id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20334 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-26.3.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000203847100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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, chimerax.surface._surface, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, pyKVFinder._pyKVFinder (total: 60) {""app_name"":""ChimeraX"",""timestamp"":""2026-05-16 10:09:39.00 +0800"",""app_version"":""1.11.1"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.3.2 (25D2150)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""1A1011BC-0D86-4CC9-A2C9-25A12115D35C""} { ""uptime"" : 780000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac17,3"", ""coalitionID"" : 25454, ""osVersion"" : { ""train"" : ""macOS 26.3.2"", ""build"" : ""25D2150"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-05-16 10:09:31.5717 +0800"", ""codeSigningMonitor"" : 2, ""incident"" : ""1A1011BC-0D86-4CC9-A2C9-25A12115D35C"", ""pid"" : 39987, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procLaunch"" : ""2026-05-16 00:16:34.0988 +0800"", ""procStartAbsTime"" : 18438480464728, ""procExitAbsTime"" : 18748646517359, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.1"",""CFBundleVersion"":""1.11.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""62A0F0CF-7BC2-5430-9622-BCF66C5ABE12"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""CD2A6953-0FC6-6033-F008-A566D47AA6E0"", ""appleIntelligenceStatus"" : {""reasons"":[""regionIneligible"",""countryLocationIneligible"",""selectedLanguageDoesNotMatchSelectedSiriLanguage"",""selectedLanguageDoesNotMatchSelectedSiriLanguageInfo(system: zh, siri: en-GB)""],""state"":""unavailable""}, ""developerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""CF1B2F98-2564-4DC5-B96E-342D69679BC3"", ""wakeTime"" : 50, ""sleepWakeUUID"" : ""0F3D1E74-4F09-4601-AF5B-4EC322AEBD9B"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= .note.gnu.proper 320 1 Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 864K 26 ColorSync 96K 6 CoreAnimation 2992K 145 CoreGraphics 112K 6 CoreServices 624K 2 CoreUI image data 5376K 41 Foundation 48K 2 Kernel Alloc Once 640K 16 MALLOC 1.0G 265 MALLOC guard page 3328K 4 Mach message 96K 4 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 768K 48 Stack 213.1M 49 Stack Guard 56.0M 1 VM_ALLOCATE 248.1M 586 VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated) __AUTH 5968K 656 __AUTH_CONST 90.5M 1042 __CTF 824 1 __DATA 43.0M 1143 __DATA_CONST 59.8M 1188 __DATA_DIRTY 8499K 899 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 620.4M 142 __OBJC_RO 78.4M 1 __OBJC_RW 2571K 1 __TEXT 1.5G 1206 __TEXT (graphics) 1792K 5 __TPRO_CONST 128K 2 dyld private memory 2992K 26 mapped file 721.8M 115 page table in kernel 1747K 1 shared memory 3280K 27 =========== ======= ======= TOTAL 4.8G 7668 TOTAL, minus reserved VM space 4.6G 7668 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f31f03f675416ce734b24a903751cb5008b1578c"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : [ ""6526e111d0c9ce2f459b54a8"" ], ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > ""/Users/fahn/Desktop/2026-01/20240323_4u9l_TM1TM2loopRemodeling_for_Hattori- > sensei > 2/ColabFold/good_structures/d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"" > format pdb Chain information for d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1 --- Chain | Description A B | No description available Computing secondary structure > select add #1 2684 atoms, 2712 bonds, 346 residues, 1 model selected > hide sel atoms > style sel ball Changed 2684 atom styles > select subtract #1 Nothing selected > select add #1 2684 atoms, 2712 bonds, 346 residues, 1 model selected > select subtract #1 Nothing selected > color #1 #0096ffff > color #1 #d4fb79ff > color #1 #73fcd6ff > color #1 #ff8ad8ff > color #1 #ff7e79ff > show cartoons > show atoms > hide atoms > style stick Changed 2684 atom styles > style sphere Changed 2684 atom styles > volume planes z style image imageMode ""full region"" No volumes specified > volume showOutlineBox true No volumes specified > volume showOutlineBox true No volumes specified > view orient > volume step 2 No volumes specified > volume step 1 No volumes specified > ui mousemode right ""tape measure"" > marker segment #2 position 6.684,-4.699,6.742 toPosition 6.684,-4.699,6.742 > color yellow radius 0.1 label 0 labelHeight 0.2 labelColor yellow > select add #1 2684 atoms, 2712 bonds, 346 residues, 1 model selected > volume showOutlineBox true No volumes specified > ui mousemode right ""tape measure"" > ui mousemode right windowing > segmentations mouseModes true > ui mousemode shift wheel 'resize segmentation cursor' > ui mousemode right 'create segmentations' > ui mousemode shift right 'erase segmentations' > ui mousemode shift middle 'move segmentation cursor' > select subtract #1 Nothing selected > volume projectionMode 2d-xyz No volumes specified > volume appearance airways No volumes specified > ui mousemode right ""crop volume"" > ui mousemode right ""tape measure"" > segmentations mouseModes false > ui mousemode shift wheel 'none' > ui mousemode right 'windowing' > ui mousemode shift right 'none' > ui mousemode shift middle 'none' > segmentations mouseModes true > ui mousemode shift wheel 'resize segmentation cursor' > ui mousemode right 'create segmentations' > ui mousemode shift right 'erase segmentations' > ui mousemode shift middle 'move segmentation cursor' > ui mousemode right ""tape measure"" > select clear > select #1/A:113 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:117 9 atoms, 8 bonds, 1 residue, 1 model selected Drag select of 1 residues > select #1/A:113 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right select > ui mousemode right ""tape measure"" > marker delete #2 > open /Users/fahn/Desktop/2026-01/SSRF-20251218_refine_10-dimer.pdb Summary of feedback from opening /Users/fahn/Desktop/2026-01/SSRF-20251218_refine_10-dimer.pdb --- note | Combining 2 symmetry atoms into CA /C:2 CA Chain information for SSRF-20251218_refine_10-dimer.pdb #2 --- Chain | Description A E | No description available Computing secondary structure > ui tool show Matchmaker > matchmaker #2/E to #1/B 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 d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#1) with SSRF-20251218_refine_10-dimer.pdb, chain E (#2), sequence alignment score = 876.3 RMSD between 173 pruned atom pairs is 0.473 angstroms; (across all 173 pairs: 0.473) > open /Users/fahn/Desktop/2026-01/MgtE-sol-d940_refine_22-dimer.pdb Chain information for MgtE-sol-d940_refine_22-dimer.pdb #3 --- Chain | Description A C | No description available 54 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > ui tool show H-Bonds > ui tool show Matchmaker > open /Users/fahn/Desktop/2026-01/20240321_4u9l_redesign1_result_for_Hattori- > sensei/ColabFold/good_designs/d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb Chain information for d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb #4 --- Chain | Description A B | No description available Computing secondary structure > ui tool show Matchmaker > matchmaker #3/C to #4/B 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 d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb, chain B (#4) with MgtE-sol-d940_refine_22-dimer.pdb, chain C (#3), sequence alignment score = 896.8 RMSD between 177 pruned atom pairs is 0.464 angstroms; (across all 177 pairs: 0.464) > hide #1 models > hide #2 models > show #2 models > hide #3 models > hide #4 models > show #3 models > hide #2 models > hide #3 models > ui tool show Matchmaker > matchmaker #4/B to #1/B 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 d923_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#1) with d940_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000_AB.pdb, chain B (#4), sequence alignment score = 644.6 RMSD between 135 pruned atom pairs is 0.523 angstroms; (across all 173 pairs: 14.724) > show #1 models > show #2 models > hide #2 models > hide #1 models > show #3 models > show #4 models > hide #4 models > show #1 models > hide #1 models > hide #3 models > show #4 models > show #2 models > hide #2 models > show #1 models > sequence chain #1/A Alignment identifier is 1/A > select #1/A:8 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:8-35 229 atoms, 230 bonds, 28 residues, 1 model selected > hide #1 models > show #1 models > hide #4 models > hide #1 models > show #4 models > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > select #1/A:8 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:8-35 229 atoms, 230 bonds, 28 residues, 1 model selected > select add #4 3025 atoms, 3060 bonds, 384 residues, 2 models selected > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > sequence chain #4/A,B Alignment identifier is 1 > select #4/A:8/B:186 10 atoms, 8 bonds, 2 residues, 1 model selected > select #4/A:8-42/B:186-220 584 atoms, 588 bonds, 70 residues, 1 model selected > show #1 models > hide #1 models > select #4/A:43-44/B:221-222 38 atoms, 40 bonds, 4 residues, 1 model selected > select #4/A:43-45/B:221-223 56 atoms, 58 bonds, 6 residues, 1 model selected > show #1 models > hide #4 models > select #1/A:8 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:8-35 229 atoms, 230 bonds, 28 residues, 1 model selected > show #4 models > select #1/A:40 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:40-69 225 atoms, 229 bonds, 30 residues, 1 model selected > select > #4/A:8-42,44-73,79-111,114-144,149-151,153-177/B:186-220,222-251,257-289,292-322,327-329,331-355 2474 atoms, 2494 bonds, 314 residues, 1 model selected > select #4/A:44/B:222 14 atoms, 14 bonds, 2 residues, 1 model selected > select #4/A:44-73/B:222-251 434 atoms, 440 bonds, 60 residues, 1 model selected > hide #1 models > sequence chain #4/A,B Alignment identifier is 1 > show #1 models > select add #1 3118 atoms, 3152 bonds, 406 residues, 2 models selected > select add #4 5480 atoms, 5542 bonds, 702 residues, 2 models selected > hide #4 models > select subtract #4 2684 atoms, 2712 bonds, 346 residues, 1 model selected > sequence chain #1/A,B Alignment identifier is 2 > select #4/A:8/B:186 10 atoms, 8 bonds, 2 residues, 1 model selected > select #4/A:8-42/B:186-220 584 atoms, 588 bonds, 70 residues, 1 model selected > show #4 models > select #4/A:44/B:222 14 atoms, 14 bonds, 2 residues, 1 model selected > select #4/A:44-73/B:222-251 434 atoms, 440 bonds, 60 residues, 1 model selected > select #4/A:8/B:186 10 atoms, 8 bonds, 2 residues, 1 model selected > select #4/A:8-42/B:186-220 584 atoms, 588 bonds, 70 residues, 1 model selected > select #1/A-B:8 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/A-B:8-36 482 atoms, 486 bonds, 58 residues, 1 model selected > select #1/A-B:36 24 atoms, 24 bonds, 2 residues, 1 model selected > select #1/A-B:34-36 60 atoms, 60 bonds, 6 residues, 1 model selected > select #1/A-B:8 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/A-B:8-35 458 atoms, 460 bonds, 56 residues, 1 model selected > select #4/A:8-9/B:186-187 28 atoms, 26 bonds, 4 residues, 1 model selected > select #4/A:8-41/B:186-219 566 atoms, 570 bonds, 68 residues, 1 model selected > select #1/A-B:8 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/A-B:8-35 458 atoms, 460 bonds, 56 residues, 1 model selected > select #1/A-B:40 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A-B:40-68 434 atoms, 442 bonds, 58 residues, 1 model selected > select #1/A-B:8 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/A-B:8-35 458 atoms, 460 bonds, 56 residues, 1 model selected > hide #4 models > select #1/A-B:40 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A-B:40-68 434 atoms, 442 bonds, 58 residues, 1 model selected > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #1 models > show #1 models > hide #4 models > select #1/A-B:8-9 28 atoms, 26 bonds, 4 residues, 1 model selected > select #1/A-B:8-36 482 atoms, 486 bonds, 58 residues, 1 model selected > select #1/A-B:40 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A-B:40-81 646 atoms, 654 bonds, 84 residues, 1 model selected > select #1/A-B:73-74 28 atoms, 26 bonds, 4 residues, 1 model selected > select #1/A-B:68-74 114 atoms, 112 bonds, 14 residues, 1 model selected > select #1/A-B:40 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A-B:40-67 416 atoms, 424 bonds, 56 residues, 1 model selected > select #1/A-B:8 10 atoms, 8 bonds, 2 residues, 1 model selected > select #1/A-B:8-35 458 atoms, 460 bonds, 56 residues, 1 model selected > hide #1 models > show #4 models > select #4/A:8-9/B:186-187 28 atoms, 26 bonds, 4 residues, 1 model selected > select #4/A:8-42/B:186-220 584 atoms, 588 bonds, 70 residues, 1 model selected > select #4/A:44/B:222 14 atoms, 14 bonds, 2 residues, 1 model selected > select #4/A:44-73/B:222-251 434 atoms, 440 bonds, 60 residues, 1 model selected > show #1 models > hide #4 models > show #4 models > hide #4 models > hide #1 models > show #4 models > hide #4 models > show #1 models > hide #1 models > show #4 models > open /Applications/ChimeraX-1.11.1.app/ '/Applications/ChimeraX-1.11.1.app/' has no suffix > show #1 models > hide #1 models > hide #4 models > show #4 models > show #2 models > show #3 models > hide #4 models > select add #4 2796 atoms, 2830 bonds, 356 residues, 1 model selected > select subtract #4 Nothing selected > ui tool show Matchmaker > matchmaker #3/C to #2/E 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 SSRF-20251218_refine_10-dimer.pdb, chain E (#2) with MgtE- sol-d940_refine_22-dimer.pdb, chain C (#3), sequence alignment score = 635.4 RMSD between 135 pruned atom pairs is 0.755 angstroms; (across all 172 pairs: 14.868) > select #1/B 1342 atoms, 1356 bonds, 173 residues, 1 model selected > hide #2-3 cartoons > show #2-3 cartoons > hide #2 models > hide #3 models > show #3 models > show #2 models > select #3/C 1343 atoms, 1357 bonds, 178 residues, 1 model selected > hide sel cartoons > select #2/E 1331 atoms, 1345 bonds, 173 residues, 1 model selected > hide sel cartoons > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > hide #2 models > hide #3 models > show #1 models > show #4 models > save /Users/fahn/Desktop/vs.cxs > close session > open /Users/fahn/Desktop/vs.cxs format session > view name session-start opened ChimeraX session > interfaces selAtoms 0 buried areas: > hide #4 models > hide #1 models > show #2 models > show #3 models > hide #3 models > show #3 models > hide #2 models > select #3/C 1343 atoms, 1357 bonds, 178 residues, 1 model selected > hide sel atoms > select #3/C 1343 atoms, 1357 bonds, 178 residues, 1 model selected > hide #3 models > show #3 models > select ::name=""SO4"" 10 atoms, 10 bonds, 2 residues, 1 model selected > select ::name=""GOL"" 32 atoms, 26 bonds, 6 residues, 1 model selected > hide sel atoms > select #3/C 1343 atoms, 1357 bonds, 178 residues, 1 model selected > show sel cartoons > select add #3 2905 atoms, 2740 bonds, 549 residues, 1 model selected > select subtract #3 Nothing selected > select add #3 2905 atoms, 2740 bonds, 549 residues, 1 model selected > marker segment #5 position 11.82,13.91,-2.299 toPosition 7.594,10.1,-3.389 > color yellow radius 0.1 label 5.793 labelHeight 0.5793 labelColor yellow > hide #!5 models > hide #!5 target m > show #!5 models > hide #!5 models > hide #5.1 models > ui tool show ""Find Cavities"" > kvfinder #2-3 19 cavities found for SSRF-20251218_refine_10-dimer.pdb #2 SSRF-20251218_refine_10-dimer.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 2.1.1 | | 556.42 | 488.24 | 2576 | 6.12 | 1.63 2.1.11 | | 235.44 | 215.62 | 1090 | 0 | 0 2.1.15 | | 111.02 | 145.03 | 514 | 0 | 0 2.1.3 | | 60.91 | 71.95 | 282 | 2.47 | 0.85 2.1.2 | | 58.1 | 70.01 | 269 | 2.62 | 0.84 2.1.19 | | 26.14 | 35.19 | 121 | 1.2 | 0.46 2.1.13 | | 24.62 | 59.09 | 114 | 0 | 0 2.1.7 | | 21.17 | 39.07 | 98 | 0 | 0 2.1.9 | | 14.26 | 21.68 | 66 | 1.2 | 0.32 2.1.18 | | 12.74 | 23.11 | 59 | 1.2 | 0.31 2.1.6 | | 12.31 | 29.54 | 57 | 0 | 0 2.1.14 | | 12.31 | 29.54 | 57 | 0 | 0 2.1.17 | | 12.31 | 29.54 | 57 | 0 | 0 2.1.8 | | 9.94 | 18.46 | 46 | 0.85 | 0.25 2.1.5 | | 8.64 | 19.12 | 40 | 1.34 | 0.55 2.1.10 | | 8.21 | 15.89 | 38 | 1.2 | 0.34 2.1.4 | | 7.56 | 17.2 | 35 | 1.34 | 0.5 2.1.12 | | 7.34 | 13.6 | 34 | 0.6 | 0.19 2.1.16 | | 5.4 | 12.94 | 25 | 0.6 | 0.12 Populating font family aliases took 40 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. 13 cavities found for MgtE-sol-d940_refine_22-dimer.pdb #3 MgtE-sol-d940_refine_22-dimer.pdb Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 3.1.6 | | 1481.11 | 1075.87 | 6857 | 18.26 | 5.23 3.1.9 | | 41.04 | 56.06 | 190 | 2.68 | 0.7 3.1.8 | | 38.02 | 50.49 | 176 | 1.9 | 0.52 3.1.2 | | 33.26 | 50.42 | 154 | 0 | 0 3.1.13 | | 29.16 | 37.97 | 135 | 1.8 | 0.56 3.1.5 | | 23.33 | 39.8 | 108 | 0 | 0 3.1.7 | | 19.87 | 36.19 | 92 | 0 | 0 3.1.4 | | 19.01 | 38.34 | 88 | 0 | 0 3.1.12 | | 19.01 | 27.91 | 88 | 1.7 | 0.38 3.1.1 | | 17.5 | 40.83 | 81 | 2.16 | 0.9 3.1.11 | | 12.31 | 29.54 | 57 | 0 | 0 3.1.10 | | 8.21 | 15.58 | 38 | 1.2 | 0.39 3.1.3 | | 6.7 | 11.6 | 31 | 0.85 | 0.24 > show #1 models > hide #1 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > view #2.1.1 @ zoom 0.75 moved plane near -40.53221842010549 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -40.53221842010549 [-0.96498108 -0.24989624 0.0797706 ] > surface #2.1.1-19 transparency 50 > ~surface #2.1 > surface #2.1.1 > select #2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #!2.1.11 @ zoom 0.75 moved plane near -24.572493455153815 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -24.572493455153815 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.1 @ zoom 0.75 moved plane near -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #!2.1.11 @ zoom 0.75 moved plane near -28.20274909595857 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -28.20274909595857 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.1 @ zoom 0.75 moved plane near -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -50.8656777460205 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #3.1.6 @ zoom 0.75 moved plane near -48.861023411397944 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -48.861023411397944 [-0.96498108 -0.24989624 0.0797706 ] > surface #3.1.1-13 transparency 50 > ~surface #3.1 > surface #3.1.6 > select #3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162 > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #1 models > show #!2 models > hide #1 models > show #!3 models > hide #!2 models > select add #3 11000 atoms, 2740 bonds, 562 residues, 16 models selected > select subtract #3 13 models selected > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > view #!2.1.11 @ zoom 0.75 moved plane near -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.1 @ zoom 0.75 moved plane near -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > select add #2 8285 atoms, 2700 bonds, 402 residues, 22 models selected > select subtract #2 19 models selected > select add #2 8285 atoms, 2700 bonds, 402 residues, 21 models selected > select #2/E 1331 atoms, 1345 bonds, 173 residues, 1 model selected > show sel cartoons > select add #2 8285 atoms, 2700 bonds, 402 residues, 21 models selected > select subtract #2 19 models selected > view #!3.1.9 @ zoom 0.75 moved plane near -21.271883453837066 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -21.271883453837066 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #3.1 > surface #!3.1.9 > select #!3.1.9 190 atoms, 1 residue, 1 model selected > show #!3/A:57,126-128,130-131,134,160-161,164-165,168 > view #!3.1.6 @ zoom 0.75 moved plane near -60.072447736261914 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -60.072447736261914 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #3.1 > surface #!3.1.6 > select #!3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162 > view #!2.1.11 @ zoom 0.75 moved plane near -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -32.22259946335476 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.1 @ zoom 0.75 moved plane near -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ] moved plane far -53.53413084780411 [-0.96498108 -0.24989624 0.0797706 ] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #!2.1.11 @ zoom 0.75 moved plane near -34.46109721666628 [-0.14067287 0.33287003 -0.93242086] moved plane far -34.46109721666628 [-0.14067287 0.33287003 -0.93242086] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!3.1.9 @ zoom 0.75 moved plane near -26.76603627620702 [-0.14067287 0.33287003 -0.93242086] moved plane far -26.76603627620702 [-0.14067287 0.33287003 -0.93242086] > ~surface #3.1 > surface #!3.1.9 > select #!3.1.9 190 atoms, 1 residue, 1 model selected > show #!3/A:57,126-128,130-131,134,160-161,164-165,168 > show #!3 models > hide #!2 models > view #!3.1.6 @ zoom 0.75 moved plane near -57.88501970624285 [-0.13673975 0.28194493 -0.94963638] moved plane far -57.88501970624285 [-0.13673975 0.28194493 -0.94963638] > ~surface #3.1 > surface #!3.1.6 > select #!3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162 > view #!3.1.9 @ zoom 0.75 moved plane near -27.629945024598456 [-0.13673975 0.28194493 -0.94963638] moved plane far -27.629945024598456 [-0.13673975 0.28194493 -0.94963638] > ~surface #3.1 > surface #!3.1.9 > select #!3.1.9 190 atoms, 1 residue, 1 model selected > show #!3/A:57,126-128,130-131,134,160-161,164-165,168 > view #!3.1.6 @ zoom 0.75 moved plane near -57.88501970624285 [-0.13673975 0.28194493 -0.94963638] moved plane far -57.88501970624285 [-0.13673975 0.28194493 -0.94963638] > ~surface #3.1 > surface #!3.1.6 > select #!3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162 > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > view #!2.1.1 @ zoom 0.75 moved plane near -55.31161885335286 [-0.13673975 0.28194493 -0.94963638] moved plane far -55.31161885335286 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #!2.1.11 @ zoom 0.75 moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.1 @ zoom 0.75 moved plane near -55.31161885335286 [-0.13673975 0.28194493 -0.94963638] moved plane far -55.31161885335286 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #!2.1.11 @ zoom 0.75 moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.15 @ zoom 0.75 moved plane near -28.403875210640678 [-0.13673975 0.28194493 -0.94963638] moved plane far -28.403875210640678 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.15 > select #!2.1.15 514 atoms, 1 residue, 1 model selected > show #!2/A:33,38,42,45-46,49/E:33,41-42,45-46,49,164-165 > view #!2.1.11 @ zoom 0.75 moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!2.1.1 @ zoom 0.75 moved plane near -55.31161885335286 [-0.13673975 0.28194493 -0.94963638] moved plane far -55.31161885335286 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58-62,64-66,68,71,145-146,149/E:1-3,11,14-15,18,58-62,64-66,68,144-150 > view #!2.1.11 @ zoom 0.75 moved plane near -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] moved plane far -33.83089111949969 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49-50,52-54,57,153-154,156-157 > view #!3.1.9 @ zoom 0.75 moved plane near -27.629945024598456 [-0.13673975 0.28194493 -0.94963638] moved plane far -27.629945024598456 [-0.13673975 0.28194493 -0.94963638] > ~surface #3.1 > surface #!3.1.9 > select #!3.1.9 190 atoms, 1 residue, 1 model selected > show #!3/A:57,126-128,130-131,134,160-161,164-165,168 > view #!3.1.6 @ zoom 0.75 moved plane near -57.88501970624285 [-0.13673975 0.28194493 -0.94963638] moved plane far -57.88501970624285 [-0.13673975 0.28194493 -0.94963638] > ~surface #3.1 > surface #!3.1.6 > select #!3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54-56,58-59,62-63,65-67,69-70,149-159,161-162/C:18-19,22-23,26,50-51,54-59,62-63,65-67,69-70,149-155,157-159,161-162 > show #!2 models > hide #!3 models > hide #!2/E,A:50,52-54,154 > hide #!3/A:55,58,67,149,152,156/C:55,57-58,67,149 > view #!2.1.1 @ zoom 0.75 moved plane near -45.87686358887427 [-0.13673975 0.28194493 -0.94963638] moved plane far -45.87686358887427 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.1 > select #!2.1.1 2576 atoms, 1 residue, 1 model selected > show > #!2/A:1,3,11,14-15,18,58,61-62,64-66,68,71,145-146,149/E:1,3,11,14-15,18,58,61-62,64-66,68,145-146,148-150 > view #!2.1.11 @ zoom 0.75 moved plane near -31.144026255720505 [-0.13673975 0.28194493 -0.94963638] moved plane far -31.144026255720505 [-0.13673975 0.28194493 -0.94963638] > ~surface #2.1 > surface #!2.1.11 > select #!2.1.11 1090 atoms, 1 residue, 1 model selected > show #!2/A,E:49,57,153,156-157 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > marker delete #5 > ui windowfill toggle > select #1/A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A-B:9 18 atoms, 16 bonds, 2 residues, 1 model selected > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > show #!2 models > hide #!3 models > hide #4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > view #!3.1.9 @ zoom 0.75 moved plane near -36.97371809266014 [-0.50665092 0.48323984 -0.71399164] moved plane far -36.97371809266014 [-0.50665092 0.48323984 -0.71399164] > ~surface #3.1 > surface #!3.1.9 > select #!3.1.9 190 atoms, 1 residue, 1 model selected > show #!3/A:127,130-131,134,160-161,164,168 > view #!3.1.6 @ zoom 0.75 moved plane near -77.06418463062619 [-0.50665092 0.48323984 -0.71399164] moved plane far -77.06418463062619 [-0.50665092 0.48323984 -0.71399164] > ~surface #3.1 > surface #!3.1.6 > select #!3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-151,153-155,157-159,161-162/C:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-155,157-159,161-162 > view #!3.1.9 @ zoom 0.75 moved plane near -36.97371809266014 [-0.50665092 0.48323984 -0.71399164] moved plane far -36.97371809266014 [-0.50665092 0.48323984 -0.71399164] > ~surface #3.1 > surface #!3.1.9 > select #!3.1.9 190 atoms, 1 residue, 1 model selected > show #!3/A:127,130-131,134,160-161,164,168 > view #!3.1.6 @ zoom 0.75 moved plane near -77.06418463062619 [-0.50665092 0.48323984 -0.71399164] moved plane far -77.06418463062619 [-0.50665092 0.48323984 -0.71399164] > ~surface #3.1 > surface #!3.1.6 > select #!3.1.6 6857 atoms, 1 residue, 1 model selected > show > #!3/A:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-151,153-155,157-159,161-162/C:18-19,22-23,26,50-51,54,56,59,62-63,65-66,69-70,150-155,157-159,161-162 > select #!2 & (#!2.1.11 @ select #!3 & (#!3.1.6 @ ~select #!2 & (#!2.1.11 @ ~select #!3 & (#!3.1.6 @ select #!2 & (#!2.1.11 @ select #!3 & (#!3.1.6 @ ~select #!2 & (#!2.1.11 @ ~select #!3 & (#!3.1.6 @ select #!2 & (#!2.1.11 @ select #!3 & (#!3.1.6 @ view sel > volume showOutlineBox true No volumes specified > volume showOutlineBox true No volumes specified > volume showOutlineBox true No volumes specified > volume showOutlineBox true No volumes specified > volume showOutlineBox true No volumes specified > select add #3 11000 atoms, 2740 bonds, 562 residues, 15 models selected > select subtract #3 13 models selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M5 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac17,3 Model Number: Z1L90002MCH/A Chip: Apple M5 Total Number of Cores: 10 (4 Super and 6 Efficiency) Memory: 16 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.2 (25D2150) Kernel Version: Darwin 25.3.0 Time since boot: 22天19小时49分钟 Graphics/Displays: Apple M5: Chipset Model: Apple M5 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 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: No Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.21.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 2.4.4 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.1 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.15.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned