id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18321 mshMIGPerform crash chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x000000020d581f00 (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, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 59) {""app_name"":""ChimeraX"",""timestamp"":""2025-07-31 02:34:31.00 +0800"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.5 (24F74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""FCCFF855-2918-4FA1-8352-679A13040F8C""} { ""uptime"" : 380000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,12"", ""coalitionID"" : 41501, ""osVersion"" : { ""train"" : ""macOS 15.5"", ""build"" : ""24F74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-07-31 02:34:31.0977 +0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""FCCFF855-2918-4FA1-8352-679A13040F8C"", ""pid"" : 81221, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-07-31 01:38:46.1045 +0800"", ""procStartAbsTime"" : 9184357185182, ""procExitAbsTime"" : 9264635709622, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""2CDE3E10-BCC2-5CE8-ADD8-9545F3BAAD71"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""4F206021-E1E0-3AF2-F2BE-B563ABAFF9DA"", ""appleIntelligenceStatus"" : {""reasons"":[""regionIneligible"",""countryBillingIneligible"",""countryLocationIneligible""],""state"":""unavailable""}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""7615A680-4F44-4819-9EB4-E89338A0F41D"", ""wakeTime"" : 5989, ""sleepWakeUUID"" : ""6E097701-6185-4B14-BA99-19EC102F75DA"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x3 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open > ""/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application > Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4 > Model/WT-4cGMP-Open-coot-9-final.pdb"" Chain information for WT-4cGMP-Open-coot-9-final.pdb #1 --- Chain | Description A B C D | No description available > open > ""/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application > Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4 > Model/apo-WT-zx-coot-10-final.pdb"" Chain information for apo-WT-zx-coot-10-final.pdb #2 --- Chain | Description A B C D | No description available > open > ""/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application > Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4 > Model/3WT-1EA-3cGMP-Open-coot-28-Final.pdb"" Chain information for 3WT-1EA-3cGMP-Open-coot-28-Final.pdb #3 --- Chain | Description A B C | No description available D | No description available > open > ""/Users/daisy/Library/Containers/com.tencent.xinWeChat/Data/Library/Application > Support/com.tencent.xinWeChat/2.0b4.0.9/4ab61b2092f657967c9150833138310e/Message/MessageTemp/217b9cf35a6b26eec7e599641c75feb8/File/TAX-4 > Model/3EA-1WT-1cGMP-Clsoed-coot-24-Final.pdb"" Chain information for 3EA-1WT-1cGMP-Clsoed-coot-24-Final.pdb #4 --- Chain | Description A | No description available B C D | No description available > open ""/Users/daisy/Library/Mobile > Documents/com~apple~CloudDocs/Documents/TAX4/Finnal PDB and map/3WT-EA > close/3WT-EA close.pdb"" Chain information for 3WT-EA close.pdb #5 --- Chain | Description A B C | No description available D | No description available > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Computing secondary structure 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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with apo-WT-zx- coot-10-final.pdb, chain A (#2), sequence alignment score = 2609 RMSD between 285 pruned atom pairs is 0.573 angstroms; (across all 513 pairs: 3.486) > matchmaker #3/A to #1/A pairing ss Computing secondary structure 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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3WT-1EA-3cGMP- Open-coot-28-Final.pdb, chain A (#3), sequence alignment score = 2669.9 RMSD between 486 pruned atom pairs is 0.607 angstroms; (across all 518 pairs: 0.860) > matchmaker #4/A to #1/A pairing ss Computing secondary structure 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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3EA-1WT-1cGMP- Clsoed-coot-24-Final.pdb, chain A (#4), sequence alignment score = 2587.4 RMSD between 416 pruned atom pairs is 0.938 angstroms; (across all 513 pairs: 1.681) > matchmaker #4/A to #1/A pairing ss Computing secondary structure 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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3EA-1WT-1cGMP- Clsoed-coot-24-Final.pdb, chain A (#4), sequence alignment score = 2587.4 RMSD between 416 pruned atom pairs is 0.938 angstroms; (across all 513 pairs: 1.681) > matchmaker #5/A to #1/A pairing ss Computing secondary structure 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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 3WT-EA close.pdb, chain A (#5), sequence alignment score = 2452 RMSD between 477 pruned atom pairs is 0.828 angstroms; (across all 514 pairs: 1.248) > hide #!4 models > hide #3 models > hide #!2 models > hide #1 models > show #1 models > show #!2 models > hide #!2 models > hide #!5 models > hide #1 models > show #!4 models > show #1 models > select: 421 Unknown command: select: 421 > select :421 220 atoms, 200 bonds, 20 residues, 5 models selected > show sel & #1#!4 atoms > select clear > show #3 models > hide #3 models > show #3 models > show #!5 models > show #!2 models > select :421 220 atoms, 200 bonds, 20 residues, 5 models selected > show sel atoms > ui tool show ""Side View"" > select clear > color #2 light gray > color byhetero > color #5 lavender > color #5 Lavender Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5 bubblegum Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5 #d783ffff > color #3 #ff9300ff > color #3 #ff7e79ff > color byattribute hetero No known/registered numeric attribute hetero > color byhetero > open ""/Users/daisy/Library/Mobile > Documents/com~apple~CloudDocs/Documents/TAX4/Finnal PDB and map/2WT-2EA > close/2WT-2EA close.pdb"" Chain information for 2WT-2EA close.pdb #6 --- Chain | Description A B C | No description available D | No description available > ui tool show Matchmaker > matchmaker #6/A to #1/A pairing ss Computing secondary structure 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 WT-4cGMP-Open-coot-9-final.pdb, chain A (#1) with 2WT-2EA close.pdb, chain A (#6), sequence alignment score = 2481.4 RMSD between 386 pruned atom pairs is 1.019 angstroms; (across all 514 pairs: 1.896) > select :421 264 atoms, 240 bonds, 24 residues, 6 models selected > show sel atoms > color #6 #941751ff > color #6 #0096ffff > color #6 #76d6ffff > color byhetero > select clear > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #1 models > hide #3 models > hide #!4 models > hide #!5 models > select #2/D:456 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > color sel bychain > select #2/A:299 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:302 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/A:299 13 atoms, 11 bonds, 2 residues, 1 model selected > select add #2/A:304 20 atoms, 18 bonds, 3 residues, 1 model selected > select add #2/A:305 28 atoms, 25 bonds, 4 residues, 1 model selected > select subtract #2/A:304 21 atoms, 18 bonds, 3 residues, 1 model selected > show sel atoms > select #2/A:300 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/A:301 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color byhetero > select #2/D:420 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/D:421 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/D:421 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/D:420 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/D:419 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #2/D:417 18 atoms, 15 bonds, 3 residues, 1 model selected > select add #2/D:418 24 atoms, 20 bonds, 4 residues, 1 model selected > select add #2/D:416 32 atoms, 27 bonds, 5 residues, 1 model selected > select add #2/D:415 38 atoms, 32 bonds, 6 residues, 1 model selected > select add #2/D:414 46 atoms, 39 bonds, 7 residues, 1 model selected > select add #2/D:413 54 atoms, 46 bonds, 8 residues, 1 model selected > show sel atoms > show #3 models > show #!4 models > show #!5 models > show #!6 models > select: 413-421 Unknown command: select: 413-421 > select :413-421 1560 atoms, 1536 bonds, 216 residues, 6 models selected > show sel & #3#!2,4-6 atoms > select :456 336 atoms, 360 bonds, 24 residues, 6 models selected > select #3/B:452 11 atoms, 11 bonds, 1 residue, 1 model selected > select :452 264 atoms, 264 bonds, 24 residues, 6 models selected > show sel & #3#!2,4-6 atoms > select :456 336 atoms, 360 bonds, 24 residues, 6 models selected > show sel & #3#!2,4-6 atoms > select :452 264 atoms, 264 bonds, 24 residues, 6 models selected > hide sel & #3#!2,4-6 atoms > show #1 models > select up 3662 atoms, 3782 bonds, 387 residues, 6 models selected > select :456 336 atoms, 360 bonds, 24 residues, 6 models selected > show sel atoms > select :413-421 1560 atoms, 1536 bonds, 216 residues, 6 models selected > show sel atoms > select :299 168 atoms, 144 bonds, 24 residues, 6 models selected > show sel atoms > select :301-302 288 atoms, 264 bonds, 48 residues, 6 models selected > show sel atoms > select :301-305 840 atoms, 840 bonds, 120 residues, 6 models selected > show sel atoms > hide sel atoms > select :301-302 288 atoms, 264 bonds, 48 residues, 6 models selected > show sel atoms > select :305 192 atoms, 168 bonds, 24 residues, 6 models selected > show sel atoms > hide #!6 models > hide #!5 models > hide #3 models > hide #!2 models > hide #!4 models > show #!2 models > show #3 models > show #!4 models > show #!5 models > show #!6 models > select :298 216 atoms, 192 bonds, 24 residues, 6 models selected > show sel atoms > select :305 192 atoms, 168 bonds, 24 residues, 6 models selected > hide sel atoms > hide #!6 models > hide #!5 models > hide #!4 models > hide #3 models > hide #!2 models > save /Users/daisy/Desktop/00001.cxs > select #1/B:456@NE1 1 atom, 1 residue, 1 model selected > select #1/B:421@NH1 1 atom, 1 residue, 1 model selected > select add #1/B:456@NE1 2 atoms, 2 residues, 1 model selected > distance #1/B:421@NH1 #1/B:456@NE1 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B ARG 421 NH1 and TRP 456 NE1: 3.205Å > select #1/B:421@NH2 1 atom, 1 residue, 1 model selected > select add #1/A:299@OG1 2 atoms, 2 residues, 1 model selected > select subtract #1/A:299@OG1 1 atom, 1 residue, 1 model selected > select add #1/A:299@OG1 2 atoms, 2 residues, 1 model selected > distance #1/B:421@NH2 #1/A:299@OG1 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B ARG 421 NH2 and /A THR 299 OG1: 4.342Å > select #1/A:299@OG1 1 atom, 1 residue, 1 model selected > select #1/A:299@OG1 1 atom, 1 residue, 1 model selected > select clear > select #1/B:421@NH2 1 atom, 1 residue, 1 model selected > select add #1/A:298@OE2 2 atoms, 2 residues, 1 model selected > select subtract #1/A:298@OE2 1 atom, 1 residue, 1 model selected > select add #1/A:298@OE2 2 atoms, 2 residues, 1 model selected > select subtract #1/A:298@OE2 1 atom, 1 residue, 1 model selected > select add #1/A:298@OE2 2 atoms, 2 residues, 1 model selected > select #1/A:298@OE2 1 atom, 1 residue, 1 model selected > select add #1/B:421@NH2 2 atoms, 2 residues, 1 model selected > select subtract #1/B:421@NH2 1 atom, 1 residue, 1 model selected > select add #1/B:421@NH2 2 atoms, 2 residues, 1 model selected > select subtract #1/B:421@NH2 1 atom, 1 residue, 1 model selected > select add #1/B:421@NH2 2 atoms, 2 residues, 1 model selected > distance #1/A:298@OE2 #1/B:421@NH2 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/A GLU 298 OE2 and /B ARG 421 NH2: 2.313Å > select #1/A:295 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select add #1/A:295@OE2 1 atom, 1 bond, 1 residue, 1 model selected > select subtract #1/A:295@OE2 1 bond, 1 model selected > select add #1/A:295@OE2 1 atom, 1 bond, 1 residue, 1 model selected > select clear > select #1/B:421@NE 1 atom, 1 residue, 1 model selected > select #1/A:295@OE2 1 atom, 1 residue, 1 model selected > select add #1/B:421@NE 2 atoms, 2 residues, 1 model selected > distance #1/A:295@OE2 #1/B:421@NE Distance between WT-4cGMP-Open-coot-9-final.pdb #1/A GLU 295 OE2 and /B ARG 421 NE: 4.807Å > select #1/B:456@NE1 1 atom, 1 residue, 1 model selected > select add #1/B:421@NE 2 atoms, 1 pseudobond, 2 residues, 2 models selected > select subtract #1/B:421@NE 1 atom, 1 residue, 1 model selected > select add #1/B:421@NE 2 atoms, 2 residues, 1 model selected > distance #1/B:456@NE1 #1/B:421@NE Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B TRP 456 NE1 and ARG 421 NE: 4.599Å > ui tool show Distances > ~distance #1/B:456@NE1 #1/B:421@NE > ~distance #1/A:295@OE2 #1/B:421@NE > hide sel atoms > select add #1/A:295@OE1 1 atom, 5 bonds, 1 residue, 1 model selected > select add #1/A:295@OE2 2 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1/A:295@CD 3 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1/A:295@CG 4 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select add #1/A:295@CB 5 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > hide #1 models > show #1 models > select #1/D:456@NE1 1 atom, 1 residue, 1 model selected > select add #1/D:421@NH1 2 atoms, 2 residues, 1 model selected > distance #1/D:456@NE1 #1/D:421@NH1 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/D TRP 456 NE1 and ARG 421 NH1: 3.330Å > select #1/C:299@OG1 1 atom, 1 residue, 1 model selected > select add #1/D:421@NH2 2 atoms, 2 residues, 1 model selected > distance #1/C:299@OG1 #1/D:421@NH2 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C THR 299 OG1 and /D ARG 421 NH2: 4.330Å > select #1/C:298@OE2 1 atom, 1 residue, 1 model selected > select add #1/D:421@NH2 2 atoms, 2 residues, 1 model selected > distance #1/C:298@OE2 #1/D:421@NH2 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C GLU 298 OE2 and /D ARG 421 NH2: 2.313Å > select clear > select #1/A:456@NE1 1 atom, 1 residue, 1 model selected > select add #1/A:421@NH1 2 atoms, 2 residues, 1 model selected > select subtract #1/A:421@NH1 1 atom, 1 residue, 1 model selected > select add #1/A:421@NH1 2 atoms, 2 residues, 1 model selected > distance #1/A:456@NE1 #1/A:421@NH1 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/A TRP 456 NE1 and ARG 421 NH1: 2.939Å > select #1/D:299@OG1 1 atom, 1 residue, 1 model selected > select add #1/A:421@NH2 2 atoms, 2 residues, 1 model selected > distance #1/D:299@OG1 #1/A:421@NH2 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/D THR 299 OG1 and /A ARG 421 NH2: 4.018Å > select #1/D:298@OE1 1 atom, 1 residue, 1 model selected > select add #1/A:421@NH2 2 atoms, 2 residues, 1 model selected > distance #1/D:298@OE1 #1/A:421@NH2 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/D GLU 298 OE1 and /A ARG 421 NH2: 3.663Å > select clear > select #1/C:421@NH1 1 atom, 1 residue, 1 model selected > select add #1/C:456@NE1 2 atoms, 2 residues, 1 model selected > distance #1/C:421@NH1 #1/C:456@NE1 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C ARG 421 NH1 and TRP 456 NE1: 2.877Å > select #1/B:299@OG1 1 atom, 1 residue, 1 model selected > select add #1/C:421@NH1 2 atoms, 1 pseudobond, 2 residues, 2 models selected > select #1/B:299@OG1 1 atom, 1 residue, 1 model selected > select add #1/C:421@NH1 2 atoms, 2 residues, 1 model selected > distance #1/B:299@OG1 #1/C:421@NH1 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/B THR 299 OG1 and /C ARG 421 NH1: 4.568Å > select #1/C:421@NH2 1 atom, 1 residue, 1 model selected > select add #1/B:298@OE2 2 atoms, 2 residues, 1 model selected > distance #1/C:421@NH2 #1/B:298@OE2 Distance between WT-4cGMP-Open-coot-9-final.pdb #1/C ARG 421 NH2 and /B GLU 298 OE2: 2.518Å > select clear > hide #1 models > show #!2 models > select #2/C:421@NH2 1 atom, 1 residue, 1 model selected > select add #2/D:298@OE2 2 atoms, 2 residues, 1 model selected > select subtract #2/D:298@OE2 1 atom, 1 residue, 1 model selected > select add #2/D:298@OE2 2 atoms, 2 residues, 1 model selected > distance #2/C:421@NH2 #2/D:298@OE2 Distance between apo-WT-zx-coot-10-final.pdb #2/C ARG 421 NH2 and /D GLU 298 OE2: 3.218Å > select #2/C:421@NH2 1 atom, 1 residue, 1 model selected > select add #2/D:299@OG1 2 atoms, 2 residues, 1 model selected > distance #2/C:421@NH2 #2/D:299@OG1 Distance between apo-WT-zx-coot-10-final.pdb #2/C ARG 421 NH2 and /D THR 299 OG1: 3.485Å > select add #2/C:456@NE1 3 atoms, 3 residues, 1 model selected > select clear > select #2/C:456@NE1 1 atom, 1 residue, 1 model selected > select add #2/C:421@NH2 2 atoms, 1 pseudobond, 2 residues, 2 models selected > distance #2/C:456@NE1 #2/C:421@NH2 Distance between apo-WT-zx-coot-10-final.pdb #2/C TRP 456 NE1 and ARG 421 NH2: 5.925Å > select clear > select #2/C:456@NE1 1 atom, 1 residue, 1 model selected > select clear > select #2/C:421@NE 1 atom, 1 residue, 1 model selected > select add #2/C:456@NE1 2 atoms, 2 residues, 1 model selected > distance #2/C:421@NE #2/C:456@NE1 Distance between apo-WT-zx-coot-10-final.pdb #2/C ARG 421 NE and TRP 456 NE1: 4.569Å > select clear > select #2/C:298@OE1 1 atom, 1 residue, 1 model selected > select add #2/B:421@NE 2 atoms, 2 residues, 1 model selected > distance #2/C:298@OE1 #2/B:421@NE Distance between apo-WT-zx-coot-10-final.pdb #2/C GLU 298 OE1 and /B ARG 421 NE: 3.456Å > select add #2/C:299@OG1 3 atoms, 3 residues, 1 model selected > select add #2/B:421@NH2 4 atoms, 3 residues, 1 model selected > select clear > select #2/B:421@NH2 1 atom, 1 residue, 1 model selected > select add #2/C:299@OG1 2 atoms, 2 residues, 1 model selected > distance #2/B:421@NH2 #2/C:299@OG1 Distance between apo-WT-zx-coot-10-final.pdb #2/B ARG 421 NH2 and /C THR 299 OG1: 7.036Å > select clear > select #2/B:421@NH2 1 atom, 1 residue, 1 model selected > select add #2/C:298@OE1 2 atoms, 2 residues, 1 model selected > distance #2/B:421@NH2 #2/C:298@OE1 Distance between apo-WT-zx-coot-10-final.pdb #2/B ARG 421 NH2 and /C GLU 298 OE1: 4.335Å > select #2/B:421@NH1 1 atom, 1 residue, 1 model selected > select add #2/B:456@NE1 2 atoms, 2 residues, 1 model selected > select clear > select #2/B:456@NE1 1 atom, 1 residue, 1 model selected > select add #2/B:421@NH2 2 atoms, 2 residues, 1 model selected > distance #2/B:456@NE1 #2/B:421@NH2 Distance between apo-WT-zx-coot-10-final.pdb #2/B TRP 456 NE1 and ARG 421 NH2: 3.135Å > hide #!7 models > show #!7 models > hide #7.1 models > show #7.1 models > hide #7.1 models > show #7.1 models > hide #!7 models > show #!7 models > distance style symbol false > distance style symbol true ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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 Air Model Identifier: Mac15,12 Model Number: Z1HY00019CH/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 8天16小时2分钟 Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal XSN-27Q: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported 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 Platform duplicate all ChimeraX