id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17231 Crash on Mac waking from sleep psrini7@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-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 0x00000001fc574840 (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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-28 14:05:21.00 -0700"",""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 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""F33AA3F3-3BF6-4F70-B776-F01935A464ED""} { ""uptime"" : 320000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,5"", ""coalitionID"" : 21145, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-28 14:05:10.9707 -0700"", ""codeSigningMonitor"" : 1, ""incident"" : ""F33AA3F3-3BF6-4F70-B776-F01935A464ED"", ""pid"" : 39485, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-28 10:48:27.3204 -0700"", ""procStartAbsTime"" : 7570135006179, ""procExitAbsTime"" : 7853421525233, ""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"":""8130645D-BEAB-5776-BE53-C039A7FAE8AE"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""34646E04-77D9-22C8-5CBA-A82BA218D2EA"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""0C17CBEB-30D5-476A-8EB6-962600B7C5A8"", ""wakeTime"" : 24437, ""sleepWakeUUID"" : ""3BB03096-279A-42CD-A91D-F49A1B352983"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x1ab64af36b58 is not in any region. 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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/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/bft-1_project/structures/bft1_8h3y_nanbody.pdb1 Summary of feedback from opening /Users/poojasrinivas/Library/CloudStorage/OneDrive- UW/Desktop/mougouslab/bft-1_project/structures/bft1_8h3y_nanbody.pdb1 --- warnings | Start residue of secondary structure not found: HELIX 15 AB6 SER B 44 ASP B 54 1 11 Start residue of secondary structure not found: HELIX 16 AB7 ARG B 96 ASP B 99 5 4 Start residue of secondary structure not found: HELIX 17 AB8 GLU B 128 ALA B 141 1 14 Start residue of secondary structure not found: HELIX 18 AB9 PRO B 142 LYS B 144 5 3 Start residue of secondary structure not found: HELIX 19 AC1 ASN B 150 GLU B 153 5 4 94 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (22 ) Cannot find LINK/SSBOND residue CYS (22 ) Cannot find LINK/SSBOND residue ASP (194 ) Cannot find LINK/SSBOND residue ASP (194 ) Cannot find LINK/SSBOND residue HIS (348 ) 7 messages similar to the above omitted bft1_8h3y_nanbody.pdb1 title: Bacteroide fragilis toxin In complex with nanobody 327 [more info...] Chain information for bft1_8h3y_nanbody.pdb1 #1 --- Chain | Description A | No description available F | No description available Non-standard residues in bft1_8h3y_nanbody.pdb1 #1 --- ZN — zinc ion 11 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > 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 > lighting soft > select /F:2-121 918 atoms, 939 bonds, 120 residues, 1 model selected > hide sel cartoons > hide pseudobondes Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide pseudobonds > select :221 13 atoms, 12 bonds, 2 residues, 1 model selected > select :211 1 atom, 1 residue, 1 model selected > color :1-199 white > color :199-500 purple > color sel byhetero > ui mousemode right select > color sel byhetero > select add #1 3868 atoms, 3739 bonds, 7 pseudobonds, 675 residues, 3 models selected > color sel byhetero > select clear > select /A:401@ZN 1 atom, 1 residue, 1 model selected > color sel green > hbonds sel reveal true 0 hydrogen bonds found > select clear > hbonds reveal true 912 hydrogen bonds found > ~hbonds > hide :HOH > hide atoms > ui tool show ""Side View"" > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > graphics silhouettes true > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/prodomaincloseup.png width > 1800 height 1800 supersample 4 transparentBackground true > hbonds reveal true 912 hydrogen bonds found > clip off > ~hbonds > hide #1 > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/bft-1_project/structures/BFT_Minibinder_3.pdb Chain information for BFT_Minibinder_3.pdb #2 --- Chain | Description A | No description available B | No description available > matchmaker #2 to #` Invalid ""to"" argument: invalid atoms specifier > matchmaker #2 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 bft1_8h3y_nanbody.pdb1, chain A (#1) with BFT_Minibinder_3.pdb, chain A (#2), sequence alignment score = 971.5 RMSD between 186 pruned atom pairs is 0.400 angstroms; (across all 186 pairs: 0.400) > hide #2/A > hide #2/A cartoons > color #2/B #EAAE11 Drag select of 1 residues > color sel white > select clear > open /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/bft-1_project/newminibinders/fold_bft1_fold_kl_d2_3_model_0_7_b/fold_bft1_fold_kl_d2_3_model_0_7_b_model_0.cif Chain information for fold_bft1_fold_kl_d2_3_model_0_7_b_model_0.cif #3 --- Chain | Description A | . B | . > matchmaker #3 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 bft1_8h3y_nanbody.pdb1, chain A (#1) with fold_bft1_fold_kl_d2_3_model_0_7_b_model_0.cif, chain B (#3), sequence alignment score = 960.7 RMSD between 183 pruned atom pairs is 0.430 angstroms; (across all 186 pairs: 0.592) > hide #3/B surfaces > hide #3/B cartoons > hide #3 models > hide #2#!1 atoms > transparency #1/ :1-199 target c Missing or invalid ""percent"" argument: Expected a number > transparency 100 #1/ :1-199 target c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 100 #1/ :1-199 target cartoons Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #1/ :1-199 100 target cartoons Missing or invalid ""percent"" argument: Expected a number > transparency #1/:1-199 100 target cartoons Missing or invalid ""percent"" argument: Expected a number > transparency #1/:1-199 100 target cartoons Missing or invalid ""percent"" argument: Expected a number > transparency #1/:1-199 100 target cartoons Missing or invalid ""percent"" argument: Expected a number > transparency #1:1-199 100 target cartoons Invalid ""target"" argument: Character 't' is not an allowed target, must be one of acrsbmpfl > transparency #1:1-199 100 cartoons > hide #1:1-199 cartoons > hide #2 models > show #2 models > show #1:1-199 cartoons > show #1/A:1-199 cartoons > color #1:1-199 white > color #1/A:1-199 white > transparency #1:1-199 0 cartoons Drag select of 4 residues > show sel cartoons > show #1 cartoons > undo > select clear > show pseudobonds Drag select of 2 residues, 1 pseudobonds > hide sel pseudobonds > select clear > hide #2 models > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/fulllengthBFT_backside.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #1:1-199 cartoons > hide pseudobonds Drag select of 2 atoms, 1 pseudobonds > hide sel atoms > select #1/A:199@C 1 atom, 1 residue, 1 model selected > hide sel atoms > select clear > hide #!1 atoms > show #2 models > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft_mb03_backside.png width > 1800 height 1800 supersample 4 transparentBackground true > show #1/A > show #1/A cartoons > hide #2 models Drag select of 1 residues, 1 pseudobonds > hide sel pseudobonds > select clear > show sel pseudobonds > select clear > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/fulllengthBFT_backside2.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #1:1-199 cartoons > hide #1:1-199 pseudobonds > select clear > hide #!1 atoms > select clear > show #2 models > show #1:1-199 cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A :RENG Nothing selected > select #1/A :R,E,N,G Nothing selected > select #1/A @R,E,N,G 348 atoms, 348 residues, 1 model selected > select clear > select #1/A :Arg,Glu 302 atoms, 271 bonds, 32 residues, 1 model selected > select #1/A :Arg,Glu,Gln,Gly 467 atoms, 412 bonds, 62 residues, 1 model selected > select #1/A:226 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:226 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel green > select #1/A:238 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:238 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel green > select #1/A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel green > select #1/A:255 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:254-255 17 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:254-255 17 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:254-255 17 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:255 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:255 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel green > select #1/A:262 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:262 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel green > select #1/A:265 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:265 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel green > select #1/A:296 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:296-297 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:296-297 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:296-297 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:296 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:296 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel green > select clear > hide #!1 models > show #!1 models > hide #1/F > hide #1/F cartoons > hide #1:1-199 cartoons > hide #2 models > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bftcartoon_interactingresidues.png > width 1800 height 1800 supersample 4 transparentBackground true > select #1 :238,246,255,262,265,296 59 atoms, 55 bonds, 7 residues, 1 model selected > select clear > show #2 models > select #1 :238,246,255,262,265,296 59 atoms, 55 bonds, 7 residues, 1 model selected > color sel purple > show sel > color byhetero > select #1 :238,246,255,262,265,296,226 71 atoms, 65 bonds, 9 residues, 1 model selected > color sel purple > color byhetero > select #1/A:226 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear Drag select of 1 atoms > hide sel atoms > select clear > show #2 models > hbonds #2#!1 reveal true 2575 hydrogen bonds found > delete /F > delete :HOH > select #1 :238,246,255,262,265,296,226 69 atoms, 65 bonds, 1 pseudobond, 7 residues, 2 models selected > color sel red > hide #!1 models > select add #1 2744 atoms, 2800 bonds, 324 pseudobonds, 349 residues, 4 models selected > select subtract #1 Nothing selected > show #!1 models > hide #!1 models > show #2 cartoons > color #2/A purple > select #2 :238,246,255,262,265,296,226 Nothing selected > select #2 :27,35,44,51,54,85,15 116 atoms, 107 bonds, 1 pseudobond, 13 residues, 2 models selected > select #2 :27,35,44,51,54,85,15,50 133 atoms, 125 bonds, 2 pseudobonds, 15 residues, 2 models selected > select #2/A :27,35,44,51,54,85,15,50,55 86 atoms, 83 bonds, 3 pseudobonds, 9 residues, 2 models selected > select #2/A :35,44,51,54,85,15,50,55 80 atoms, 78 bonds, 3 pseudobonds, 8 residues, 2 models selected > select #2/A :35,44,51,54,15,50,55 68 atoms, 66 bonds, 3 pseudobonds, 7 residues, 2 models selected > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 3 pseudobonds, 8 residues, 2 models selected > hide sel atoms > hide #2 atoms > ~hbonds > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > show sel atoms > color sel byhetero > select #2/B:42 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hbonds sel reveal true 11 hydrogen bonds found > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > hbonds sel reveal true 43 hydrogen bonds found > select clear Drag select of 5 residues > show sel atoms > hbonds sel reveal true 8 hydrogen bonds found > ui mousemode right distance > ui mousemode right select > select clear > ui mousemode right distance > distance #2/A:54@OH #2/B:36@SD Distance between BFT_Minibinder_3.pdb #2/A TYR 54 OH and /B MET 36 SD: 3.392Å > hide #!5 models > hide #5.1 models > hide #4 models > ui mousemode right select Drag select of 1 residues > hide sel cartoons > select #2/B:56 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #2/B:57@C 1 atom, 1 residue, 1 model selected > show sel cartoons > show sel atoms > select #2/B:57 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 2 residues > show sel atoms > select #2/B:56 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/B:57 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Rotamers Populating font family aliases took 149 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > swapaa interactive sel THR rotLib Dunbrack BFT_Minibinder_3.pdb #2/B THR 57: phi -136.0, psi none trans Changed 12 bond radii > swapaa #!2/B:57 THR criteria 3 rotLib Dunbrack retain false Using Dunbrack library BFT_Minibinder_3.pdb #!2/B THR 57: phi -136.0, psi none trans Applying THR rotamer (chi angles: -173.3) to BFT_Minibinder_3.pdb #!2/B THR 57 > select clear > ui mousemode right distance > distance #2/A:35@OD1 #2/B:57@OG1 Distance between BFT_Minibinder_3.pdb #2/A ASN 35 OD1 and /B THR 57 OG1: 3.186Å > ui mousemode right select > select #2/B:57 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > ui mousemode right distance > distance #2/A:44@NZ #2/B:57@OXT Distance between BFT_Minibinder_3.pdb #2/A LYS 44 NZ and /B THR 57 OXT: 2.213Å > distance #2/A:44@NZ #2/B:57@OXT Distance already exists; modify distance properties with 'distance style' > show sel cartoons > ui mousemode right select > select clear > show #4 models > select #2/B:39 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/B:46 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:32 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/B:31 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:53 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:53 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #2/A:51 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:31 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #2/B:33 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/B:47 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > hide #4 models > ui tool show ""Side View"" > select #2/B:57 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #2/A:44 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/A:35 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > hide #2 cartoons > undo > hide #2 cartoons > select clear > ui mousemode right translate > undo > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > ui mousemode right select > select #2/B:57@CA 1 atom, 1 residue, 1 model selected > select #2/B:46 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:42 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:36 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:25 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > hide #2 cartoons > select clear Drag select of 17 atoms, 15 bonds > select clear Drag select of 16 atoms, 14 bonds Drag select of 9 atoms, 8 bonds Drag select of 4 atoms, 4 bonds Drag select of 23 atoms, 21 bonds Drag select of 23 atoms, 22 bonds > select ~sel 6661 atoms, 6793 bonds, 16 pseudobonds, 849 residues, 8 models selected > hide sel Drag select of 8 atoms, 7 bonds Drag select of 6 atoms, 5 bonds Drag select of 14 atoms, 12 bonds > show sel cartoons > select clear > select #2/A:35 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/MB03thr_bftasnlys.png width > 1800 height 1800 supersample 4 transparentBackground true Drag select of 19 atoms, 2 residues, 16 bonds > hide sel atoms > show sel cartoons > undo > select clear > hide #2 cartoons > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > show sel atoms > show sel cartoons > Sel #2/B :46,42,36,25 Unknown command: Sel #2/B :46,42,36,25 > ael #2/B :46,42,36,25 Unknown command: ael #2/B :46,42,36,25 > select #2/B :46,42,36,25 36 atoms, 33 bonds, 4 residues, 1 model selected > show sel atoms > show sel cartoons > select #2/A:51 11 atoms, 11 bonds, 1 residue, 1 model selected Drag select of 39 atoms, 7 residues, 35 bonds > hide sel atoms > hide sel cartoons Drag select of 10 atoms, 2 residues, 8 bonds Drag select of 11 atoms, 2 residues, 9 bonds > hide sel atoms > hide sel cartoons > select #2/A:51 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > select #2/A:50 10 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > undo > select #2/A:50 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A :51 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel cartoons Drag select of 2 residues > hide sel cartoons > undo > select #2/A:51 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms Drag select of 1 atoms, 2 residues, 1 bonds > hide sel cartoons > select clear Drag select of 30 atoms, 1 residues, 31 bonds > hbonds sel reveal true 14 hydrogen bonds found > undo > ~hbonds > select clear Drag select of 28 atoms, 1 residues, 30 bonds Drag select of 29 atoms, 1 residues, 31 bonds Drag select of 1 atoms, 1 bonds > select clear Drag select of 4 atoms, 3 bonds > hide sel atoms Drag select of 7 atoms, 6 bonds Drag select of 8 atoms, 6 bonds > hide sel atoms Drag select of 3 atoms, 3 bonds Drag select of 4 atoms, 3 bonds > hide sel atoms > select #2/A:51@CA 1 atom, 1 residue, 1 model selected > ~hbonds > ui mousemode right distance > distance #2/A:51@N #2/B:25@OH Distance between BFT_Minibinder_3.pdb #2/A PHE 51 N and /B TYR 25 OH: 3.034Å > distance #2/A:50@N #2/B:25@OH Distance between BFT_Minibinder_3.pdb #2/A HIS 50 N and /B TYR 25 OH: 4.527Å > ui mousemode right select > select clear Drag select of 14 atoms, 14 bonds Drag select of 16 atoms, 17 bonds > show sel cartoons > select clear > select #2/A:51 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel cartoons > hide sel atoms > ui mousemode right distance > distance #2/B:25@CD2 #2/A:50@CE1 Distance between BFT_Minibinder_3.pdb #2/B TYR 25 CD2 and /A HIS 50 CE1: 3.616Å > select ~sel & ##selected 1911 atoms, 1952 bonds, 6 pseudobonds, 243 residues, 2 models selected > select up 1913 atoms, 1952 bonds, 6 pseudobonds, 244 residues, 2 models selected > ui mousemode right select > select clear > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/MB03tyr_bfthis.png width > 1800 height 1800 supersample 4 transparentBackground true Drag select of 16 atoms, 2 residues, 16 bonds > hide sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > select clear > select add #2 1922 atoms, 1963 bonds, 6 pseudobonds, 244 residues, 2 models selected > close #5 > show sel cartoons > select clear > select #2/B:57 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A :His 70 atoms, 70 bonds, 7 residues, 1 model selected > select #1/A @His Nothing selected > select #2/A :His 60 atoms, 60 bonds, 6 residues, 1 model selected > select clear > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > show sel atoms > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > select clear Drag select of 15 atoms, 29 residues, 13 bonds > show sel atoms > select clear > select #2/A:55 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:57 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:54 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:55 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:15 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/B:42 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > hide #2 atoms > hide #2 cartoons > show #2/A:55,15 > show #2/A:55,15 cartoons > show #2/B :42 > show #2/B :42 cartoons > select #2/A:55 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/minibinder_bftinteractions.cxs > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/MB03asp_bftlysthr.png width > 1800 height 1800 supersample 4 transparentBackground true > hide #2 atoms > show #2 cartoons > select #2/A :35,44,51,54,15,50,55,53 76 atoms, 74 bonds, 8 residues, 1 model selected > show sel atoms > select clear > hbonds #2 reveal true 985 hydrogen bonds found > interfaces #2 & ~solvent 1 buried areas: A B 989 > hide #2 atoms > hide #2 cartoons > show #2 cartoons > ~hbonds > hbonds #2 reveal true 985 hydrogen bonds found > select #2/B:46 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:53@C 1 atom, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > ~hbonds > select add #2 1922 atoms, 1963 bonds, 244 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #2/B:46 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > show sel cartoons > select #2/A:53 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > interfaces #2 & ~solvent 1 buried areas: A B 989 > select add #2 1922 atoms, 1963 bonds, 244 residues, 1 model selected > show sel cartoons > hbonds sel reveal true 985 hydrogen bonds found > ~hbonds > hide sel atoms > undo > show sel cartoons > hide sel atoms > show sel atoms > select add #2 1922 atoms, 1963 bonds, 244 residues, 1 model selected > show sel cartoons > show sel atoms > hide sel atoms > select #2/C 1 atom, 1 residue, 1 model selected > show sel surfaces > hide sel atoms > hide sel cartoons > hide sel atoms > select #2/C 1 atom, 1 residue, 1 model selected > hide sel atoms Drag select of BFT_Minibinder_3.pdb_C SES surface, 25 of 44 triangles > select #2/C:1@ZN 1 atom, 1 residue, 1 model selected > hide sel > hide /C > select clear Drag select of BFT_Minibinder_3.pdb_C SES surface, 22 of 44 triangles > select #2/C:1@ZN 1 atom, 1 residue, 1 model selected > delete sel > interfaces #2 & ~solvent 1 buried areas: A B 989 > select interfaces #2 Expected an objects specifier or a keyword > hide /B cartoons Drag select of 144 atoms, 141 bonds Drag select of 146 atoms, 142 bonds > color sel red > hide sel atoms > show sel surfaces > color sel red > show #2/A surfaces > select clear > undo > color sel green > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:49 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:49 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel red > select clear > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select #2/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:101-102 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > select #2/A:49@O 1 atom, 1 residue, 1 model selected > select #2/A:66 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:66 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > select #2/A:64@CG 1 atom, 1 residue, 1 model selected Drag select of BFT_Minibinder_3.pdb_A SES surface, 36340 of 157062 triangles Drag select of BFT_Minibinder_3.pdb_A SES surface, 16801 of 157062 triangles > select #2/A:101@CD 1 atom, 1 residue, 1 model selected > select #2/A:101@O 1 atom, 1 residue, 1 model selected Drag select of BFT_Minibinder_3.pdb_A SES surface, 35472 of 157062 triangles > color sel purple > select #2/A:49 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:49 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:66-67 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:66-67 18 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:66 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:66 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > color #1/A :64 > color #1/A :64 purple > color #2/A :64 purple > select #2/A:108 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:108 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel red > select #2/A:144 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:144 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel red > select #2/A:146 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:146 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > select #2/A:148-149 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:148-149 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:148 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:148 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select #2/A:151-152 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:151-152 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:151 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:151 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > select #2/A:158-159 18 atoms, 18 bonds, 2 residues, 1 model selected > select #2/A:158-159 18 atoms, 18 bonds, 2 residues, 1 model selected > select #2/A:158 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:158 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red\ Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel red > select #2/A:164 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:164 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > select #2/A:172 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:172 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:172 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:172-173 16 atoms, 15 bonds, 2 residues, 1 model selected > color sel red > select #2/A:182 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:182 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel red > select #2/A:59 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:59 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > select #2/A:64-65 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:64-65 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:64-65 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:63-64 12 atoms, 11 bonds, 2 residues, 1 model selected > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:64 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select #2/A:78 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:78 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > select #2/A:105 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:105 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select #2/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select #2/A:120 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:120 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > select #2/A:146 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:146 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:148 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:148 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:149 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:150 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:150 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > select #2/A:157 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:157 5 atoms, 4 bonds, 1 residue, 1 model selected > color sel red > select #2/A:159 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:159 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel red > select #2/A:164-165 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:164-165 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:164-165 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:164 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:164 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel purple > select #2/A:169 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:169 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > select #2/A:172 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:172-173 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:182 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:182 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft_interactingresiduees_nonconservedresidues_nomb03.png > width 1800 height 1638 supersample 4 transparentBackground true > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft_nonconservedresidues.png > width 1800 height 1800 supersample 4 transparentBackground true > hide #!2 surfaces > undo > show #!2 surfaces > hide /B surfaces > select #2/A:44@CD 1 atom, 1 residue, 1 model selected > select #2/A:35@CB 1 atom, 1 residue, 1 model selected > select #2/A:35@ND2 1 atom, 1 residue, 1 model selected > select #2/A:31@NE2 1 atom, 1 residue, 1 model selected > select #2/A:27@OG 1 atom, 1 residue, 1 model selected > hide sel surfaces > select clear > hide #!2 surfaces > show #!2 cartoons > select ~sel & ##selected Nothing selected > hide /B cartoons > select #2/A:23-38,43-45,65-78,80-82,99-101,134-142,168-178,182-184 468 atoms, 466 bonds, 62 residues, 1 model selected > select #2/A:7-15,47-55,89-94,104-106,122-126 263 atoms, 265 bonds, 32 residues, 1 model selected Drag select of 5 residues > select #2/A:51 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:51-63 102 atoms, 105 bonds, 13 residues, 1 model selected > select clear > select #2/A:55 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:50 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:55 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:50 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:50-61 102 atoms, 106 bonds, 12 residues, 1 model selected > select #2/A:56 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:50-56 62 atoms, 64 bonds, 7 residues, 1 model selected > select #2/A:7-15,47-55,89-94,104-106,122-126 263 atoms, 265 bonds, 32 residues, 1 model selected > select #2/A:55 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:50-55 55 atoms, 57 bonds, 6 residues, 1 model selected > select #2/A:10 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:15 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:23 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/A:27 13 atoms, 12 bonds, 2 residues, 2 models selected > select add #2/A:30 21 atoms, 19 bonds, 3 residues, 2 models selected > select add #2/A:31 30 atoms, 27 bonds, 4 residues, 2 models selected > select add #2/A:35 38 atoms, 34 bonds, 5 residues, 2 models selected > select #2/A:44 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:81 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/A:85 21 atoms, 20 bonds, 2 residues, 2 models selected > select clear > select #2/A:44 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/A:35 17 atoms, 15 bonds, 2 residues, 2 models selected > select add #2/A:31 26 atoms, 23 bonds, 3 residues, 2 models selected > select add #2/A:30 34 atoms, 30 bonds, 4 residues, 2 models selected > select add #2/A:27 40 atoms, 35 bonds, 5 residues, 2 models selected > select add #2/A:23 47 atoms, 42 bonds, 6 residues, 2 models selected > select add #2/A:15 58 atoms, 52 bonds, 7 residues, 2 models selected > select add #2/A:81 67 atoms, 60 bonds, 8 residues, 2 models selected > select add #2/A:85 79 atoms, 72 bonds, 9 residues, 2 models selected > select add #2/A:10 91 atoms, 84 bonds, 10 residues, 2 models selected Drag select of 3 residues > select add #2/A:52 125 atoms, 90 bonds, 14 residues, 2 models selected > select add #2/A:51 136 atoms, 101 bonds, 15 residues, 2 models selected > select add #2/A:50 146 atoms, 111 bonds, 16 residues, 2 models selected > select ~sel 6537 atoms, 6658 bonds, 7 pseudobonds, 834 residues, 5 models selected > color sel purple > select clear > show /B > color /B #EAAE11 > hide #!2 atoms > show #!2 cartoons > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft-mb03_1.png width 1800 > height 1800 supersample 4 transparentBackground true > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft-mb03_2.png width 1800 > height 1800 supersample 4 transparentBackground true > save /Users/poojasrinivas/Library/CloudStorage/OneDrive- > UW/Desktop/mougouslab/hhmiepimeeting/josephstalk/bft-mb03_3.png width 1800 > height 1800 supersample 4 transparentBackground true > select #2/A:81 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > interfaces #!2 & ~solvent 1 buried areas: A B 989 > hbonds #!2 reveal true 986 hydrogen bonds found > undo > select clear > ~hbonds > color #!2 byhetero > color /A purple > color #!2 byhetero Drag select of 4 atoms, 4 bonds > show sel surfaces > undo > hide sel cartoons > hide sel surfaces > show sel cartoons Drag select of 3 atoms, 3 bonds > show sel cartoons Drag select of 4 atoms, 4 bonds > show sel cartoons Drag select of 32 atoms, 1 residues, 29 bonds > show sel cartoons Drag select of 11 atoms, 9 bonds > show sel cartoons > select clear Drag select of 5 atoms, 2 residues, 3 bonds > show sel cartoons Drag select of 9 atoms, 3 residues, 5 bonds > select clear > undo > show sel atoms > show #2/B cartoons > select clear Drag select of 7 atoms, 14 residues, 4 bonds > select clear Drag select of 12 atoms, 15 residues, 9 bonds > show sel cartoons > select clear > ui mousemode right distance > distance #2/B:56@OD1 #2/A:31@OE1 Distance between BFT_Minibinder_3.pdb #2/B ASN 56 OD1 and /A GLN 31 OE1: 4.367Å > distance #2/B:56@ND2 #2/A:31@NE2 Distance between BFT_Minibinder_3.pdb #2/B ASN 56 ND2 and /A GLN 31 NE2: 4.112Å ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M2 Max 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 Pro Model Identifier: Mac14,5 Model Number: MPHG3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 11 days, 22 hours, 44 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 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