id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15634 Crash waking Mac from sleep bullitt@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit 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. After using ChimeraX, I left it running. After my computer came back from sleep mode, ChimeraX had crashed (in other words, it occurred when I was not actively using it) Fatal Python error: Segmentation fault Current thread 0x00007ff84774dfc0 (most recent call first): File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/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 ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/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 ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 59) {""app_name"":""ChimeraX"",""timestamp"":""2024-07-16 16:15:29.00 -0400"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""09A40133-1CC6-402A-867B-BC15945661FE""} { ""uptime"" : 300000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 2107, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-07-16 16:15:25.8974 -0400"", ""codeSigningMonitor"" : 0, ""incident"" : ""09A40133-1CC6-402A-867B-BC15945661FE"", ""pid"" : 19493, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-07-14 16:07:16.1944 -0400"", ""procStartAbsTime"" : 180994552496464, ""procExitAbsTime"" : 302489009432235, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/private\/var\/folders\/*\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D7D3B377-4527-5057-A8B7-1D0ECDF18636"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D6D0BAE5-DDDC-7E4B-A5C4-407F474777DB"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 34165, ""bridgeVersion"" : {""build"":""21P5077"",""train"":""8.5""}, ""sleepWakeUUID"" : ""5BC695A2-F0BD-48A6-876E-4E7A6FE06145"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet > camera ortho 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/eb1MacPro/Dropbox/Hflu/Compare_Hflu_oldnew_2023.11.06.cxs format > session Opened hibs53mbrix.brix as #1, grid size 60,60,100, pixel 3.5, shown at level 3.3e+04, step 1, values float32 Opened postprocess_Hib_job113.mrc as #2, grid size 280,280,280, pixel 1.08, shown at level 0.00681, step 1, values float32 Opened hibs53mbrix.brix as #3, grid size 60,60,100, pixel 3.5, shown at level 6.91e+04, step 1, values float32 Opened hibs53mbrix.brix z flip as #4, grid size 60,60,100, pixel 3.5, shown at level 4.61e+04, step 1, values float32 Opened postprocess_Hib_job113.mrc as #5, grid size 280,280,280, pixel 1.08, shown at level 0.00487, step 2, values float32 Opened postprocess_Hib_job113.mrc as #6, grid size 280,280,280, pixel 1.08, shown at level 0.00501, step 2, values float32 opened ChimeraX session The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open > /Users/eb1MacPro/Dropbox/EB/Hflu_Cryo/Hib_Purdue_2022/PostProcess/PostProcjob183/HifA_3_subunits_try1.pdb Chain information for HifA_3_subunits_try1.pdb #7 --- Chain | Description A B C | No description available > view > select #7 8808 atoms, 8883 bonds, 588 residues, 1 model selected > ui mousemode right ""move picked models"" > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,11.791,0,1,0,-137.6,0,0,1,-146.84 > view matrix models #7,1,0,0,-124.93,0,1,0,-101.01,0,0,1,-138.43 > view matrix models #7,1,0,0,-150.37,0,1,0,-137.73,0,0,1,-135.05 > view matrix models #7,1,0,0,-137.23,0,1,0,-140.06,0,0,1,-139.34 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.95822,-0.037597,-0.28355,-83.072,0.04805,0.99839,0.029997,-151.49,0.28197,-0.042369,0.95849,-169.05 > ui tool show ""Fit in Map"" > fitmap #7 inMap #5 Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc (#5) using 8808 atoms average map value = 0.004288, steps = 144 shifted from previous position = 13.5 rotated from previous position = 14.2 degrees atoms outside contour = 4767, contour level = 0.0048659 Position of HifA_3_subunits_try1.pdb (#7) relative to postprocess_Hib_job113.mrc (#5) coordinates: Matrix rotation and translation -0.01196724 -0.99804550 -0.06133493 311.73301767 0.99240991 -0.00434703 -0.12289701 20.45345436 0.12239018 -0.06234013 0.99052232 -11.50163111 Axis 0.03028095 -0.09187019 0.99531047 Axis point 146.07531995 164.34851109 0.00000000 Rotation angle (degrees) 90.73890521 Shift along axis -3.88718354 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.99794,-0.004421,-0.063998,-137.2,0.01323,0.99036,0.13789,-161.5,0.062771,-0.13845,0.98838,-131.96 > view matrix models > #7,0.99794,-0.004421,-0.063998,-144.47,0.01323,0.99036,0.13789,-163.66,0.062771,-0.13845,0.98838,-135.82 > fitmap #7 inMap #5 Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc (#5) using 8808 atoms average map value = 0.005834, steps = 360 shifted from previous position = 26 rotated from previous position = 69.9 degrees atoms outside contour = 3895, contour level = 0.0048659 Position of HifA_3_subunits_try1.pdb (#7) relative to postprocess_Hib_job113.mrc (#5) coordinates: Matrix rotation and translation 0.93491632 -0.35244470 -0.04140315 69.31164057 0.34981181 0.93492622 -0.05953720 -32.69981073 0.05969247 0.04117898 0.99736714 -6.51118911 Axis 0.14054554 -0.14107503 0.97997183 Axis point 122.06161474 170.93956117 0.00000000 Rotation angle (degrees) 20.99610141 Shift along axis 7.97378663 > hide #!2 models > hide #!1 models > hide #!6 models > view matrix models > #7,0.34935,0.93699,-0.00041691,-188.6,-0.93042,0.34696,0.11803,70.305,0.11073,-0.040845,0.99301,-137.88 > view matrix models > #7,0.34935,0.93699,-0.00041691,-187.65,-0.93042,0.34696,0.11803,69.11,0.11073,-0.040845,0.99301,-137.75 > fitmap #7 inMap #5 Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc (#5) using 8808 atoms average map value = 0.005834, steps = 68 shifted from previous position = 1.55 rotated from previous position = 0.00717 degrees atoms outside contour = 3895, contour level = 0.0048659 Position of HifA_3_subunits_try1.pdb (#7) relative to postprocess_Hib_job113.mrc (#5) coordinates: Matrix rotation and translation 0.93494566 -0.35235739 -0.04148369 69.30915042 0.34972297 0.93496136 -0.05950720 -32.69882289 0.05975346 0.04112819 0.99736559 -6.51171261 Axis 0.14046494 -0.14130487 0.97995027 Axis point 122.07519356 170.98390585 0.00000000 Rotation angle (degrees) 20.99106952 Shift along axis 7.97485413 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.4828,-0.8523,-0.20121,92.415,-0.84972,-0.40034,-0.34309,238.72,0.21187,0.33661,-0.9175,75.448 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.4828,-0.8523,-0.20121,92.183,-0.84972,-0.40034,-0.34309,242.36,0.21187,0.33661,-0.9175,83.318 > fitmap #7 inMap #5 Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc (#5) using 8808 atoms average map value = 0.008534, steps = 160 shifted from previous position = 0.744 rotated from previous position = 32.4 degrees atoms outside contour = 2324, contour level = 0.0048659 Position of HifA_3_subunits_try1.pdb (#7) relative to postprocess_Hib_job113.mrc (#5) coordinates: Matrix rotation and translation 0.99996228 0.00866391 0.00061478 -1.36469757 0.00866306 -0.99996154 0.00137123 300.18455070 0.00062664 -0.00136585 -0.99999893 313.89919247 Axis -0.99999056 -0.00433343 -0.00031056 Axis point 0.00000000 150.20263009 156.84710274 Rotation angle (degrees) 179.92158780 Shift along axis -0.03363141 > combine #7 modelId #8 name HifA pdb v2 Expected a keyword > combine modelId #7 modelId #8 name HifA pdb v2 Repeated keyword argument ""modelId"" > combine modelId #7 modelId #8 name HifA_pdb_v2 Repeated keyword argument ""modelId"" > combine modelId #7 name HifA_pdb_v2 Traceback (most recent call last): File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/cmd.py"", line 169, in combine_cmd session.models.add([combination]) File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 756, in add p = self._parent_for_added_model(model, parent, root_model = root_model) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 825, in _parent_for_added_model raise ValueError('Tried to add model %s with the same id as another model %s' ValueError: Tried to add model HifA_pdb_v2 #7 with the same id as another model HifA_3_subunits_try1.pdb #7 ValueError: Tried to add model HifA_pdb_v2 #7 with the same id as another model HifA_3_subunits_try1.pdb #7 File ""/private/var/folders/7v/7mk1h4t57d3fdgl6w3z2f1440000gp/T/AppTranslocation/E4BA0D7C-66CE-430A-9DF4-D23CD4D77191/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/models.py"", line 825, in _parent_for_added_model raise ValueError('Tried to add model %s with the same id as another model %s' See log for complete Python traceback. > combine #7 name HifA_pdb_v2 > combine #7 name HifA_pdb_v3 > hide #7 models > hide #9 models > show #!6 models > show #!1 models > hide #!1 models > show #!2 models > hide #!5 models > hide #!6 models > cofr #8 > turn y -163 models #8 > move y 27.5 models #8 > turn y -163 models #8 > fitmap #8 inMap #2 Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using 8808 atoms average map value = 0.0085, steps = 200 shifted from previous position = 1.56 rotated from previous position = 44.1 degrees atoms outside contour = 3224, contour level = 0.0068059 Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2) coordinates: Matrix rotation and translation -0.95318800 0.30236388 0.00295348 248.66109660 0.30236175 0.95319255 -0.00115465 -38.29418254 -0.00316440 -0.00020758 -0.99999515 286.90580071 Axis 0.15298091 0.98822908 -0.00034421 Axis point 127.51924242 0.00000000 143.25152578 Rotation angle (degrees) 179.82264785 Shift along axis 0.09822127 > hide #!2 models > hide #8 models > show #9 models > show #!6 models > turn y -163 models #9 > move y -27.5 models #9 > select #9 8808 atoms, 8883 bonds, 588 residues, 1 model selected > view matrix models > #9,0.28727,0.95747,0.027111,-189.2,0.95329,-0.28303,-0.10549,-90.473,-0.093334,0.05615,-0.99405,210.91 > cofr #9 > turn y 163 models #9 > fitmap #8 inMap #2 Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using 8808 atoms average map value = 0.0085, steps = 40 shifted from previous position = 0.0221 rotated from previous position = 0.0167 degrees atoms outside contour = 3225, contour level = 0.0068059 Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2) coordinates: Matrix rotation and translation -0.95311199 0.30260477 0.00280789 248.63710695 0.30260267 0.95311610 -0.00115333 -38.31853444 -0.00302528 -0.00024958 -0.99999557 286.91339264 Axis 0.15310569 0.98820976 -0.00035449 Axis point 127.50116796 0.00000000 143.26419024 Rotation angle (degrees) 179.83089826 Shift along axis 0.09929828 > fitmap #9 inMap #6 Fit molecule HifA_pdb_v3 (#9) to map postprocess_Hib_job113.mrc (#6) using 8808 atoms average map value = 0.008534, steps = 176 shifted from previous position = 0.96 rotated from previous position = 45.1 degrees atoms outside contour = 2382, contour level = 0.0050147 Position of HifA_pdb_v3 (#9) relative to postprocess_Hib_job113.mrc (#6) coordinates: Matrix rotation and translation 0.99996207 0.00867876 0.00074810 -1.39113756 0.00867779 -0.99996151 0.00130162 300.17943356 0.00075933 -0.00129503 -0.99999910 313.88525898 Axis -0.99999057 -0.00432749 -0.00037586 Axis point 0.00000000 150.19461045 156.84545615 Rotation angle (degrees) 179.92561049 Shift along axis -0.02587769 > hide #9 models > hide #!6 models > show #9 models > show #8 models > show #7 models > show #!6 models > select add #8 17616 atoms, 17766 bonds, 1176 residues, 2 models selected > select subtract #8 8808 atoms, 8883 bonds, 588 residues, 1 model selected > select add #8 17616 atoms, 17766 bonds, 1176 residues, 2 models selected > select subtract #8 8808 atoms, 8883 bonds, 588 residues, 1 model selected > select subtract #9 Nothing selected > select add #8 8808 atoms, 8883 bonds, 588 residues, 1 model selected > cofr #8 > move y -27.5 models #8 > turn y -163 models #8 > hide #!6 models > hide #7 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #9 models > hide #8 models > show #9 models > show #!6 models > hide #!6 models > hide #9 models > show #7 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > show #!5 models > show #!2 models > hide #!5 models > hide #7 models > show #8 models > turn y -163 models #8 > fitmap #8 inMap #2 Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using 8808 atoms average map value = 0.008367, steps = 228 shifted from previous position = 3.33 rotated from previous position = 59.4 degrees atoms outside contour = 3364, contour level = 0.0068059 Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2) coordinates: Matrix rotation and translation -0.94902635 -0.31518023 0.00323087 341.05552209 -0.31518598 0.94902883 -0.00144759 55.55309347 -0.00261003 -0.00239217 -0.99999413 341.93603023 Axis -0.15964364 0.98717423 -0.00097149 Axis point 175.27590480 0.00000000 170.73982106 Rotation angle (degrees) 179.83049618 Shift along axis 0.06104816 > hide #!2 models > show #7 models > show #9 models > show #!6 models > show #!5 models > show #!2 models > save > /Users/eb1MacPro/Dropbox/Hflu/2024HIB/3newHib_into_oldHib_w_pdbs_2024.07.15.cxs > show #!1 models > graphics silhouettes true > graphics silhouettes false > transparency #1.1#2.1#5.1#6.1 0 > transparency #1.1#2.1#5.1#6.1 50 > select subtract #8 Nothing selected > select add #2 2 models selected > transparency sel 0 > transparency sel 50 > hide #!1 models > hide #!2 models > hide #!5 models > hide #!6 models > select subtract #2 Nothing selected > show #!1 models > hide #!1 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > hide #8 models > show #8 models > hide #8 models > show #8 models > ortho Unknown command: ortho > camera ortho > color #8 #75edebff > show #!2 models > color #8 #dbee40ff > color #8 #eee923ff > color #8 #eec544ff > color #8 #eeba37ff > hide #!2 models > show #!5 models > hide #8 models > hide #9 models > show #9 models > show #7 models > hide #9 models > show #9 models > show #!6 models > hide #!5 models > hide #7 models > color #9 #5dedeaff > color #9 #53dfedff > color #9 #42daedff > color #9 #3ec1edff > show #8 models > show #7 models > hide #!6 models > hide #8 models > hide #9 models > show #!5 models > select #7 8808 atoms, 8883 bonds, 588 residues, 1 model selected > move y 27.5 models #7 > turn y -163 models #7 > fitmap #7 inMap #5 Fit molecule HifA_3_subunits_try1.pdb (#7) to map postprocess_Hib_job113.mrc (#5) using 8808 atoms average map value = 0.008367, steps = 120 shifted from previous position = 1.04 rotated from previous position = 15.6 degrees atoms outside contour = 2409, contour level = 0.0048659 Position of HifA_3_subunits_try1.pdb (#7) relative to postprocess_Hib_job113.mrc (#5) coordinates: Matrix rotation and translation -0.94904213 -0.31513324 0.00317530 341.05130751 -0.31513944 0.94904390 -0.00167804 55.59108791 -0.00248469 -0.00259317 -0.99999350 341.96468820 Axis -0.15961106 0.98717939 -0.00108181 Axis point 175.26801244 0.00000000 170.76519349 Rotation angle (degrees) 179.83574708 Shift along axis 0.07287375 > hide #!5 models > show #8 models > show #9 models > select subtract #7 Nothing selected > show #!5 models > show #!6 models > show #!2 models > save > /Users/eb1MacPro/Dropbox/Hflu/2024HIB/3newHib_into_oldHib_w_pdbs_2024.07.15.cxs > select #7-9 26424 atoms, 26649 bonds, 1764 residues, 3 models selected > move y -27.5 > move y 27.5 > move y -27.5 sel Expected an integer >= 1 or a keyword > move y -27.5 models #7-9 > turn y -163 models #7-9 > close session > open > /Users/eb1MacPro/Dropbox/Hflu/2024HIB/3newHib_into_oldHib_w_pdbs_2024.07.15.cxs > format session Opened hibs53mbrix.brix as #1, grid size 60,60,100, pixel 3.5, shown at level 3.3e+04, step 1, values float32 Opened postprocess_Hib_job113.mrc as #2, grid size 280,280,280, pixel 1.08, shown at level 0.00681, step 1, values float32 Opened hibs53mbrix.brix as #3, grid size 60,60,100, pixel 3.5, shown at level 6.91e+04, step 1, values float32 Opened hibs53mbrix.brix z flip as #4, grid size 60,60,100, pixel 3.5, shown at level 4.61e+04, step 1, values float32 Opened postprocess_Hib_job113.mrc as #5, grid size 280,280,280, pixel 1.08, shown at level 0.00487, step 2, values float32 Opened postprocess_Hib_job113.mrc as #6, grid size 280,280,280, pixel 1.08, shown at level 0.00501, step 2, values float32 opened ChimeraX session > set bgColor white > hide #!5 models > hide #!6 models > hide #!2 models > hide #7/a-b #8/a-b #9/a-b > hide #7/A-B #8/A-B #9/A-B > hide #8 models > hide #9 models > show #8 models > hide #8 models > show #8 models > hide #8 models > hide #7/B > hide ribbons #7/A-B #8/A-B #9/A-B Expected ',' or a keyword > hide #7/A-B #8/A-B #9/A-B ribbons > show #8 models > show #9 models > hide #8 models > show #8 models > hide #9 models > show #!2 models > hide #7 models > hide #8 models > show #!1 models > hide #!1 models > show #!5 models > cofr #2 > turn y 120 models #2 > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.046908,0.99771,-0.048765,-150.74,-0.99724,0.049588,0.055283,133.07,0.057574,0.046037,0.99728,-150.25 > view matrix models > #2,0.084098,0.99576,-0.037145,-157.82,-0.99496,0.085955,0.051611,127.81,0.054585,0.032618,0.99798,-147.89 > view matrix models > #2,-0.16048,0.9867,-0.025882,-121.17,-0.98618,-0.15919,0.045883,164.22,0.041152,0.032888,0.99861,-145.99 > view matrix models > #2,-0.15228,0.98686,0.053939,-134.43,-0.98684,-0.15483,0.046672,163.54,0.054411,-0.046122,0.99745,-135.94 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.15228,0.98686,0.053939,-130.8,-0.98684,-0.15483,0.046672,163.58,0.054411,-0.046122,0.99745,-135.99 > view matrix models > #2,-0.15228,0.98686,0.053939,-131.44,-0.98684,-0.15483,0.046672,165.28,0.054411,-0.046122,0.99745,-135.91 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.00057809,0.99966,0.02597,-152.09,-0.99983,-0.0010498,0.018154,148.39,0.018175,-0.025955,0.9995,-133.78 > view matrix models > #2,-0.0051394,0.99923,0.038881,-153.27,-0.99986,-0.0045252,-0.015867,154.03,-0.015679,-0.038958,0.99912,-126.65 > view matrix models > #2,0.0033244,0.9999,0.01364,-150.86,-0.99874,0.0026356,0.050211,142.86,0.05017,-0.01379,0.99865,-140.32 > view matrix models > #2,-0.042504,0.99837,0.038117,-147.38,-0.99704,-0.044833,0.0625,147.9,0.064107,-0.035347,0.99732,-138.98 > view matrix models > #2,-0.042928,0.99829,0.039602,-147.53,-0.99725,-0.045211,0.058663,148.56,0.060354,-0.036975,0.99749,-138.19 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.042928,0.99829,0.039602,-146.57,-0.99725,-0.045211,0.058663,146.36,0.060354,-0.036975,0.99749,-137.32 > show #!6 models > turn y -120 models #2 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.87596,-0.45732,0.15346,-88.876,0.45571,0.88885,0.047646,-207.94,-0.15819,0.028196,0.98701,-112.41 > ui tool show ""Side View"" > show #8 models > show #7-9 ribbons Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 3 maps. > ui tool show ""Fit in Map"" > fitmap #8 inMap #2 Fit molecule HifA_pdb_v2 (#8) to map postprocess_Hib_job113.mrc (#2) using 8808 atoms average map value = 0.008367, steps = 108 shifted from previous position = 5.47 rotated from previous position = 10.3 degrees atoms outside contour = 3358, contour level = 0.0068059 Position of HifA_pdb_v2 (#8) relative to postprocess_Hib_job113.mrc (#2) coordinates: Matrix rotation and translation -0.94903779 -0.31514582 0.00322349 341.04744198 -0.31515186 0.94903995 -0.00156823 55.56803627 -0.00256507 -0.00250424 -0.99999386 341.96153508 Axis -0.15962651 0.98717694 -0.00103040 Axis point 175.27030012 0.00000000 170.75653587 Rotation angle (degrees) 179.83201567 Shift along axis 0.06291469 > show #9 models > show #7 models > hide #!2 models > hide #!5 models > hide #!6 models > ui tool show ""Side View"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet > camera ortho 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 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 10 days, 2 hours, 22 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal B247W: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: TD3AA0018532 Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: ff.c8 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