id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16077 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001ebb98f40 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2024-10-06 00:27:56.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.6.1 (23G93)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""1B6C1DD4-1951-4068-89D9-EF769B17D5C4""} { ""uptime"" : 270000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir10,1"", ""coalitionID"" : 32209, ""osVersion"" : { ""train"" : ""macOS 14.6.1"", ""build"" : ""23G93"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-10-06 00:27:31.0548 +0100"", ""codeSigningMonitor"" : 1, ""incident"" : ""1B6C1DD4-1951-4068-89D9-EF769B17D5C4"", ""pid"" : 52873, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-10-05 19:35:28.8394 +0100"", ""procStartAbsTime"" : 6335876266617, ""procExitAbsTime"" : 6643992767187, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""95EA9875-E798-50C2-A70E-4ADB9E064864"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""436138E8-7B98-5034-1A43-08D6C4D3F078"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 3842, ""sleepWakeUUID"" : ""11B08CCA-B400-45A8-9AEF-9AB13D637A6B"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x45a347a48a58 is not in any region. 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""\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox"", ""name"" : ""HIToolbox"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6502977536, ""size"" : 562440, ""uuid"" : ""f635824e-318b-3f0c-842c-c369737f2b68"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6505754624, ""size"" : 577528, ""uuid"" : ""aaa5636d-6f3f-3fa7-9f4a-cf966f0308fe"", ""path"" : ""\/usr\/lib\/libc++.1.dylib"", ""name"" : ""libc++.1.dylib"" } ], ""sharedCache"" : { ""base"" : 6502219776, ""size"" : 4214358016, ""uuid"" : ""bb3df3d3-38bd-304c-9233-e43de95f1903"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 848K 34 \nColorSync 656K 31 \nCoreAnimation 2896K 142 \nCoreGraphics 48K 3 \nCoreUI image data 5440K 43 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.8G 96 \nMALLOC guard page 192K 12 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.6M 36 \nStack 153.8M 36 \nVM_ALLOCATE 214.7M 170 \nVM_ALLOCATE (reserved) 128.0M 4 reserved VM address space (unallocated)\n__AUTH 3602K 489 \n__AUTH_CONST 37.7M 723 \n__CTF 824 1 \n__DATA 27.7M 876 \n__DATA_CONST 47.9M 885 \n__DATA_DIRTY 2212K 264 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 555.4M 158 \n__OBJC_RO 71.9M 2 \n__OBJC_RW 2200K 1 \n__TEXT 1.1G 903 \ndyld private memory 592K 6 \nmapped file 275.1M 86 \nshared memory 3136K 24 \n=========== ======= ======= \nTOTAL 5.4G 5041 \nTOTAL, minus reserved VM space 5.3G 5041 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6adeb57a55f13df3622dee06b3c3cc10cf749019"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 }, { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : { }, ""deploymentId"" : 240000031 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/3ltm_A_A_solenoid.pdb"" Chain information for 3ltm_A_A_solenoid.pdb #1 --- Chain | Description A | No description available 13 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/4gpm_A_A_solenoid.pdb"" Chain information for 4gpm_A_A_solenoid.pdb #2 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/4pjs_A_A_solenoid.pdb"" Chain information for 4pjs_A_A_solenoid.pdb #3 --- Chain | Description A | No description available 90 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/4r5c_A_A_solenoid.pdb"" Chain information for 4r5c_A_A_solenoid.pdb #4 --- Chain | Description A | No description available 18 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/5di5_A_A_solenoid.pdb"" Chain information for 5di5_A_A_solenoid.pdb #5 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/5i9d_A_A_solenoid.pdb"" Chain information for 5i9d_A_A_solenoid.pdb #6 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/6veh_A_A_solenoid.pdb"" Chain information for 6veh_A_A_solenoid.pdb #7 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/6xt4_A_A_solenoid.pdb"" Chain information for 6xt4_A_A_solenoid.pdb #8 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/7udo_A_A_solenoid.pdb"" Chain information for 7udo_A_A_solenoid.pdb #9 --- Chain | Description A | No description available 27 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/8c3w_A_A_solenoid.pdb"" Chain information for 8c3w_A_A_solenoid.pdb #10 --- Chain | Description A | No description available 35 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/8eov_A_A_solenoid.pdb"" Chain information for 8eov_A_A_solenoid.pdb #11 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/8erw_A_A_solenoid.pdb"" Chain information for 8erw_A_A_solenoid.pdb #12 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/8ga9_A_A_solenoid.pdb"" Chain information for 8ga9_A_A_solenoid.pdb #13 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/8k84_A_A_solenoid.pdb"" Chain information for 8k84_A_A_solenoid.pdb #14 --- Chain | Description A | No description available > open ""/Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/solenoid from > PDA/8ump_A_A_solenoid.pdb"" Chain information for 8ump_A_A_solenoid.pdb #15 --- Chain | Description A | No description available > set bgColor white > ui tool show Matchmaker > matchmaker #3,8,11-12,14-15#!2,4-7,9-10,13 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 4pjs_A_A_solenoid.pdb, chain A (#3), sequence alignment score = 128.4 RMSD between 16 pruned atom pairs is 0.688 angstroms; (across all 117 pairs: 12.275) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 6xt4_A_A_solenoid.pdb, chain A (#8), sequence alignment score = 135.5 RMSD between 17 pruned atom pairs is 1.420 angstroms; (across all 110 pairs: 10.804) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8eov_A_A_solenoid.pdb, chain A (#11), sequence alignment score = 98.4 RMSD between 14 pruned atom pairs is 0.850 angstroms; (across all 82 pairs: 13.869) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8erw_A_A_solenoid.pdb, chain A (#12), sequence alignment score = 164.3 RMSD between 6 pruned atom pairs is 1.110 angstroms; (across all 119 pairs: 11.426) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8k84_A_A_solenoid.pdb, chain A (#14), sequence alignment score = 108.3 RMSD between 8 pruned atom pairs is 1.276 angstroms; (across all 90 pairs: 15.171) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8ump_A_A_solenoid.pdb, chain A (#15), sequence alignment score = 114.9 RMSD between 14 pruned atom pairs is 1.333 angstroms; (across all 80 pairs: 9.335) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 4gpm_A_A_solenoid.pdb, chain A (#2), sequence alignment score = 71.5 RMSD between 16 pruned atom pairs is 0.997 angstroms; (across all 96 pairs: 14.746) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 4r5c_A_A_solenoid.pdb, chain A (#4), sequence alignment score = 3.1 Fewer than 3 residues aligned; cannot match 3ltm_A_A_solenoid.pdb, chain A with 4r5c_A_A_solenoid.pdb, chain A Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 5di5_A_A_solenoid.pdb, chain A (#5), sequence alignment score = 10.1 Fewer than 3 residues aligned; cannot match 3ltm_A_A_solenoid.pdb, chain A with 5di5_A_A_solenoid.pdb, chain A Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 5i9d_A_A_solenoid.pdb, chain A (#6), sequence alignment score = 120.5 RMSD between 28 pruned atom pairs is 1.148 angstroms; (across all 119 pairs: 13.891) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 6veh_A_A_solenoid.pdb, chain A (#7), sequence alignment score = 238.3 RMSD between 31 pruned atom pairs is 0.602 angstroms; (across all 77 pairs: 8.452) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 7udo_A_A_solenoid.pdb, chain A (#9), sequence alignment score = 122.4 RMSD between 6 pruned atom pairs is 1.061 angstroms; (across all 106 pairs: 15.627) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8c3w_A_A_solenoid.pdb, chain A (#10), sequence alignment score = 130.8 RMSD between 10 pruned atom pairs is 1.222 angstroms; (across all 113 pairs: 14.589) Matchmaker 3ltm_A_A_solenoid.pdb, chain A (#1) with 8ga9_A_A_solenoid.pdb, chain A (#13), sequence alignment score = 84.6 RMSD between 11 pruned atom pairs is 1.500 angstroms; (across all 93 pairs: 15.029) > ui tool show Matchmaker > matchmaker #3,8,11-12,14-15#!2,4-7,9-10,13 & sel to #1/A & sel pairing bs No 'to' chains specified > lighting gentle > graphics silhouettes true > hide #15 models > hide #14 models > hide #!13 models > hide #12 models > hide #11 models > hide #!10 models > hide #!9 models > hide #8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #3 models > hide #!2 models > show #!2 models > show #3 models > show #!4 models > hide #!4 models > hide #3 models > hide #!2 models > hide #1 target a > color #1 #fd5901ff > show #!2 models > hide #!1 models > color #2 #fd5901ff > show #3 models > hide #!2 models > color #3 #fd5901ff > show #!4 models > hide #3 models > color #4 #ff8500ff > show #3 models > hide #3 models > show #!5 models > hide #!4 models > color #5 #faab36ff > show #!6 models > hide #!5 models > color #6 #fd5901ff > show #!7 models > hide #!6 models > color #7 #fd5901ff > show #8 models > hide #!7 models > color #8 #fd5901ff > show #!9 models > hide #8 models > color #9 #fd5901ff > show #!10 models > hide #!9 models > color #10 #fd5901ff > show #11 models > hide #!10 models > color #11 #fd5901ff > show #12 models > hide #11 models > color #12 #fd5901ff > show #!13 models > hide #12 models > color #13 #fd5901ff > show #14 models > hide #!13 models > color #14 #fd5901ff > show #15 models > hide #14 models > color #15 #fd5901ff > hide #15 models > show #!1 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/3ltm.png > transparentBackground true width 3000 height 3000 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/4gpm.png > transparentBackground true width 3000 height 3000 > show #3 models > hide #!2 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/4pjs.png > transparentBackground true width 3000 height 3000 > show #!4 models > hide #3 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/4r5c.png > transparentBackground true width 3000 height 3000 > show #!5 models > hide #!4 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5di5.png > transparentBackground true width 3000 height 3000 > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!6 models > show #!6 models > hide #!6 models > open 5di5 Summary of feedback from opening 5di5 fetched from pdb --- note | Fetching compressed mmCIF 5di5 from http://files.rcsb.org/download/5di5.cif 5di5 title: beta1 t801 loop variant in P3221 [more info...] Chain information for 5di5 #16 --- Chain | Description A | beta1 t801 loop variant 5di5 mmCIF Assemblies --- 1| author_and_software_defined_assembly > select add #16 1388 atoms, 1379 bonds, 210 residues, 1 model selected > delete atoms sel > delete bonds sel > open 5i9d Summary of feedback from opening 5i9d fetched from pdb --- note | Fetching compressed mmCIF 5i9d from http://files.rcsb.org/download/5i9d.cif 5i9d title: Crystal structure of designed pentatricopeptide repeat protein dPPR-U8A2 in complex with its target RNA U8A2 [more info...] Chain information for 5i9d #16 --- Chain | Description A | pentatricopeptide repeat protein dPPR-U8A2 B | RNA (5'-R(*GP*GP*GP*G*UP*UP*UP*UP*AP*AP*UP*UP*UP*UP*CP*CP*CP*C)-3') > select nucleic-acid 198 atoms, 218 bonds, 11 residues, 1 model selected > delete atoms sel > delete bonds sel > color #16 #fd5901ff > ui tool show ""Side View"" > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5i9d.png > transparentBackground true width 3000 height 3000 > hide #!16 models > show #!5 models > hide #!5 models > show #!6 models > show #!7 models > hide #!6 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/6veh.png > transparentBackground true width 3000 height 3000 > show #8 models > hide #!7 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/6xt4.png > transparentBackground true width 3000 height 3000 > show #!9 models > hide #8 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/7udo.png > transparentBackground true width 3000 height 3000 > show #!10 models > hide #!9 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8c3w.png > transparentBackground true width 3000 height 3000 > show #11 models > hide #!10 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8eov.png > transparentBackground true width 3000 height 3000 > show #12 models > hide #11 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8erw.png > transparentBackground true width 3000 height 3000 > show #!13 models > hide #12 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8ga9.png > transparentBackground true width 3000 height 3000 > show #14 models > hide #!13 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8k84.png > transparentBackground true width 3000 height 3000 > show #15 models > hide #14 models > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/8ump.png > transparentBackground true width 3000 height 3000 > show #!16 models > hide #15 models > hide #!16 models > open /Users/georginikov/Downloads/5DN0.cxs opened ChimeraX session > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0.png > transparentBackground true width 3000 height 3000 > transparency /A 50 cartoons > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0_50.png > transparentBackground true width 3000 height 3000 > lighting gentle > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0_50.png > transparentBackground true width 3000 height 3000 > ui tool show ""Side View"" > save > /Users/georginikov/Desktop/DP_chimeraX_PDA_solenoids/chimera_images/5DN0_50.png > transparentBackground true width 3000 height 3000 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/georginikov/Downloads/All_pdbs_colored_plddt_GA_plot.cxs Log from Mon Oct 7 10:50:42 2024 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_96/Sequence_1/1Sequence_1_unrelaxed_rank_1_model_5.pdb Chain information for 1Sequence_1_unrelaxed_rank_1_model_5.pdb #1 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_101/Sequence_1/2_newSequence_1_unrelaxed_rank_1_model_2.pdb Chain information for 2_newSequence_1_unrelaxed_rank_1_model_2.pdb #2 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_112/Sequence_1/3newSequence_1_unrelaxed_rank_1_model_3.pdb Chain information for 3newSequence_1_unrelaxed_rank_1_model_3.pdb #3 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/B_solenoid/Round_12_122/Sequence_1/4Sequence_1_unrelaxed_rank_1_model_5.pdb Chain information for 4Sequence_1_unrelaxed_rank_1_model_5.pdb #4 --- Chain | Description A | No description available > colorConfidence truecartoon Unknown command: colorConfidence truecartoon > color bfactor palette alphafold 5244 atoms, 600 residues, atom bfactor range 20.2 to 97.3 > set bgColor white > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_332/Sequence_1/1Sequence_1_unrelaxed_rank_1_model_3.pdb Chain information for 1Sequence_1_unrelaxed_rank_1_model_3.pdb #5 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_337/Sequence_1/2newSequence_1_unrelaxed_rank_1_model_4.pdb Chain information for 2newSequence_1_unrelaxed_rank_1_model_4.pdb #6 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_355/Sequence_1/3new_Sequence_1_unrelaxed_rank_1_model_4.pdb Chain information for 3new_Sequence_1_unrelaxed_rank_1_model_4.pdb #7 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_372/Sequence_1/4newSequence_1_unrelaxed_rank_1_model_2.pdb Chain information for 4newSequence_1_unrelaxed_rank_1_model_2.pdb #8 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/AB_solenoid/Round_3_404/Sequence_1/5Sequence_1_unrelaxed_rank_1_model_4.pdb Chain information for 5Sequence_1_unrelaxed_rank_1_model_4.pdb #9 --- Chain | Description A | No description available > color bfactor palette alphafold 11172 atoms, 1290 residues, atom bfactor range 20.2 to 97.3 > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_68/Sequence_1/1Sequence_1_unrelaxed_rank_1_model_2.pdb Chain information for 1Sequence_1_unrelaxed_rank_1_model_2.pdb #10 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_102/Sequence_1/2newSequence_1_unrelaxed_rank_1_model_2.pdb Chain information for 2newSequence_1_unrelaxed_rank_1_model_2.pdb #11 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_108/Sequence_1/3Sequence_1_unrelaxed_rank_1_model_2.pdb Chain information for 3Sequence_1_unrelaxed_rank_1_model_2.pdb #12 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_130/Sequence_1/4Sequence_1_unrelaxed_rank_1_model_4.pdb Chain information for 4Sequence_1_unrelaxed_rank_1_model_4.pdb #13 --- Chain | Description A | No description available > open > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/A_solenoid/Round_3_155/Sequence_1/5Sequence_1_unrelaxed_rank_1_model_3.pdb Chain information for 5Sequence_1_unrelaxed_rank_1_model_3.pdb #14 --- Chain | Description A | No description available > color bfactor palette alphafold 17600 atoms, 2050 residues, atom bfactor range 20.2 to 97.3 > graphics silhouettes true > save > /Users/daniellapretorius/Desktop/PhD_year_1/PhD_thesis/in_silico_evolution_solenoid_generation/Genetic_algorithm_trajectory/All_pdbs_colored_plddt_GA_plot.cxs \u2014\u2014\u2014 End of log from Mon Oct 7 10:50:42 2024 \u2014\u2014\u2014 opened ChimeraX session OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z1240001TB/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 34 days, 13 hours, 39 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX