id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19465 Crash closing tool till.dorendorf@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.11.dev202508070056 (2025-08-07 00:56:19 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 0x00000002029860c0 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1058 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1223 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.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 57) {""app_name"":""ChimeraX"",""timestamp"":""2025-12-02 10:51:10.00 +0100"",""app_version"":""1.11.0"",""slice_uuid"":""9cf8124a-d876-34ad-b7ee-c011183ebc15"",""build_version"":""1.11.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.6.1 (24G90)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""EDF473E8-9912-404C-876D-D139439F1FAF""} { ""uptime"" : 7400, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 504, ""deployVersion"" : 210, ""modelCode"" : ""Mac13,1"", ""coalitionID"" : 1603, ""osVersion"" : { ""train"" : ""macOS 15.6.1"", ""build"" : ""24G90"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-12-02 10:51:06.3181 +0100"", ""codeSigningMonitor"" : 1, ""incident"" : ""EDF473E8-9912-404C-876D-D139439F1FAF"", ""pid"" : 1697, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-12-02 09:12:11.0086 +0100"", ""procStartAbsTime"" : 36371676765, ""procExitAbsTime"" : 178819269318, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.0"",""CFBundleVersion"":""1.11.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""FD0CFA27-A212-50A1-8CF0-62FF1D8A0863"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D93E1587-7AA2-780C-4174-19F7D9E4F252"", ""appleIntelligenceStatus"" : {""state"":""available""}, ""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"" : ""4C9E9285-DFD3-4864-8640-BFF8757E4B21"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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""name"" : ""Foundation"", ""CFBundleVersion"" : ""3603"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 7429861376, ""CFBundleShortVersionString"" : ""20621"", ""CFBundleIdentifier"" : ""com.apple.WebKit"", ""size"" : 21306528, ""uuid"" : ""fb40cbe5-eb40-3ba6-b806-be1abc73a678"", ""path"" : ""\/System\/Library\/Frameworks\/WebKit.framework\/Versions\/A\/WebKit"", ""name"" : ""WebKit"", ""CFBundleVersion"" : ""20621.3.11.11.3"" } ], ""sharedCache"" : { ""base"" : 6783762432, ""size"" : 5040898048, ""uuid"" : ""4c1223e5-cace-3982-a003-6110a7a8a25c"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=3.5G written=2104K(0%) resident=2104K(0%) swapped_out=0K(0%) unallocated=3.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 960K 38 \nColorSync 624K 33 \nCoreAnimation 2768K 133 \nCoreGraphics 48K 3 \nCoreServices 1248K 5 \nCoreUI image data 5408K 39 \nFoundation 64K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.9G 119 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 256K 3 \nPROTECTED_MEMORY 16K 1 \nSTACK GUARD 624K 39 \nStack 200.8M 40 \nStack Guard 56.0M 1 \nVM_ALLOCATE 275.2M 245 \nVM_ALLOCATE (reserved) 192.0M 2 reserved VM address space (unallocated)\n__AUTH 5520K 696 \n__AUTH_CONST 77.4M 943 \n__CTF 824 1 \n__DATA 33.5M 1069 \n__DATA_CONST 53.5M 1088 \n__DATA_DIRTY 2777K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.5M 139 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1097 \n__TEXT (graphics) 9424K 11 \n__TPRO_CONST 128K 2 \ndyld private memory 1840K 17 \nmapped file 592.7M 88 \npage table in kernel 2104K 1 \nshared memory 3680K 24 \n=========== ======= ======= \nTOTAL 6.3G 6251 \nTOTAL, minus reserved VM space 6.1G 6251 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""d30782e577659b2cbc5e15433d07d485ac058d88"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""5fb4245a1bbfe8005e33a1e1"", ""factorPackIds"" : { }, ""deploymentId"" : 240000021 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.dev202508070056 (2025-08-07) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/till/Desktop/titinasingTwcK/molecularReplacement/test/CCP4_DATABASE/tmp/2/2_TitTwcKDtoEAMPPNPE4X3setHeF_warpNtrace.pdb Chain information for 2_TitTwcKDtoEAMPPNPE4X3setHeF_warpNtrace.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available Q | No description available Drag select of 8542 atoms, 48 pseudobonds > show sel cartoons Computing secondary structure > hide sel atoms > select clear > open /Users/till/Downloads/TTN1_final.pdb Chain information for TTN1_final.pdb #2 --- Chain | Description A | No description available 46 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3551 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Computing secondary structure > close #1 > select clear > select /A:82 19 atoms, 18 bonds, 1 residue, 1 model selected > sequence chain #2/A Alignment identifier is 2/A > select clear > hide atoms > select /A:306 16 atoms, 15 bonds, 1 residue, 1 model selected > select clear > select /A:320 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /A:312 18 atoms, 16 bonds, 2 residues, 1 model selected > hide sel atoms > label delete #2 > select clear > select /A:5 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:5-35 499 atoms, 503 bonds, 31 residues, 1 model selected > color sel yellow > ui tool show ""Color Actions"" > select /A:293 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:293-370 1037 atoms, 1045 bonds, 2 pseudobonds, 65 residues, 2 models selected > select /A:367 12 atoms, 11 bonds, 1 residue, 1 model selected > select /A:293-367 1003 atoms, 1010 bonds, 2 pseudobonds, 62 residues, 2 models selected > color sel red > select /A:368 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:368-463 1440 atoms, 1451 bonds, 96 residues, 1 model selected > color sel forest green > set bgColor white > set bgColor #ffffff00 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select /A:36 21 atoms, 21 bonds, 1 residue, 1 model selected > select /A:36-292 4106 atoms, 4151 bonds, 257 residues, 1 model selected > color sel light gray > select clear > lighting simple > lighting full > lighting soft > lighting simple > select clear > select /A:293 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:293-306 114 atoms, 114 bonds, 1 pseudobond, 8 residues, 2 models selected > select > /A:8-13,32-35,75-87,118-123,131-151,160-162,197-199,202-205,212-228,238-247,255-257,262-269,276-278,282-286,289-292,303-309,338-343,347-349,436-438 2093 atoms, 2098 bonds, 129 residues, 1 model selected > select /A:307 22 atoms, 21 bonds, 1 residue, 1 model selected > select /A:293-307 136 atoms, 136 bonds, 1 pseudobond, 9 residues, 2 models selected > color (#!2 & sel) #fffeffff > color (#!2 & sel) #fff2ffff > color (#!2 & sel) #ffc8ffff > color (#!2 & sel) #ff80ffff > color (#!2 & sel) #ff48ffff > color (#!2 & sel) #ff17ffff > color (#!2 & sel) #ff00ffff > color (#!2 & sel) #ff00feff > color (#!2 & sel) #ff00edff > color (#!2 & sel) #ff00c8ff > color (#!2 & sel) #ff009dff > color (#!2 & sel) #ff0070ff > color (#!2 & sel) #ff0041ff > color (#!2 & sel) #ff001cff > color (#!2 & sel) #ff000aff > color (#!2 & sel) #ff0004ff > color (#!2 & sel) #ff0001ff > color (#!2 & sel) #ff0000ff > color (#!2 & sel) #ff0100ff > color (#!2 & sel) #ff0300ff > color (#!2 & sel) #ff0600ff > color (#!2 & sel) #ff0800ff > color (#!2 & sel) #ff0900ff > color (#!2 & sel) #ff0a00ff > color (#!2 & sel) #ff0e00ff > color (#!2 & sel) #ff0f00ff > color (#!2 & sel) #ff1000ff > color (#!2 & sel) #ff1200ff > color (#!2 & sel) #ff1400ff > color (#!2 & sel) #ff1700ff > color (#!2 & sel) #ff1a00ff > color (#!2 & sel) #ff1d00ff > color (#!2 & sel) #ff1f00ff > color (#!2 & sel) #ff2000ff > color (#!2 & sel) #ff2200ff > color (#!2 & sel) #ff2500ff > color (#!2 & sel) #ff2600ff > color (#!2 & sel) #ff2700ff > color (#!2 & sel) #ff2800ff > color (#!2 & sel) #ff2a00ff > color (#!2 & sel) #ff2b00ff > color (#!2 & sel) #ff2c00ff > color (#!2 & sel) #ff2d00ff > color (#!2 & sel) #ff2e00ff > color (#!2 & sel) #ff3000ff > color (#!2 & sel) #ff3200ff > color (#!2 & sel) #ff3300ff > color (#!2 & sel) #ff3400ff > color (#!2 & sel) #ff3600ff > color (#!2 & sel) #ff3800ff > color (#!2 & sel) #ff3900ff > color (#!2 & sel) #ff3a00ff > color (#!2 & sel) #ff3800ff > color (#!2 & sel) #fc3800ff > color (#!2 & sel) #fa3800ff > color (#!2 & sel) #f83800ff > color (#!2 & sel) #f63800ff > color (#!2 & sel) #f53800ff > color (#!2 & sel) #f23800ff > color (#!2 & sel) #f03800ff > color (#!2 & sel) #ef3800ff > color (#!2 & sel) #eb3800ff > color (#!2 & sel) #e93800ff > color (#!2 & sel) #e83800ff > color (#!2 & sel) #e63800ff > color (#!2 & sel) #e33800ff > color (#!2 & sel) #e23800ff > color (#!2 & sel) #e13800ff > color (#!2 & sel) #e03800ff > color (#!2 & sel) #de3800ff > color (#!2 & sel) #dc3800ff > color (#!2 & sel) #db3800ff > color (#!2 & sel) #d83800ff > color (#!2 & sel) #d63800ff > color (#!2 & sel) #d73800ff > color (#!2 & sel) #d73802ff > color (#!2 & sel) #d73804ff > color (#!2 & sel) #d73806ff > color (#!2 & sel) #d73807ff > color (#!2 & sel) #d73809ff > color (#!2 & sel) #d7380aff > color (#!2 & sel) #d7380dff > color (#!2 & sel) #d73810ff > color (#!2 & sel) #d73812ff > color (#!2 & sel) #d73813ff > color (#!2 & sel) #d73814ff > color (#!2 & sel) #d73816ff > color (#!2 & sel) #d73818ff > color (#!2 & sel) #d7381cff > color (#!2 & sel) #d7381dff > color (#!2 & sel) #d7381fff > color (#!2 & sel) #d73821ff > color (#!2 & sel) #d73824ff > color (#!2 & sel) #d73825ff > color (#!2 & sel) #d7382aff > color (#!2 & sel) #d7382cff > color (#!2 & sel) #d7392cff > color (#!2 & sel) #d73a2cff > color (#!2 & sel) #d73e2cff > color (#!2 & sel) #d7432cff > color (#!2 & sel) #d7442cff > color (#!2 & sel) #d7452cff > color (#!2 & sel) #d7462cff > color (#!2 & sel) #d7482cff > color (#!2 & sel) #d74b2cff > color (#!2 & sel) #d74b28ff > color (#!2 & sel) #d74b22ff > color (#!2 & sel) #d74b20ff > color (#!2 & sel) #d74b1cff > color (#!2 & sel) #d74b18ff > color (#!2 & sel) #d74b15ff > color (#!2 & sel) #d74b14ff > color (#!2 & sel) #d74b13ff > color (#!2 & sel) #d74b11ff > color (#!2 & sel) #d74b10ff > color (#!2 & sel) #d74b0fff > color (#!2 & sel) #d74b0eff > color (#!2 & sel) #d74b0dff > color (#!2 & sel) #d74b0bff > color (#!2 & sel) #d74b0aff > color (#!2 & sel) #d74b05ff > color (#!2 & sel) #d74b00ff > color (#!2 & sel) #d74b04ff > color (#!2 & sel) #d74b11ff > color (#!2 & sel) #d74b17ff > color (#!2 & sel) #d74b19ff > color (#!2 & sel) #d74b1aff > color (#!2 & sel) #d74b1eff > color (#!2 & sel) #d74b22ff > color (#!2 & sel) #d74b25ff > color (#!2 & sel) #d74b26ff > color (#!2 & sel) #d74b28ff > color (#!2 & sel) #d74b2cff > color (#!2 & sel) #d74b37ff > color (#!2 & sel) #d74b3dff > color (#!2 & sel) #d74b3eff > color (#!2 & sel) #d74b40ff > color (#!2 & sel) #d74b42ff > color (#!2 & sel) #d74b44ff > color (#!2 & sel) #d74b47ff > color (#!2 & sel) #d74b50ff > color (#!2 & sel) #d74b54ff > color (#!2 & sel) #d74b55ff > color (#!2 & sel) #d74b56ff > color (#!2 & sel) #d74b5aff > color (#!2 & sel) #d74b5fff > color (#!2 & sel) #d74b68ff > color (#!2 & sel) #d74b6cff > color (#!2 & sel) #d74b75ff > color (#!2 & sel) #d74b7bff > color (#!2 & sel) #d74b80ff > color (#!2 & sel) #d74b8aff > color (#!2 & sel) #d74b8cff > color (#!2 & sel) #d74b93ff > color (#!2 & sel) #d74b9dff > color (#!2 & sel) #d74ba1ff > color (#!2 & sel) #d74ba7ff > color (#!2 & sel) #d74ba9ff > color (#!2 & sel) #d74ba8ff > color (#!2 & sel) #d74b9eff > color (#!2 & sel) #d74b8bff > color (#!2 & sel) #d74b7aff > color (#!2 & sel) #d74b66ff > color (#!2 & sel) #d74b51ff > color (#!2 & sel) #d74b43ff > color (#!2 & sel) #d74b40ff > color (#!2 & sel) #d74b39ff > color (#!2 & sel) #d74b38ff > color (#!2 & sel) #d74b36ff > color (#!2 & sel) #d74b32ff > color (#!2 & sel) #d74b2eff > color (#!2 & sel) #d74b2dff > color (#!2 & sel) #d74b28ff > color (#!2 & sel) #d74b25ff > color (#!2 & sel) #d74b22ff > color (#!2 & sel) #d74b1dff > color (#!2 & sel) #d74b1aff > color (#!2 & sel) #d74b14ff > color (#!2 & sel) #d74b11ff > color (#!2 & sel) #d74b0eff > color (#!2 & sel) #d74b0bff > color (#!2 & sel) #d74b08ff > color (#!2 & sel) #d74b05ff > color (#!2 & sel) #d74b00ff > color (#!2 & sel) #d94b00ff > color (#!2 & sel) #ff4b00ff > color (#!2 & sel) #ff4b02ff > color (#!2 & sel) #ff4b03ff > color (#!2 & sel) #ff4b06ff > color (#!2 & sel) #ff4b08ff > color (#!2 & sel) #ff4b0aff > color (#!2 & sel) #ff4b0bff > color (#!2 & sel) #ff4b0cff > color (#!2 & sel) #ff4b0dff > color (#!2 & sel) #ff4b10ff > color (#!2 & sel) #ff4b12ff > color (#!2 & sel) #ff4b16ff > color (#!2 & sel) #ff4b19ff > color (#!2 & sel) #ff4b1aff > color (#!2 & sel) #ff4b1dff > color (#!2 & sel) #ff4b1eff > color (#!2 & sel) #ff4b1fff > color (#!2 & sel) #ff4c1fff > color (#!2 & sel) #ff531fff > color (#!2 & sel) #ff581fff > color (#!2 & sel) #ff5a1fff > color (#!2 & sel) #ff5c1fff > color (#!2 & sel) #ff5f1fff > color (#!2 & sel) #ff601fff > color (#!2 & sel) #ff611fff > color (#!2 & sel) #ff631fff > color (#!2 & sel) #ff651fff > color (#!2 & sel) #ff661fff > color (#!2 & sel) #ff671fff > color (#!2 & sel) #ff691fff > color (#!2 & sel) #ff6b1fff > color (#!2 & sel) #ff6c1fff > color (#!2 & sel) #ff6d1fff > color (#!2 & sel) #ff6e1fff > color (#!2 & sel) #ff6f1fff > color (#!2 & sel) #ff701fff > color (#!2 & sel) #ff711fff > color (#!2 & sel) #ff721fff > color (#!2 & sel) #ff731fff > color (#!2 & sel) #ff741fff > color (#!2 & sel) #ff751fff > color (#!2 & sel) #ff761fff > color (#!2 & sel) #ff771fff > color (#!2 & sel) #ff781fff > color (#!2 & sel) #ff791fff > select clear > turn 0,180,0 40 > turn 0,180,0 -40 > turn 0,180,0 40 > turn 0,180,0 90 > turn 0,180,0 -90 > turn 0,180,0 90 > turn 0,180,0 -90 > save /Users/till/Desktop/TTN-1/Figures/fullView-TTN1.cxs > save /Users/till/Desktop/TTN-1/Figures/fullViewFront.jpg width 2000 height > 1712 supersample 3 > turn 0,180,0 90 > save /Users/till/Desktop/TTN-1/Figures/fullViewSide.jpg width 2000 height > 1712 supersample 3 > turn 0,180,0 -90 > open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb Chain information for TTN1_final.pdb #1 --- Chain | Description A | No description available 46 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3551 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Computing secondary structure > hide #!1 models > show #!1 models > hide #!2 models > label delete #1 > open 6ygn 6ygn title: Titin kinase and its flanking domains [more info...] Chain information for 6ygn #3 --- Chain | Description | UniProt A B | Titin | TITIN_HUMAN 5-553 Non-standard residues in 6ygn #3 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) 6ygn mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 8852 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > open 3uto 3uto title: Twitchin kinase region from C.elegans (Fn31-NL-kin-CRD-Ig26) [more info...] Chain information for 3uto #4 --- Chain | Description | UniProt A B | Twitchin | UNC22_CAEEL 1-570 Non-standard residues in 3uto #4 --- FLC — citrate anion GOL — glycerol (glycerin; propane-1,2,3-triol) P33 — 3,6,9,12,15,18-hexaoxaicosane-1,20-diol (heptaethylene glycol; PEG330) PEG — di(hydroxyethyl)ether 3uto mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 8784 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > ui tool show Matchmaker > matchmaker #3#!2,4 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 TTN1_final.pdb, chain A (#1) with 6ygn, chain A (#3), sequence alignment score = 978 RMSD between 214 pruned atom pairs is 0.865 angstroms; (across all 427 pairs: 10.485) Matchmaker TTN1_final.pdb, chain A (#1) with TTN1_final.pdb, chain A (#2), sequence alignment score = 2363.7 RMSD between 446 pruned atom pairs is 0.000 angstroms; (across all 446 pairs: 0.000) Matchmaker TTN1_final.pdb, chain A (#1) with 3uto, chain A (#4), sequence alignment score = 1132.3 RMSD between 247 pruned atom pairs is 0.874 angstroms; (across all 425 pairs: 12.959) > select #3/B:512 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 47 atoms, 47 bonds, 6 residues, 1 model selected > select up 4426 atoms, 4512 bonds, 549 residues, 1 model selected > select up 4586 atoms, 4534 bonds, 687 residues, 1 model selected > select up 9213 atoms, 9068 bonds, 1415 residues, 1 model selected > select down 4586 atoms, 4534 bonds, 687 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/B:430 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 106 atoms, 107 bonds, 12 residues, 1 model selected > select up 4545 atoms, 4661 bonds, 566 residues, 1 model selected > select up 4781 atoms, 4682 bonds, 781 residues, 1 model selected > delete atoms sel > delete bonds sel > label delete #4 > select #1/A:339 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear Drag select of 1 residues > sequence chain #4/A Alignment identifier is 4/A > select #4/A:124 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/A:5-124 882 atoms, 904 bonds, 1 pseudobond, 113 residues, 2 models selected > hide sel atoms > hide sel cartoons > select ::name=""EDO""::name=""FLC""::name=""GOL""::name=""HOH""::name=""PEG"" 1217 atoms, 45 bonds, 1172 residues, 4 models selected > hide sel & #3#!1,4 atoms > select #3/A:99 8 atoms, 7 bonds, 1 residue, 1 model selected > sequence chain #3/A Alignment identifier is 3/A > select #3/A:97 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:5-97 727 atoms, 743 bonds, 93 residues, 1 model selected > hide sel cartoons > hide sel atoms > select clear Drag select of 1348 residues, 2 pseudobonds, 112 atoms, 101 bonds > hide sel cartoons > show sel atoms > hide sel atoms > show sel cartoons > select clear > select #3/A:98 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:98-553 3699 atoms, 3768 bonds, 456 residues, 1 model selected > color sel cornflower blue > select clear > select #3/A:98 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:98-454 2895 atoms, 2946 bonds, 357 residues, 1 model selected > color sel cornflower blue > color sel #ff791fff > color sel #6495edff > color sel #6195edff > color sel #6095edff > color sel #5e95edff > color sel #5c95edff > color sel #5a95edff > color sel #5995edff > color sel #5895edff > color sel #5795edff > color sel #5695edff > color sel #5295edff > color sel #4f95edff > color sel #4e95edff > color sel #4c95edff > color sel #4b95edff > color sel #4b95ecff > color sel #4b95e6ff > color sel #4b95e0ff > color sel #4b95dfff > color sel #4b95deff > color sel #4b95dcff > color sel #4b95d9ff > color sel #4b95d8ff > color sel #4b95d7ff > color sel #4b95d6ff > color sel #4b95d5ff > color sel #4b95d4ff > color sel #4b95d2ff > color sel #4b95ceff > color sel #4b95cbff > color sel #4b95caff > color sel #4b95c8ff > color sel #4b95c7ff > color sel #4b95c6ff > color sel #4b95c5ff > color sel #4b95c7ff > color sel #4b95cdff > color sel #4b95ceff > color sel #4b95cdff > color sel #4b92cdff > color sel #4b8fcdff > color sel #4b8ecdff > color sel #4b8dcdff > color sel #4b8ccdff > color sel #4b8bcdff > color sel #4b8ccdff > color sel #4b90cdff > color sel #4b92cdff > color sel #4b99cdff > color sel #4ba3cdff > color sel #4ba4cdff > color sel #4ba6cdff > color sel #4ba8cdff > color sel #4ba9cdff > color sel #4babcdff > color sel #4baccdff > color sel #4baecdff > color sel #4bb0cdff > color sel #4bafcdff > color sel #4aafcdff > color sel #47afcdff > color sel #45afcdff > color sel #42afcdff > color sel #41afcdff > color sel #3fafcdff > color sel #3eafcdff > color sel #3dafcdff > color sel #3cafcdff > color sel #3bafcdff > color sel #38afcdff > color sel #37afcdff > color sel #36afcdff > color sel #34afcdff > color sel #33afcdff > color sel #c1d4f9ff > color sel #c1d4f7ff > select #3/A:98 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:98-442 2811 atoms, 2862 bonds, 345 residues, 1 model selected > select #3/A:510 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 47 atoms, 47 bonds, 6 residues, 1 model selected > select up 4426 atoms, 4512 bonds, 549 residues, 1 model selected > color sel #c1d3f7ff > color sel #c1ccf7ff > color sel #c1bdf7ff > color sel #c1bcf7ff > color sel #c1bff7ff > color sel #c1c7f7ff > color sel #c1cef7ff > color sel #c1d4f7ff > color sel #b1caf6ff > select clear > select #3/A:98 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/A:5 7 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:5-9 39 atoms, 41 bonds, 5 residues, 1 model selected > select clear > select #1/A:380 16 atoms, 15 bonds, 1 residue, 1 model selected > select up 59 atoms, 58 bonds, 4 residues, 1 model selected > select up 2235 atoms, 2253 bonds, 144 residues, 1 model selected > select up 2268 atoms, 2286 bonds, 147 residues, 1 model selected > select up 2422 atoms, 2441 bonds, 156 residues, 1 model selected > select down 2268 atoms, 2286 bonds, 147 residues, 1 model selected > select up 2422 atoms, 2441 bonds, 156 residues, 1 model selected > select #4/A:20-21 17 atoms, 16 bonds, 2 residues, 1 model selected > select #4/A:20-23 29 atoms, 28 bonds, 4 residues, 1 model selected > select #4/A:558 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 18 atoms, 18 bonds, 2 residues, 1 model selected > select up 3731 atoms, 3824 bonds, 463 residues, 1 model selected > select up 3746 atoms, 3839 bonds, 465 residues, 1 model selected > select up 4482 atoms, 4597 bonds, 559 residues, 1 model selected > select down 3746 atoms, 3839 bonds, 465 residues, 1 model selected > color sel #81c487ff > color sel #81c787ff > color sel #81c784ff > select clear > color #1,3-4 #c0e3c1ff > undo > select #4/A:108-110 27 atoms, 27 bonds, 3 residues, 1 model selected > select #4/A:108-111 35 atoms, 35 bonds, 4 residues, 1 model selected > select #4/A:462 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 61 atoms, 61 bonds, 7 residues, 1 model selected > select up 3731 atoms, 3824 bonds, 463 residues, 1 model selected > select up 3746 atoms, 3839 bonds, 465 residues, 1 model selected > select down 3731 atoms, 3824 bonds, 463 residues, 1 model selected > select clear > select #4/A:462 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 61 atoms, 61 bonds, 7 residues, 1 model selected > select up 3731 atoms, 3824 bonds, 463 residues, 1 model selected > color sel #c0e3c2ff > color sel #c0e3c1ff > select clear > select #4/A:460 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 61 atoms, 61 bonds, 7 residues, 1 model selected > select up 3731 atoms, 3824 bonds, 463 residues, 1 model selected > color sel #b3ddb1ff > color sel #b3ddb5ff > select clear > select #1/A:373 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 71 atoms, 70 bonds, 4 residues, 1 model selected > select up 2235 atoms, 2253 bonds, 144 residues, 1 model selected > select up 2268 atoms, 2286 bonds, 147 residues, 1 model selected > select up 2422 atoms, 2441 bonds, 156 residues, 1 model selected > select up 2443 atoms, 2462 bonds, 158 residues, 1 model selected > select up 7048 atoms, 7118 bonds, 446 residues, 1 model selected > color sel coral > select clear > lighting simple > lighting soft > lighting simple > lighting shadows true > lighting shadows false > ui tool show ""Side View"" > select #1/A:373 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 71 atoms, 70 bonds, 4 residues, 1 model selected > select up 2235 atoms, 2253 bonds, 144 residues, 1 model selected > select up 2268 atoms, 2286 bonds, 147 residues, 1 model selected > select up 2422 atoms, 2441 bonds, 156 residues, 1 model selected > select up 2443 atoms, 2462 bonds, 158 residues, 1 model selected > select up 7048 atoms, 7118 bonds, 446 residues, 1 model selected > color sel #ff7f50ff > select clear > save /Users/till/Desktop/TTN-1/Figures/fullView-TTN1-compTK-TwcK.cxs > turn 0,180,0 -90 > turn 0,180,0 90 > undo > select #1/A:370 14 atoms, 14 bonds, 1 residue, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select #1/A:368 10 atoms, 9 bonds, 1 residue, 1 model selected > select #1/A:368-463 1440 atoms, 1451 bonds, 96 residues, 1 model selected > hide sel cartoons > select #3/A:454 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:453 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:453-553 816 atoms, 833 bonds, 101 residues, 1 model selected > hide sel cartoons > select #4/A:479 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:479-480 16 atoms, 16 bonds, 2 residues, 1 model selected > select #4/A:479-570 744 atoms, 760 bonds, 92 residues, 1 model selected > hide sel cartoons > select #4/A:438 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 106 atoms, 107 bonds, 12 residues, 1 model selected > select up 3731 atoms, 3824 bonds, 463 residues, 1 model selected > color sel #b3ddb5ff > color sel #d9eedaff > select clear > select #4/A:458 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 61 atoms, 61 bonds, 7 residues, 1 model selected > select up 3731 atoms, 3824 bonds, 463 residues, 1 model selected > color sel #cce8cdff > select clear > save /Users/till/Desktop/TTN-1/Figures/fullView-TTN1-compTK-TwcK.cxs > select #4/A:412 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/A:412-478 549 atoms, 566 bonds, 67 residues, 1 model selected > hide sel cartoons > select clear > select #1/A:301-446 2187 atoms, 2205 bonds, 1 pseudobond, 139 residues, 2 models selected > hide sel cartoons > select #3/A:435 8 atoms, 7 bonds, 1 residue, 1 model selected > sequence chain #3/A Alignment identifier is 3/A > select #3/A:392 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:392-553 1295 atoms, 1316 bonds, 162 residues, 1 model selected > hide sel cartoons > select clear > save /Users/till/Desktop/TTN-1/Figures/KinaseOnly-TTN1-compTK-TwcK.cxs > save /Users/till/Desktop/TTN-1/Figures/KinaseDomainComp.jpg width 2000 > height 2201 supersample 3 > hide #3 models > hide #!4 models > select #1/A:65 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:65 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:157 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:157 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:177 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:177-179 39 atoms, 39 bonds, 3 residues, 1 model selected > show sel atoms > select #1/A:81 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:161 15 atoms, 14 bonds, 1 residue, 1 model selected > select H 6996 atoms, 884 residues, 3 models selected > hide sel & #!1 atoms > select up 14034 atoms, 14166 bonds, 884 residues, 3 models selected > select add #1/A:177@CG 1 atom, 2 bonds, 1 residue, 1 model selected > select add #1/A:178@CB 2 atoms, 2 bonds, 2 residues, 1 model selected > select up 8 atoms, 3 bonds, 5 residues, 1 model selected > select up 81 atoms, 78 bonds, 5 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #ff7f50ff target a > color sel #ff7b50ff target a > color sel #ff7a50ff target a > color sel #ff7850ff target a > color sel #ff7750ff target a > color sel #ff7650ff target a > color sel #ff7550ff target a > color sel #ff7250ff target a > color sel #ff7050ff target a > color sel #ff6e50ff target a > color sel #ff6c50ff target a > color sel #ff6a50ff target a > color sel #ff6850ff target a > color sel #ff6750ff target a > color sel #ff6650ff target a > color sel #ff6450ff target a > color sel #ff6350ff target a > color sel #ff6250ff target a > color sel #ff6050ff target a > color sel #ff5f50ff target a > color sel #ff5d50ff target a > color sel #ff5c50ff target a > color sel #ff5a50ff target a > color sel #ff5950ff target a > color sel #ff5850ff target a > color sel #ff5750ff target a > color sel #ff5550ff target a > color sel #ff5350ff target a > color sel #ff5250ff target a > color sel #ff4f50ff target a > color sel #ff4e50ff target a > color sel #ff4d50ff target a > color sel #ff4c50ff target a > color sel #ff4b50ff target a > color sel #ff4950ff target a > color sel #ff4850ff target a > color sel #ff4750ff target a > color sel #ff4650ff target a > color sel #ff4550ff target a > color sel #ff4450ff target a > color sel #ff4550ff target a > color sel #ff4650ff target a > color sel #ff464fff target a > color sel #ff464eff target a > color sel #ff464cff target a > color sel #ff464aff target a > color sel #ff4648ff target a > color sel #ff4647ff target a > color sel #ff4646ff target a > color sel #ff4645ff target a > color sel #ff4644ff target a > color sel #ff4643ff target a > color sel #ff463fff target a > color sel #ff463bff target a > color sel #ff4639ff target a > color sel #ff4638ff target a > color sel #ff4635ff target a > color sel #ff4633ff target a > color sel #ff4632ff target a > color sel #ff4631ff target a > color sel #ff4630ff target a > color sel #ff462fff target a > color sel #ff462eff target a > color sel #ff462dff target a > color sel #ff462cff target a > color sel #ff462bff target a > color sel #ff4629ff target a > color sel #ff4628ff target a > color sel #ff4627ff target a > color sel #ff4626ff target a > color sel #ff4625ff target a > color sel #ff4624ff target a > color sel #ff4623ff target a > color sel #ff4620ff target a > color sel #ff461eff target a > color sel #ff461dff target a > color sel #ff461cff target a > color sel #ff461bff target a > color sel #ff461aff target a > color sel #ff4619ff target a > color sel #ff4618ff target a > color sel #ff4617ff target a > color sel #ff4616ff target a > color sel #ff4316ff target a > color sel #ff4116ff target a > color sel #ff3d16ff target a > color sel #ff3c16ff target a > color sel #ff3b16ff target a > color sel #ff3a16ff target a > color sel #ff3916ff target a > color sel #ff3516ff target a > color sel #ff3416ff target a > color sel #ff3316ff target a > color sel #ff3216ff target a > color sel #ff3116ff target a > color sel #ff2f16ff target a > color sel #ff2c16ff target a > color sel #ff2a16ff target a > color sel #ff2a15ff target a > color sel #ff2a14ff target a > color sel #ff2a10ff target a > color sel #ff2a0fff target a > color sel #ff2a0eff target a > select clear > select #1/A:65@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 4 bonds, 5 residues, 1 model selected > select up 81 atoms, 78 bonds, 5 residues, 1 model selected > color sel byhetero target a > color sel #ff7f50ff target a > color sel #ff8050ff target a > color sel #ff8650ff target a > color sel #ff8c50ff target a > color sel #ff8d50ff target a > color sel #ff8e50ff target a > color sel #ff8f50ff target a > color sel #ff9050ff target a > color sel #ff9250ff target a > color sel #ff9450ff target a > color sel #ff9550ff target a > color sel #ff9650ff target a > color sel #ff9850ff target a > color sel #ff9950ff target a > color sel #ff9b50ff target a > color sel #ff9d50ff target a > color sel #ff9e50ff target a > color sel #ff9f50ff target a > color sel #ffa250ff target a > color sel #ffa650ff target a > color sel #ffa750ff target a > color sel #ffa850ff target a > color sel #ffaa50ff target a > color sel #ffab50ff target a > color sel #ffac50ff target a > color sel #ffae50ff target a > color sel #ffb050ff target a > color sel #ffb450ff target a > color sel #ffb550ff target a > color sel #ffb650ff target a > color sel #ffb750ff target a > color sel #ffb950ff target a > color sel #ffba50ff target a > color sel #ffba4fff target a > color sel #ffba4dff target a > color sel #ffba4cff target a > color sel #ffba4bff target a > color sel #ffba4aff target a > color sel #ffba49ff target a > color sel #ffba48ff target a > select clear > select add #1/A:177@OD1 1 atom, 1 bond, 1 residue, 1 model selected > select add #1/A:81@CD 2 atoms, 2 bonds, 2 residues, 1 model selected > select up 8 atoms, 3 bonds, 5 residues, 1 model selected > select up 81 atoms, 78 bonds, 5 residues, 1 model selected > color sel byhetero target a > select #1/A:44 22 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:43 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:43-48 74 atoms, 74 bonds, 6 residues, 1 model selected > select clear > select #1/A:65@NZ 1 atom, 1 residue, 1 model selected > select add #1/A:81@OE2 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #1/A:65@NZ #1/A:81@OE2 Distance between TTN1_final.pdb #1/A LYS 65 NZ and GLU 81 OE2: 3.121Å > select #1/A:81@OE1 1 atom, 1 residue, 1 model selected > select add #1/A:65@NZ 2 atoms, 2 residues, 1 model selected > distance #1/A:81@OE1 #1/A:65@NZ Distance between TTN1_final.pdb #1/A GLU 81 OE1 and LYS 65 NZ: 3.119Å > distance style symbol false > distance style symbol true > distance style decimalPlaces 2 > distance style decimalPlaces 1 > distance style decimalPlaces 0 > distance style decimalPlaces 1 > distance style decimalPlaces 2 > hide #5.1 models > distance style color #ffd701 > distance style color #ffd734 > distance style color #ffd753 > distance style color #ffd77c > distance style color #ffd786 > distance style color #ffd78f > distance style color #ffd7a5 > distance style color #ffd7b4 > distance style color #ffd7c1 > distance style color #ffd7c9 > distance style color #ffd7cb > distance style color #ffd7cd > distance style color #ffd7d1 > distance style color #ffd7d3 > distance style color #ffd7d4 > distance style color #ffd7d5 > distance style color #ffd7d6 > distance style color #ffd7d8 > distance style color #ffd7db > distance style color #ffd7dc > distance style color #ffd7dd > distance style color #ffd7df > distance style color #ffd7e1 > distance style color #ffd7e3 > distance style color #ffd7e6 > distance style color #ffd7e9 > distance style color #ffd7ea > distance style color #ffd7eb > distance style color #ffd7ec > distance style color #ffd7ee > distance style color #ffd7f1 > distance style color #ffd7f3 > distance style color #ffd7f4 > distance style color #ffd7f5 > distance style color #ffd7f6 > distance style color #ffd7f7 > distance style color #ffd7f9 > distance style color #ffd7fa > distance style color #ffe2fa > distance style color #fffffa > distance style color #fffbfa > distance style color #ffdcfa > distance style color #ff62fa > distance style color #ff3bfa > distance style color #ff1dfa > distance style color #ff00fa > distance style color #ff00f9 > distance style color #ff00f6 > distance style color #ff00ea > distance style color #ff00b0 > distance style color #ff0075 > distance style color #ff005e > distance style color #ff0045 > distance style color #ff0033 > distance style color #ff001b > distance style color #ff0007 > distance style color red > distance style color #fe0000 > distance style color #fd0000 > distance style color #f60000 > distance style color #f00000 > distance style color #eb0000 > distance style color #e10000 > distance style color #d30000 > distance style color #c60000 > distance style color #bb0000 > distance style color #b10000 > distance style color #a30000 > distance style color #870000 > distance style color #720000 > distance style color #530000 > distance style color #400000 > distance style color #2a0000 > distance style color #1b0000 > distance style color #0b0000 > distance style color black > distance style dashes 8 > distance style dashes 7 > distance style dashes 6 > distance style dashes 5 > distance style dashes 4 > distance style dashes 3 > distance style dashes 4 > select clear > select > #1/A:8-13,32-35,75-87,118-123,131-151,160-162,197-199,202-205,212-228,238-247,255-257,262-269,276-278,282-286,289-292,303-309,338-343,347-349,436-438 2093 atoms, 2098 bonds, 129 residues, 1 model selected > select #1/A:43 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:43-48 74 atoms, 74 bonds, 6 residues, 1 model selected > distance style color #ffba48 > distance style color #ffbf48 > distance style color #ffc548 > distance style color #ffc948 > distance style color #ffc848 > distance style color #ffc648 > distance style color #ffc448 > distance style color #ffc048 > distance style color #ffbf48 > distance style color #ffbe48 > distance style color #ffbf48 > distance style color #ffc248 > distance style color #ffc448 > distance style color #ffc848 > distance style color #ffd148 > distance style color #ffd548 > distance style color #ffda48 > distance style color #ffdd48 > distance style color #ffdc48 > distance style color #ffd948 > distance style color #ffd748 > distance style color #ffd648 > distance style color #ffd148 > distance style color #ffcd48 > distance style color #ffc848 > distance style color #ffbf48 > distance style color #ffb548 > distance style color #ffad48 > distance style color #ff9d48 > distance style color #ff9548 > distance style color #ff9348 > distance style color #ff9448 > distance style color #ff9d48 > distance style color #ffc548 > distance style color #ffdc48 > distance style color #fff148 > distance style color #fff548 > distance style color #ffee48 > distance style color #ffe048 > distance style color #ffcd48 > distance style color #ff8d48 > distance style color #ff8148 > distance style color #ff7948 > distance style color #ff7748 > distance style color #ff7848 > distance style color #ff8048 > distance style color #ff8d48 > distance style color #ffb948 > distance style color #ffcd48 > distance style color #ffe548 > distance style color #ffee48 > distance style color #fff548 > distance style color #fff848 > distance style color #fffa48 > distance style color #fffb48 > distance style color #fffd48 > distance style color #fffc48 > distance style color #fff848 > distance style color #ffef48 > distance style color #ffdf48 > distance style color #ffcd48 > distance style color #ffa548 > distance style color #ff9b48 > distance style color #ff9248 > distance style color #ff9648 > distance style color #ff9e48 > distance style color #ffae48 > distance style color #ffda48 > distance style color #ffec48 > distance style color #fff648 > distance style color #fff748 > distance style color #fff848 > distance style color #fff948 > distance style color #fff448 > distance style color #ffc948 > distance style color #ff9648 > distance style color #ff6348 > distance style color #ff5248 > distance style color #ff2548 > distance style color #ff1448 > distance style color #ff1248 > distance style color #ff1148 > distance style color #ff1048 > distance style color #ff0c48 > distance style color #ff0048 > distance style color #ff0047 > distance style color #ff0046 > distance style color #ff0045 > distance style color #ff0041 > distance style color #ff003e > distance style color #ff003a > distance style color #ff0037 > distance style color #ff0035 > distance style color #ff002c > distance style color #ff0028 > distance style color #ff0023 > distance style color #ff001f > distance style color #ff001e > distance style color #ff001d > distance style color #ff001c > distance style color #ff001a > distance style color #ff0018 > distance style color #ff0014 > distance style color #ff0114 > distance style color #ff0514 > distance style color #ff0814 > distance style color #ff0914 > distance style color #ff0a14 > distance style color #ff0b14 > distance style color #ff0c14 > distance style color #ff0d14 > distance style color #ff0e14 > distance style color #ff0f14 > distance style color #ff1014 > distance style color #ff1114 > distance style color #ff1214 > distance style color #ff1314 > distance style color #ff1414 > distance style color #fe1414 > distance style color #f81414 > distance style color #ef1414 > distance style color #e61414 > distance style color #db1414 > distance style color #c31414 > distance style color #b71414 > distance style color #a81414 > distance style color #9c1414 > distance style color #891414 > distance style color #7e1414 > distance style color #761414 > distance style color #5c1414 > distance style color #4b1414 > distance style color #3b1414 > distance style color #3a1414 > distance style color #391414 > distance style color #381414 > distance style color #361414 > distance style color #2e1414 > distance style color #2b1414 > distance style color #291414 > distance style color #281414 > distance style color #261414 > distance style color #251414 > distance style color #241414 > distance style color #221414 > distance style color #211414 > distance style color #1f1414 > distance style color #1e1414 > distance style color #1d1414 > distance style color #1c1414 > distance style color #1b1414 > distance style color #1a1414 > distance style color #191414 > distance style color #181414 > distance style color #171414 > distance style color #161414 > distance style color #141414 > distance style color #131414 > distance style color #121414 > distance style color #111414 > distance style color #121414 > distance style color #131414 > distance style color #141414 > distance style color #151414 > distance style color #141414 > select #1/A:44 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > distance style color #141416 > distance style color #141419 > distance style color #141425 > distance style color #14142c > distance style color #14142f > distance style color #141430 > distance style color #141433 > distance style color #141434 > distance style color #141435 > distance style color #141437 > distance style color #14143b > distance style color #141440 > distance style color #141441 > distance style color #141442 > distance style color #141443 > distance style color #141445 > distance style color #141447 > distance style color #141449 > ui tool show ""Color Actions"" > color sel byhetero target acsp > color sel #14144aff target acsp > color sel #141453ff target acsp > color sel #141460ff target acsp > color sel #141461ff target acsp > color sel #141462ff target acsp > color sel #141464ff target acsp > color sel #141467ff target acsp > color sel #14146eff target acsp > color sel #141471ff target acsp > color sel #141472ff target acsp > color sel #141471ff target acsp > color sel #141470ff target acsp > color sel #14146fff target acsp > color sel #14146cff target acsp > color sel #141465ff target acsp > color sel #141460ff target acsp > color sel #14145fff target acsp > color sel #14145bff target acsp > undo > color sel #ff7f50ff target acsp > hide sel atoms > select #1/A:43 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:43-48 74 atoms, 74 bonds, 6 residues, 1 model selected > color sel #ffba48ff target acsp > select clear > save /Users/till/Desktop/TTN-1/Figures/TTN1-activeSite.jpg width 2000 height > 2061 supersample 3 > hide #!5 models Drag select of 30 atoms, 280 residues, 26 bonds > color sel #ff7f50ff target acsp > hide sel atoms > undo > show #!5 models > select clear > save /Users/till/Desktop/TTN-1/Figures/TTN1-ActiveSite.cxs Drag select of 30 atoms, 290 residues, 26 bonds, 2 pseudobonds > hide sel atoms > color (#!1 & sel) #ff7f50ff target acsp > color (#!1 & sel) #ff7f61ff target acsp > color (#!1 & sel) #ff7f6dff target acsp > color (#!1 & sel) #ff7f64ff target acsp > color (#!1 & sel) #ff7f5dff target acsp > color (#!1 & sel) #ff7f5bff target acsp > color (#!1 & sel) #ff7f50ff target acsp > select clear > close #3#2,4-5 > open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb Chain information for TTN1_final.pdb #2 --- Chain | Description A | No description available 46 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3551 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Computing secondary structure > open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb Chain information for TTN1_final.pdb #3 --- Chain | Description A | No description available 46 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3551 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Computing secondary structure > rename #2 C-spine > rename #3 R-spine > open /Users/till/Desktop/TTN-1/Figures/TTN1_final.pdb Chain information for TTN1_final.pdb #4 --- Chain | Description A | No description available 46 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 3551 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. Computing secondary structure ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.dev202508070056 (2025-08-07) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Max 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: 6.9.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac13,1 Model Number: Z14J000EQD/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 2 hours, 4 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: G4FQX9PD4K Display Firmware Version: Version 17.0 (Build 21A329) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.4 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2025.7.14 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.10 ChimeraX-AtomicLibrary: 14.1.21 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: 1.5.1 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.dev202508070056 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: 1.7.1 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-MatchAlign: 1.0 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.17 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.5.1 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: 1.15.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.4 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.4 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: 1.5.2 ChimeraX-Scenes: 0.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.2 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: 1.48 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.2.1 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 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.10.2 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.2 debugpy: 1.8.16 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 5.0.0 lxml: 5.3.1 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.2 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.1 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.1 PyQt6_sip: 13.10.2 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.1 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 requests: 2.32.4 roman-numerals-py: 3.1.0 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: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.5 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect feedback normal Window Toolkit all ChimeraX