A (#4), sequence alignment score = 407.7 RMSD between 121 pruned atom pairs is 1.260 angstroms; (across all 603 pairs: 20.413) > ui tool show Matchmaker > matchmaker #!4 to #2 Computing secondary structure 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 rzago_apo-tet_rsr19_mg-added_real_space_refined_021.cif, chain D (#2) with 5xq2.cif, chain A (#4), sequence alignment score = 373.4 RMSD between 124 pruned atom pairs is 1.246 angstroms; (across all 612 pairs: 26.429) > select #4/B 5187 atoms, 5312 bonds, 1 pseudobond, 681 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide sel surfaces > select #4/C 59 atoms, 66 bonds, 3 residues, 1 model selected > select #4/F 317 atoms, 354 bonds, 16 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #4/F 317 atoms, 354 bonds, 16 residues, 1 model selected > select #4/F#4/Y 634 atoms, 708 bonds, 32 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #4/C#4/D 118 atoms, 132 bonds, 6 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #4/E#4/X 720 atoms, 806 bonds, 36 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > view matrix models #2,1,0,0,-51.322,0,1,0,14.417,0,0,1,-132.39 > undo ===== Log before crash end ===== Log: Startup Messages --- warning | Registration file '/Users/ak/Library/Application Support/ChimeraX/registration' has expired note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ak/Downloads/fold_wp_106257897_1_trimer/fold_wp_106257897_1_trimer_model_0.cif Chain information for fold_wp_106257897_1_trimer_model_0.cif #1 --- Chain | Description A B C | . Computing secondary structure OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Model Number: Z15H00108LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5.1 (22G90) Kernel Version: Darwin 22.6.0 Time since boot: 42 days, 2 hours, 7 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-XMAS: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 et_xmlfile: 2.0.0 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 narwhals: 1.30.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 2.2.3 numpy: 1.26.4 openpyxl: 3.1.5 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 pandas: 2.2.3 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 plotly: 6.0.0 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pyKVFinder: 0.7.3 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 QtRangeSlider: 0.1.5 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 seaborn: 0.13.2 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 toml: 0.10.2 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX