id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16661 Crash in ~QAccessibleCache on exit chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. 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""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so"", ""name"" : ""_cmsgpack.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 14422917120, ""size"" : 737280, ""uuid"" : ""cc06500d-d418-3365-b197-36b1304a819e"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so"", ""name"" : ""QtOpenGL.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 14362460160, ""size"" : 49152, ""uuid"" : ""b32a8c32-a5e0-3a8b-9a0d-00a26b160215"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so"", ""name"" : ""QtOpenGLWidgets.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 14362607616, 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""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so"", ""name"" : ""_graphics.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 6160580608, ""size"" : 475136, ""uuid"" : ""0c6e9a11-e483-3d7d-a88f-8ad0507af167"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so"", ""name"" : ""mmcif.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 6159155200, ""size"" : 409600, ""uuid"" : ""1ab8e5e2-c699-3efb-8f77-d375e3793c8f"", ""path"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so"", ""name"" : ""_mmcif.cpython-311-darwin.so"" }, { 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======= \nTOTAL 6.5G 5864 \nTOTAL, minus reserved VM space 6.2G 5864 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""49c1a8cd5ec56f3b61da067359ff5ea9c4b328f6"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ ] } } Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"" Log from Tue Jan 21 15:01:50 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"" Log from Mon Jan 20 14:17:30 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"" Log from Mon Jan 20 11:17:03 2025 Startup Messages --- 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/qianyuxia/Tianjin University/Works/Structure/OXGR1 > 结构/LTE4/GPCR_LTE4_J460_20250114_5_real_space_refined.pdb"" Summary of feedback from opening /Users/qianyuxia/Tianjin University/Works/Structure/OXGR1 结构/LTE4/GPCR_LTE4_J460_20250114_5_real_space_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.008 0.070 9136 Ignored bad PDB record found on line 23 ANGLE : 0.960 10.549 12417 Ignored bad PDB record found on line 24 CHIRALITY : 0.056 0.198 1400 17 messages similar to the above omitted Start residue of secondary structure not found: HELIX 15 15 ILE D 29 LEU D 45 1 17 Start residue of secondary structure not found: HELIX 16 16 GLY D 50 LYS D 61 1 12 Start residue of secondary structure not found: HELIX 17 17 SER D 67 THR D 84 1 18 Start residue of secondary structure not found: HELIX 18 18 ILE D 109 VAL D 134 1 26 Start residue of secondary structure not found: HELIX 19 19 SER D 143 HIS D 145 5 3 8 messages similar to the above omitted Chain information for GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > open ""/Users/qianyuxia/Tianjin University/Works/Structure/OXGR1 > 结构/Apo/GPCR_Apo_State2_20250119_2_real_space_refined.pdb"" Summary of feedback from opening /Users/qianyuxia/Tianjin University/Works/Structure/OXGR1 结构/Apo/GPCR_Apo_State2_20250119_2_real_space_refined.pdb --- warnings | Ignored bad PDB record found on line 20 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.007 0.079 9257 Ignored bad PDB record found on line 23 ANGLE : 1.120 14.635 12550 Ignored bad PDB record found on line 24 CHIRALITY : 0.065 0.282 1424 17 messages similar to the above omitted Chain information for GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available > hide atoms > show cartoons > style stick Changed 18004 atom styles > set bgColor white > show ligand > cartoon style width 1 > transparency 80 ribbons > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | ss 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 GPCR_LTE4_J460_20250114_5_real_space_refined.pdb, chain A (#1) with GPCR_Apo_State2_20250119_2_real_space_refined.pdb, chain A (#2), sequence alignment score = 1045.1 RMSD between 228 pruned atom pairs is 0.932 angstroms; (across all 275 pairs: 1.909) > select #1/C:62 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 57 atoms, 60 bonds, 6 residues, 1 model selected > select up 2600 atoms, 2647 bonds, 338 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/C:121 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 48 atoms, 48 bonds, 6 residues, 1 model selected > select up 2600 atoms, 2647 bonds, 338 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/E:97 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 3 residues, 1 model selected > select up 925 atoms, 951 bonds, 119 residues, 1 model selected > select up 1218 atoms, 1247 bonds, 161 residues, 1 model selected > select up 1799 atoms, 1845 bonds, 235 residues, 1 model selected > select up 6461 atoms, 6610 bonds, 814 residues, 1 model selected > select down 1799 atoms, 1845 bonds, 235 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/E:23 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 57 atoms, 56 bonds, 8 residues, 1 model selected > select up 917 atoms, 943 bonds, 118 residues, 1 model selected > select up 1000 atoms, 1025 bonds, 131 residues, 1 model selected > select up 1782 atoms, 1828 bonds, 233 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/D:22 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 363 atoms, 369 bonds, 53 residues, 1 model selected > select up 4561 atoms, 4661 bonds, 563 residues, 1 model selected > select down 363 atoms, 369 bonds, 53 residues, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #2/D:15 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 72 atoms, 71 bonds, 9 residues, 1 model selected > select up 403 atoms, 409 bonds, 53 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/B:27 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 207 atoms, 206 bonds, 26 residues, 1 model selected > select up 402 atoms, 401 bonds, 52 residues, 1 model selected > select up 412 atoms, 410 bonds, 54 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > select up 4198 atoms, 4292 bonds, 510 residues, 1 model selected > select down 1896 atoms, 1929 bonds, 232 residues, 1 model selected > color sel #b18aa6ff > select #2/B:233 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 12 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > color sel #abd7b8ff > select #1/A:241 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 2237 atoms, 2299 bonds, 277 residues, 1 model selected > select up 4198 atoms, 4292 bonds, 510 residues, 1 model selected > select down 2237 atoms, 2299 bonds, 277 residues, 1 model selected > color sel #9ab67dff > select #2/A:215 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 235 atoms, 239 bonds, 31 residues, 1 model selected > select up 2363 atoms, 2427 bonds, 294 residues, 1 model selected > color sel #fdadc2ff > transparency 80 ribbons > select clear > select H 35 atoms, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 30 atoms, 29 bonds, 1 residue, 1 model selected > color sel #b180a6ff > color sel byhetero > select sel :< 5 422 atoms, 415 bonds, 45 residues, 2 models selected > select add #2 4452 atoms, 4546 bonds, 1 pseudobond, 544 residues, 3 models selected > select subtract #2 193 atoms, 190 bonds, 18 residues, 1 model selected > show sel atoms > style sel stick Changed 193 atom styles > color sel byhetero > select clear > save ""/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"" ——— End of log from Mon Jan 20 11:17:03 2025 ——— opened ChimeraX session > select #2/A:87 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > select #2/A:91 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 10 atom styles > select clear > select #2/A:92 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select #2/A:93 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select #2/A:98 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:99 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 14 atom styles > select #2/A:100 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:101 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select #2/A:105 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:106 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > select #2/A:110 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select #2/A:190 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:191 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select #2/A:195 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:198 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select clear > select #2/A:265 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select #2/A:268 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select clear > select #2/A:84 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 85 atoms, 85 bonds, 11 residues, 1 model selected > select up 2363 atoms, 2427 bonds, 294 residues, 1 model selected > select up 4259 atoms, 4356 bonds, 526 residues, 1 model selected > select up 8422 atoms, 8613 bonds, 1036 residues, 2 models selected > select up 8422 atoms, 8613 bonds, 1036 residues, 2 models selected > select up 8422 atoms, 8613 bonds, 1036 residues, 2 models selected > select up 8422 atoms, 8613 bonds, 1036 residues, 2 models selected > color sel byhetero > select clear > hide #!2 models > select #1/B:241 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 162 atoms, 162 bonds, 19 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > select ((#1/A & ::polymer_type>0 ) & ((#1/B & ::polymer_type>0 ) :<4)) | ((#1/B & ::polymer_type>0 ) & ((#1/A & ::polymer_type>0 ) :<4)) 201 atoms, 190 bonds, 23 residues, 1 model selected > show sel atoms > style sel stick Changed 201 atom styles > color sel byhetero > select clear > show #!2 models > hide #!1 models > select #2/B:238 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 12 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > select clear > select #2/B:238 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 12 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :<4)) | ((#2/B & ::polymer_type>0 ) & ((#2/A & ::polymer_type>0 ) :<4)) 357 atoms, 342 bonds, 43 residues, 1 model selected > show sel atoms > style sel stick Changed 357 atom styles > color sel byhetero > select clear > show #!1 models > save ""/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"" ——— End of log from Mon Jan 20 14:17:30 2025 ——— opened ChimeraX session > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > ui mousemode right distance > distance #2/A:145@ND1 #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS 145 ND1 and /B ARG 31 NH2: 5.289Å > ~distance #2/A:145@ND1 #2/B:31@NH2 > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 96 atoms, 99 bonds, 12 residues, 1 model selected > select down 10 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > distance #2/A:145@O #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS 145 O and /B ARG 31 NH2: 4.884Å > ~distance #2/A:145@O #2/B:31@NH2 > distance #2/A:145@N #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS 145 N and /B ARG 31 NH2: 5.708Å > ~distance #2/A:145@N #2/B:31@NH2 > select #2/A:145@CB 1 atom, 1 residue, 1 model selected > select up 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 96 atoms, 99 bonds, 12 residues, 1 model selected > show sel cartoons > select clear > distance #2/A:145@CB #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS 145 CB and /B ARG 31 NH2: 4.326Å > ~distance #2/A:145@CB #2/B:31@NH2 > select #2/A:145@CB 1 atom, 1 residue, 1 model selected > hide sel cartoons > select clear > distance #2/A:145@C #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A HIS 145 C and /B ARG 31 NH2: 4.782Å > ~distance #2/A:145@C #2/B:31@NH2 > distance #2/B:31@NH2 #2/A:145@CB Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/B ARG 31 NH2 and /A HIS 145 CB: 4.326Å > ~distance #2/B:31@NH2 #2/A:145@CB > select #2/B:238 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 12 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > hide sel atoms > select #2/A:146 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 96 atoms, 99 bonds, 12 residues, 1 model selected > select up 2363 atoms, 2427 bonds, 294 residues, 1 model selected > select up 4259 atoms, 4356 bonds, 526 residues, 1 model selected > select clear > ui mousemode right ""translate selected models"" > show ligand [Repeated 2 time(s)] > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > select #2/B:238 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 12 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :<4)) | ((#2/B & ::polymer_type>0 ) & ((#2/A & ::polymer_type>0 ) :<4)) 357 atoms, 342 bonds, 43 residues, 1 model selected > show sel atoms > style sel stick Changed 357 atom styles > select clear [Repeated 2 time(s)] > select #2/A:146 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 96 atoms, 99 bonds, 12 residues, 1 model selected > show sel cartoons > select #2/B:24 11 atoms, 10 bonds, 1 residue, 1 model selected > view matrix models > #2,0.99686,-0.06461,0.045786,-27.436,-0.065497,-0.99769,0.01815,216.05,0.044507,-0.021092,-0.99879,210.8 > show #!1 models > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 GPCR_LTE4_J460_20250114_5_real_space_refined.pdb, chain A (#1) with GPCR_Apo_State2_20250119_2_real_space_refined.pdb, chain A (#2), sequence alignment score = 1045.1 RMSD between 228 pruned atom pairs is 0.932 angstroms; (across all 275 pairs: 1.909) > select clear > hide #!2 models > ui mousemode right distance > distance #1/A:190@OD1 #1/F:1@N30 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ASP 190 OD1 and /F LIG 1 N30: 3.524Å > distance #1/A:268@NH1 #1/F:1@O28 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ARG 268 NH1 and /F LIG 1 O28: 2.318Å > distance #1/A:268@NH2 #1/F:1@O29 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ARG 268 NH2 and /F LIG 1 O29: 2.486Å > distance #1/F:1@O23 #1/A:93@OH Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1 O23 and /A TYR 93 OH: 4.409Å > ~distance #1/F:1@O23 #1/A:93@OH > ui mousemode right ""translate selected models"" > ui mousemode right distance > distance #1/A:198@OH #1/F:1@O21 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A TYR 198 OH and /F LIG 1 O21: 4.638Å > ~distance #1/A:198@OH #1/F:1@O21 > distance #1/A:198@OH #1/F:1@O22 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A TYR 198 OH and /F LIG 1 O22: 5.606Å > ~distance #1/A:198@OH #1/F:1@O22 > ui mousemode right ""translate selected models"" > ui mousemode right distance > distance #1/A:195@CD1 #1/F:1@O22 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ILE 195 CD1 and /F LIG 1 O22: 4.601Å > ~distance #1/A:195@CD1 #1/F:1@O22 > distance #1/A:195@CG2 #1/F:1@O21 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/A ILE 195 CG2 and /F LIG 1 O21: 5.171Å > ~distance #1/A:195@CG2 #1/F:1@O21 > ui mousemode right ""translate selected models"" > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > ui mousemode right distance > distance #1/F:1@O23 #1/A:110@NE Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1 O23 and /A ARG 110 NE: 4.075Å > ~distance #1/F:1@O23 #1/A:110@NE > distance #1/F:1@O23 #1/A:110@NH1 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1 O23 and /A ARG 110 NH1: 5.367Å > ~distance #1/F:1@O23 #1/A:110@NH1 > distance #1/F:1@O23 #1/A:110@NH2 Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1 O23 and /A ARG 110 NH2: 6.353Å > ~distance #1/F:1@O23 #1/A:110@NH2 > ui mousemode right ""translate selected models"" > show #!2 models > hide #!2 models > ui mousemode right distance > distance #1/F:1@O23 #1/A:93@OH Distance between GPCR_LTE4_J460_20250114_5_real_space_refined.pdb #1/F LIG 1 O23 and /A TYR 93 OH: 4.409Å > ui mousemode right distance > ~distance #1/F:1@O23 #1/A:93@OH > ui mousemode right ""translate selected models"" > transparency 80 ribbons > select down Nothing selected > show #!2 models > hide #!1 models > select #2/B:238 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 12 residues, 1 model selected > select up 1494 atoms, 1528 bonds, 180 residues, 1 model selected > select up 1554 atoms, 1587 bonds, 187 residues, 1 model selected > select up 1896 atoms, 1929 bonds, 232 residues, 1 model selected > select ((#2/A & ::polymer_type>0 ) & ((#2/B & ::polymer_type>0 ) :<4)) | ((#2/B & ::polymer_type>0 ) & ((#2/A & ::polymer_type>0 ) :<4)) 357 atoms, 342 bonds, 43 residues, 1 model selected > select clear > select #2/A:142 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms [Repeated 1 time(s)] > show sel atoms > hide sel cartoons > select clear > ui mousemode right distance > distance #2/A:142@O #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A PHE 142 O and /B ARG 31 NH2: 4.802Å > select clear > ~distance #2/A:142@O #2/B:31@NH2 > distance #2/B:31@CB #2/A:142@CB Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/B ARG 31 CB and /A PHE 142 CB: 5.464Å > ~distance #2/B:31@CB #2/A:142@CB > ui mousemode right ""translate selected models"" > ui mousemode right distance > distance #2/A:142@O #2/B:31@NE Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A PHE 142 O and /B ARG 31 NE: 4.460Å > distance #2/A:142@O #2/B:31@NH2 Distance between GPCR_Apo_State2_20250119_2_real_space_refined.pdb #2/A PHE 142 O and /B ARG 31 NH2: 4.802Å > ~distance #2/A:142@O #2/B:31@NH2 > ~distance #2/A:142@O #2/B:31@NE > ui mousemode right ""translate selected models"" > select #2/A:143 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 96 atoms, 99 bonds, 12 residues, 1 model selected > select up 2363 atoms, 2427 bonds, 294 residues, 1 model selected > show sel cartoons > select clear > show #!1 models > save ""/Users/qianyuxia/Desktop/Apo 2 与 LTE4.cxs"" ——— End of log from Tue Jan 21 15:01:50 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M4 Pro 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: Mac16,8 Model Number: MX2H3CH/A Chip: Apple M4 Pro Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.61.3 OS Loader Version: 11881.61.3 Software: System Software Overview: System Version: macOS 15.2 (24C101) Kernel Version: Darwin 24.2.0 Time since boot: 9天8小时49分钟 Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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 babel: 2.16.0 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-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-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-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 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 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 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: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 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: 1.26.4 openvr: 1.26.701 packaging: 23.2 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 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 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 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 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 tornado: 6.4.2 traitlets: 5.14.3 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-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX