id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9926 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00007ff85e9b3640 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-10-06 17:14:37.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.4.1 (22F770820d)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""DF489EEA-C095-4597-AF51-E7967E708807""} { ""uptime"" : 190000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 7336, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 541, ""osVersion"" : { ""train"" : ""macOS 13.4.1"", ""build"" : ""22F770820d"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-10-06 17:14:20.5717 +0200"", ""incident"" : ""DF489EEA-C095-4597-AF51-E7967E708807"", ""pid"" : 44652, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-10-02 16:40:10.7793 +0200"", ""procStartAbsTime"" : 22102791547119, ""procExitAbsTime"" : 191436225626022, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""1545732F-3ECF-5423-8838-9536F50DE789"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""E8834526-84A6-79EE-EAB6-12A98E7DF4C1"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 9630, ""bridgeVersion"" : {""build"":""20P5060"",""train"":""7.5""}, ""sleepWakeUUID"" : ""77BF73BC-92E2-4749-B3A9-D50ED5A4C828"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""81e34a2424b145911fcabc72e44beca7108cc2a9"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000413 }, { ""rolloutId"" : ""6391cacc75b0720ff1f8c695"", ""factorPackIds"" : { ""COREOS_ICD"" : ""63957f508061fa721c8edc4a"" }, ""deploymentId"" : 240000007 } ], ""experiments"" : [ { ""treatmentId"" : ""a092db1b-c401-44fa-9c54-518b7d69ca61"", ""experimentId"" : ""64a844035c85000c0f42398a"", ""deploymentId"" : 400000019 }, { ""treatmentId"" : ""d28d100b-301c-49ae-b6c9-57930102d4d4"", ""experimentId"" : ""64466b09a3b9440a82a18c34"", ""deploymentId"" : 400000002 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs Opened RHom Model.pdb map 3 as #4, grid size 51,73,158, pixel 1, shown at level 0.115, step 1, values float32 Opened Rhom_Flagella_Map_2RingMasked.mrc as #6, grid size 200,201,275, pixel 0.94,0.94,0.94, shown at level 0.024, step 1, values float32 Log from Thu Aug 10 13:03:26 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs Opened RHom Model.pdb map 3 as #4, grid size 51,73,158, pixel 1, shown at level 0.115, step 1, values float32 Opened Rhom_Flagella_Map_2RingMasked.mrc as #6, grid size 200,201,275, pixel 0.94,0.94,0.94, shown at level 0.024, step 1, values float32 Log from Wed Aug 2 16:13:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/mbell/sshfs/c0140_4_MotionCor2/Chimera projects/Rhom > fitting/Rhom_Modelangelo_Structure.cxs"" Opened Rhom_single_Map_3.1A.mrc as #3, grid size 62,90,171, pixel 0.94,0.94,0.94, shown at level 0.0155, step 1, values float32 Log from Tue Jul 4 11:16:35 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/mbell/sshfs/c0140_4_MotionCor2/RhFlaB_Modelangelo_1/gnn_output_round_1/output.cif Summary of feedback from opening /Users/mbell/sshfs/c0140_4_MotionCor2/RhFlaB_Modelangelo_1/gnn_output_round_1/output.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. 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/Users/mbell/sshfs/c0140_4_MotionCor2/RhFlaB_Modelangelo_SingleParticle_1/gnn_output_round_1/output.cif Summary of feedback from opening /Users/mbell/sshfs/c0140_4_MotionCor2/RhFlaB_Modelangelo_SingleParticle_1/gnn_output_round_1/output.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for output.cif #2 --- Chain | Description E | No description available [deleted to fit within ticket limits] > view matrix models > #24,-0.8641,0.49333,0.099801,217.28,-0.47285,-0.86361,0.17491,391.07,0.17248,0.10395,0.97951,-92.661 > fitmap #23 inMap #6 Fit molecule copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01533, steps = 28 shifted from previous position = 0.0129 rotated from previous position = 0.0325 degrees atoms outside contour = 1404, contour level = 0.023968 Position of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.14280944 0.98974751 0.00231057 27.01004015 -0.98974999 -0.14281056 0.00032599 384.66630155 0.00065262 -0.00224033 0.99999728 -31.14805554 Axis -0.00129645 0.00083756 -0.99999881 Axis point 180.08718705 180.60620775 0.00000000 Rotation angle (degrees) 98.21056054 Shift along axis 31.43518161 > fitmap #23 inMap #6 Fit molecule copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01533, steps = 36 shifted from previous position = 0.0091 rotated from previous position = 0.0387 degrees atoms outside contour = 1404, contour level = 0.023968 Position of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.14216106 0.98984088 0.00229308 26.89566604 -0.98984342 -0.14216180 0.00016459 384.62673223 0.00048891 -0.00224640 0.99999736 -31.11908119 Axis -0.00121786 0.00091134 -0.99999884 Axis point 180.12091039 180.62815995 0.00000000 Rotation angle (degrees) 98.17301470 Shift along axis 31.43681665 > fitmap #24 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.009696, steps = 284 shifted from previous position = 7.23 rotated from previous position = 15.8 degrees atoms outside contour = 1683, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.74511047 0.66627611 0.02977453 184.39464653 -0.66577636 -0.74570489 0.02580784 428.69480834 0.03939816 -0.00059348 0.99922342 -60.41169213 Axis -0.01981562 -0.00722306 -0.99977756 Axis point 174.68050316 179.17355950 0.00000000 Rotation angle (degrees) 138.22751284 Shift along axis 53.64787269 > view matrix models > #24,-0.6941,0.71984,-0.0080316,176.46,-0.71984,-0.69413,-0.0028391,435.73,-0.0076187,0.0038109,0.99996,-53.779 > ui mousemode right ""translate selected models"" > view matrix models > #24,-0.6941,0.71984,-0.0080316,175.95,-0.71984,-0.69413,-0.0028391,435.69,-0.0076187,0.0038109,0.99996,-59.294 > fitmap #24 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01512, steps = 56 shifted from previous position = 0.856 rotated from previous position = 3.01 degrees atoms outside contour = 1417, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65619907 0.75458425 0.00232109 161.86554090 -0.75458613 -0.65620100 0.00009757 435.00235504 0.00159673 -0.00168744 0.99999730 -59.55655411 Axis -0.00118277 0.00047998 -0.99999919 Axis point 180.05778136 180.59683287 0.00000000 Rotation angle (degrees) 131.01080821 Shift along axis 59.57384653 > view matrix models > #24,-0.6562,0.75458,0.0023211,164.45,-0.75459,-0.6562,9.7566e-05,431.75,0.0015967,-0.0016874,1,-54.315 > view matrix models > #24,-0.6562,0.75458,0.0023211,163.14,-0.75459,-0.6562,9.7566e-05,435.42,0.0015967,-0.0016874,1,-59.591 > fitmap #24 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01512, steps = 48 shifted from previous position = 1.33 rotated from previous position = 0.16 degrees atoms outside contour = 1410, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65423983 0.75628565 0.00150570 161.48783907 -0.75628690 -0.65423992 -0.00050312 435.09898571 0.00060458 -0.00146790 0.99999874 -59.42573024 Axis -0.00063784 0.00059575 -0.99999962 Axis point 180.21418966 180.60854145 0.00000000 Rotation angle (degrees) 130.86208586 Shift along axis 59.58191477 > select clear > fitmap #24 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01512, steps = 36 shifted from previous position = 0.00402 rotated from previous position = 0.0261 degrees atoms outside contour = 1413, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65450283 0.75605747 0.00177723 161.50503784 -0.75605906 -0.65450329 -0.00038929 435.07979840 0.00086888 -0.00159848 0.99999835 -59.44407111 Axis -0.00079967 0.00060071 -0.99999950 Axis point 180.17736710 180.60966239 0.00000000 Rotation angle (degrees) 130.88204248 Shift along axis 59.57624915 > combine #23 #25 > color #25 #6000cbff > select add #25 2086 atoms, 2098 bonds, 1 pseudobond, 273 residues, 2 models selected > view matrix models > #25,-0.14216,0.98984,0.0022931,31.018,-0.98984,-0.14216,0.00016459,383,0.00048891,-0.0022464,1,-34.483 > view matrix models > #25,-0.14216,0.98984,0.0022931,29.516,-0.98984,-0.14216,0.00016459,386.78,0.00048891,-0.0022464,1,-10.405 > view matrix models > #25,-0.14216,0.98984,0.0022931,35.605,-0.98984,-0.14216,0.00016459,390.49,0.00048891,-0.0022464,1,-11.887 > fitmap #25 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.006252, steps = 168 shifted from previous position = 4.09 rotated from previous position = 3.57 degrees atoms outside contour = 1879, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.19807400 0.98017507 -0.00484908 51.27967405 -0.97987378 -0.19813334 -0.02430144 401.39819748 -0.02478043 -0.00006200 0.99969292 -8.60662837 Axis 0.01236517 0.01016750 -0.99987185 Axis point 189.72003980 179.74716109 0.00000000 Rotation angle (degrees) 101.43506389 Shift along axis 13.32082319 > view matrix models > #25,-0.19807,0.98018,-0.0048491,51.973,-0.97987,-0.19813,-0.024301,400.34,-0.02478,-6.1996e-05,0.99969,-0.0019831 > fitmap #25 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01538, steps = 576 shifted from previous position = 9.94 rotated from previous position = 29.7 degrees atoms outside contour = 1415, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65713960 0.75376743 0.00148529 162.52255446 -0.75376884 -0.65713905 -0.00089866 435.27146784 0.00029867 -0.00171011 0.99999849 -7.68736589 Axis -0.00053826 0.00078713 -0.99999955 Axis point 180.25598777 180.66912945 0.00000000 Rotation angle (degrees) 131.08212199 Shift along axis 7.94249717 > fitmap #25 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01539, steps = 36 shifted from previous position = 0.0182 rotated from previous position = 0.147 degrees atoms outside contour = 1413, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65897332 0.75216327 0.00213916 162.90542091 -0.75216553 -0.65897408 -0.00042719 435.18747632 0.00108834 -0.00189051 0.99999762 -7.79995849 Axis -0.00097274 0.00069853 -0.99999928 Axis point 180.11044523 180.65927726 0.00000000 Rotation angle (degrees) 131.22173875 Shift along axis 7.94548106 > select subtract #25 Nothing selected > fitmap #1 inMap #6 Fit molecule copy of Rhom_Model_Trimmed.pdb (#1) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.0154, steps = 40 shifted from previous position = 0.0136 rotated from previous position = 0.0126 degrees atoms outside contour = 1391, contour level = 0.023968 Position of copy of Rhom_Model_Trimmed.pdb (#1) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.84103335 0.54098236 0.00099363 -69.10116854 -0.54098326 0.84103143 0.00180284 125.78058227 0.00013963 -0.00205379 0.99999788 -26.40532164 Axis -0.00356445 0.00078930 -0.99999334 Axis point 179.48397901 180.29753030 0.00000000 Rotation angle (degrees) 32.75081362 Shift along axis 26.75073115 > select add #2 4172 atoms, 4196 bonds, 2 pseudobonds, 546 residues, 2 models selected > select subtract #2 Nothing selected > select add #3 6258 atoms, 6294 bonds, 3 pseudobonds, 819 residues, 2 models selected > select subtract #3 Nothing selected > fitmap #2 inMap #6 Fit molecule combination (#2) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 4172 atoms average map value = 0.0152, steps = 40 shifted from previous position = 0.00709 rotated from previous position = 0.0482 degrees atoms outside contour = 2882, contour level = 0.023968 Position of combination (#2) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.99999862 0.00003204 -0.00166022 0.52627021 -0.00002985 0.99999912 0.00132259 -0.44175560 0.00166026 -0.00132254 0.99999775 -50.21532302 Axis -0.62301104 -0.78207719 -0.01457791 Axis point 30239.67506594 0.00000000 573.18936827 Rotation angle (degrees) 0.12163086 Shift along axis 0.74964919 > fitmap #3 inMap #6 Fit molecule combination (#3) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 6258 atoms average map value = 0.01535, steps = 40 shifted from previous position = 0.0136 rotated from previous position = 0.0207 degrees atoms outside contour = 4208, contour level = 0.023968 Position of combination (#3) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.84172143 -0.53991002 -0.00148768 126.48019137 0.53991195 0.84171988 0.00165251 -69.22746988 0.00036000 -0.00219417 0.99999753 -21.70049777 Axis -0.00356230 -0.00171109 0.99999219 Axis point 181.33851729 180.95552944 0.00000000 Rotation angle (degrees) 32.67786629 Shift along axis -22.03243458 > select add #4 2 models selected > select subtract #4 Nothing selected > select add #5 2086 atoms, 2098 bonds, 1 pseudobond, 273 residues, 2 models selected > select subtract #5 Nothing selected > fitmap #5 inMap #6 Fit molecule Rhom_Model_Trimmed.pdb (#5) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.0153, steps = 40 shifted from previous position = 0.0223 rotated from previous position = 0.00798 degrees atoms outside contour = 1414, contour level = 0.023968 Position of Rhom_Model_Trimmed.pdb (#5) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.99999197 0.00398259 -0.00044920 -0.45751742 -0.00398170 0.99999012 0.00197720 0.16247208 0.00045707 -0.00197540 0.99999794 1.71149665 Axis -0.44226160 -0.10140280 -0.89113531 Axis point 6.04202678 263.61988561 0.00000000 Rotation angle (degrees) 0.25603385 Shift along axis -1.33930783 > select add #6 2 models selected > select subtract #6 Nothing selected > fitmap #8 inMap #6 Fit molecule copy of Rhom_Model_Trimmed.pdb (#8) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01505, steps = 28 shifted from previous position = 0.017 rotated from previous position = 0.00902 degrees atoms outside contour = 1436, contour level = 0.023968 Position of copy of Rhom_Model_Trimmed.pdb (#8) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.83915204 -0.54389400 -0.00178156 127.72048235 0.54389608 0.83915199 0.00099395 -69.37353706 0.00095439 -0.00180306 0.99999792 -73.52381512 Axis -0.00257126 -0.00251513 0.99999353 Axis point 181.37040904 180.84034524 0.00000000 Rotation angle (degrees) 32.94942693 Shift along axis -73.67725868 > fitmap #9 inMap #6 Fit molecule copy of copy of Rhom_Model_Trimmed.pdb (#9) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01453, steps = 36 shifted from previous position = 0.0114 rotated from previous position = 0.0187 degrees atoms outside contour = 1498, contour level = 0.023968 Position of copy of copy of Rhom_Model_Trimmed.pdb (#9) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.41413910 -0.91020970 -0.00266769 270.92657813 0.91021120 0.41414297 -0.00108711 -58.18555016 0.00209430 -0.00197794 0.99999585 -97.17358447 Axis -0.00048935 -0.00261586 0.99999646 Axis point 180.83662047 181.20432112 0.00000000 Rotation angle (degrees) 65.53489573 Shift along axis -97.15361418 > fitmap #10 inMap #6 Fit molecule copy of copy of Rhom_Model_Trimmed.pdb (#10) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01551, steps = 28 shifted from previous position = 0.00622 rotated from previous position = 0.035 degrees atoms outside contour = 1383, contour level = 0.023968 Position of copy of copy of Rhom_Model_Trimmed.pdb (#10) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.13983960 -0.99017326 -0.00134170 384.80401362 0.99017347 -0.13983776 -0.00137490 27.49001070 0.00117377 -0.00152078 0.99999815 -17.26195379 Axis -0.00007366 -0.00127022 0.99999919 Axis point 180.47068802 180.87248773 0.00000000 Rotation angle (degrees) 98.03856492 Shift along axis -17.32520360 > fitmap #11 inMap #6 Fit molecule copy of copy of Rhom_Model_Trimmed.pdb (#11) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.0153, steps = 40 shifted from previous position = 0.00833 rotated from previous position = 0.0519 degrees atoms outside contour = 1418, contour level = 0.023968 Position of copy of copy of Rhom_Model_Trimmed.pdb (#11) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.41742880 -0.90870795 -0.00175169 269.81930859 0.90870684 0.41743152 -0.00167635 -58.37229426 0.00225453 -0.00089201 0.99999706 -45.68706120 Axis 0.00043157 -0.00220434 0.99999748 Axis point 180.52305269 181.21486497 0.00000000 Rotation angle (degrees) 65.32764408 Shift along axis -45.44182786 > fitmap #12 inMap #6 Fit molecule copy of copy of copy of Rhom_Model_Trimmed.pdb (#12) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.0152, steps = 28 shifted from previous position = 0.0183 rotated from previous position = 0.038 degrees atoms outside contour = 1416, contour level = 0.023968 Position of copy of copy of copy of Rhom_Model_Trimmed.pdb (#12) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.14420560 -0.98954703 -0.00119417 385.46259200 0.98954694 -0.14420383 -0.00145528 28.43552833 0.00126786 -0.00139154 0.99999823 -68.95440132 Axis 0.00003220 -0.00124402 0.99999923 Axis point 180.47349817 180.85651389 0.00000000 Rotation angle (degrees) 98.29128017 Shift along axis -68.97730905 > fitmap #13 inMap #6 Fit molecule copy of copy of copy of Rhom_Model_Trimmed.pdb (#13) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01543, steps = 28 shifted from previous position = 0.0113 rotated from previous position = 0.00522 degrees atoms outside contour = 1426, contour level = 0.023968 Position of copy of copy of copy of Rhom_Model_Trimmed.pdb (#13) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65377827 -0.75668616 0.00015289 434.98650437 0.75668355 -0.65377653 -0.00250094 162.70234225 0.00199238 -0.00151937 0.99999686 -40.87032994 Axis 0.00064860 -0.00121549 0.99999905 Axis point 180.29563300 180.84638586 0.00000000 Rotation angle (degrees) 130.82712958 Shift along axis -40.78592358 > fitmap #14 inMap #6 Fit molecule copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#14) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01479, steps = 40 shifted from previous position = 0.00803 rotated from previous position = 0.0181 degrees atoms outside contour = 1465, contour level = 0.023968 Position of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#14) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65470287 -0.75588630 0.00022386 435.00375875 0.75588192 -0.65470003 -0.00322228 163.32252658 0.00258224 -0.00194042 0.99999478 -92.56773102 Axis 0.00084792 -0.00156001 0.99999842 Axis point 180.27032934 180.96414755 0.00000000 Rotation angle (degrees) 130.89721416 Shift along axis -92.45352270 > fitmap #15 inMap #6 Fit molecule copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#15) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01541, steps = 28 shifted from previous position = 0.00169 rotated from previous position = 0.0556 degrees atoms outside contour = 1411, contour level = 0.023968 Position of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#15) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.95819392 -0.28611740 0.00111108 404.65508980 0.28611551 -0.95819380 -0.00159970 302.34297634 0.00152233 -0.00121492 0.99999810 -12.64928371 Axis 0.00067241 -0.00071868 0.99999952 Axis point 180.24441520 180.73014442 0.00000000 Rotation angle (degrees) 163.37439554 Shift along axis -12.59447051 > fitmap #16 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#16) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.0152, steps = 24 shifted from previous position = 0.00202 rotated from previous position = 0.0708 degrees atoms outside contour = 1420, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#16) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.95955628 -0.28151231 0.00159846 403.94390438 0.28151002 -0.95955709 -0.00151592 303.40558781 0.00196057 -0.00100462 0.99999757 -64.40554858 Axis 0.00090812 -0.00064314 0.99999938 Axis point 180.21042969 180.70171087 0.00000000 Rotation angle (degrees) 163.64957295 Shift along axis -64.23381110 > fitmap #17 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#17) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01537, steps = 28 shifted from previous position = 0.0209 rotated from previous position = 0.0247 degrees atoms outside contour = 1421, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#17) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.95986796 0.28044688 0.00174608 302.52418206 -0.28044920 -0.95986803 -0.00126688 404.68907168 0.00132071 -0.00170572 0.99999767 -36.01547225 Axis -0.00078240 0.00075837 -0.99999941 Axis point 180.22880599 180.68394135 0.00000000 Rotation angle (degrees) 163.71304315 Shift along axis 36.08565975 > fitmap #18 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#18) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01498, steps = 28 shifted from previous position = 0.00864 rotated from previous position = 0.0164 degrees atoms outside contour = 1453, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#18) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.95957585 0.28144002 0.00238970 302.00023716 -0.28144333 -0.95957712 -0.00118285 404.85440494 0.00196020 -0.00180760 0.99999645 -87.79431407 Axis -0.00110991 0.00076304 -0.99999909 Axis point 180.11740640 180.69949255 0.00000000 Rotation angle (degrees) 163.65371753 Shift along axis 87.76796138 > fitmap #19 inMap #6 Fit molecule copy of copy of Rhom_Model_Trimmed.pdb (#19) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01493, steps = 28 shifted from previous position = 0.0115 rotated from previous position = 0.0419 degrees atoms outside contour = 1444, contour level = 0.023968 Position of copy of copy of Rhom_Model_Trimmed.pdb (#19) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.84254165 0.53863119 0.00004860 -68.71619613 -0.53863008 0.84253972 0.00211011 124.94312568 0.00109562 -0.00180403 0.99999777 -78.26153068 Axis -0.00363339 -0.00097193 -0.99999293 Axis point 179.61617395 179.55410829 0.00000000 Rotation angle (degrees) 32.59072804 Shift along axis 78.38921439 > fitmap #20 inMap #6 Fit molecule copy of copy of copy of Rhom_Model_Trimmed.pdb (#20) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01534, steps = 28 shifted from previous position = 0.0159 rotated from previous position = 0.0654 degrees atoms outside contour = 1412, contour level = 0.023968 Position of copy of copy of copy of Rhom_Model_Trimmed.pdb (#20) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.41160538 0.91136090 0.00152611 -58.64798270 -0.91136177 0.41160304 0.00163385 270.10105124 0.00086087 -0.00206334 0.99999750 -3.03033913 Axis -0.00202838 0.00036497 -0.99999788 Axis point 179.85724021 180.46465256 0.00000000 Rotation angle (degrees) 65.69443003 Shift along axis 3.24787095 > fitmap #21 inMap #6 Fit molecule copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#21) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01522, steps = 24 shifted from previous position = 0.00152 rotated from previous position = 0.0182 degrees atoms outside contour = 1408, contour level = 0.023968 Position of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#21) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.41365576 0.91043332 0.00028374 -58.60331930 -0.91043041 0.41365360 0.00267859 269.23227676 0.00232130 -0.00136634 0.99999637 -55.02009813 Axis -0.00222142 -0.00111900 -0.99999691 Axis point 179.82932268 180.04982971 0.00000000 Rotation angle (degrees) 65.56549039 Shift along axis 54.84883867 > fitmap #21 inMap #6 Fit molecule copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#21) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01522, steps = 28 shifted from previous position = 0.0177 rotated from previous position = 0.0393 degrees atoms outside contour = 1407, contour level = 0.023968 Position of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#21) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation 0.41423889 0.91016813 0.00034710 -58.66743246 -0.91016582 0.41423691 0.00244018 269.14666199 0.00207719 -0.00132673 0.99999696 -55.00380759 Axis -0.00206935 -0.00095042 -0.99999741 Axis point 179.86655133 180.09059491 0.00000000 Rotation angle (degrees) 65.52876294 Shift along axis 54.86926551 > fitmap #22 inMap #6 Fit molecule copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#22) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.0149, steps = 36 shifted from previous position = 0.00498 rotated from previous position = 0.0426 degrees atoms outside contour = 1452, contour level = 0.023968 Position of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#22) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.14031145 0.99010493 0.00221808 26.42117415 -0.99010655 -0.14031393 0.00100864 384.10203892 0.00130989 -0.00205462 0.99999703 -82.94561679 Axis -0.00154693 0.00045864 -0.99999870 Axis point 180.01164114 180.50575691 0.00000000 Rotation angle (degrees) 98.06602657 Shift along axis 83.08080032 > fitmap #23 inMap #6 Fit molecule copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01533, steps = 40 shifted from previous position = 0.0144 rotated from previous position = 0.0298 degrees atoms outside contour = 1404, contour level = 0.023968 Position of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.14267480 0.98976690 0.00232231 26.98430751 -0.98976949 -0.14267561 0.00018775 384.67375794 0.00051717 -0.00227176 0.99999729 -31.12496109 Axis -0.00124247 0.00091190 -0.99999881 Axis point 180.09860100 180.61905247 0.00000000 Rotation angle (degrees) 98.20275706 Shift along axis 31.44218063 > fitmap #23 inMap #6 Fit molecule copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01533, steps = 40 shifted from previous position = 0.015 rotated from previous position = 0.011 degrees atoms outside contour = 1407, contour level = 0.023968 Position of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#23) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.14249516 0.98979264 0.00237762 26.94258213 -0.98979537 -0.14249594 0.00016303 384.66380948 0.00050016 -0.00233013 0.99999716 -31.10078363 Axis -0.00125943 0.00094841 -0.99999876 Axis point 180.10373553 180.62922421 0.00000000 Rotation angle (degrees) 98.19236090 Shift along axis 31.43163084 > fitmap #24 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01512, steps = 24 shifted from previous position = 0.00214 rotated from previous position = 0.0688 degrees atoms outside contour = 1415, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#24) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65536139 0.75531260 0.00207820 161.68803112 -0.75531443 -0.65536256 -0.00014930 435.03834750 0.00124921 -0.00166754 0.99999783 -59.49277285 Axis -0.00100504 0.00054877 -0.99999934 Axis point 180.11681860 180.60141746 0.00000000 Rotation angle (degrees) 130.94718500 Shift along axis 59.56896879 > fitmap #25 inMap #6 Fit molecule copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) to map Rhom_Flagella_Map_2RingMasked.mrc (#6) using 2086 atoms average map value = 0.01539, steps = 40 shifted from previous position = 0.00313 rotated from previous position = 0.0105 degrees atoms outside contour = 1410, contour level = 0.023968 Position of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb (#25) relative to Rhom_Flagella_Map_2RingMasked.mrc (#6) coordinates: Matrix rotation and translation -0.65895236 0.75218212 0.00195902 162.94011377 -0.75218405 -0.65895293 -0.00043265 435.18790108 0.00096547 -0.00175865 0.99999799 -7.80153019 Axis -0.00088143 0.00066045 -0.99999939 Axis point 180.13129350 180.65055489 0.00000000 Rotation angle (degrees) 131.22012104 Shift along axis 7.94532386 > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > combine #1-3,5,8-25 name 2Ring_Trimmed Remapping chain ID 'A' in combination #2 to 'C' Remapping chain ID 'A' in combination #3 to 'D' Remapping chain ID 'B' in combination #3 to 'E' Remapping chain ID 'C' in combination #3 to 'F' Remapping chain ID 'A' in Rhom_Model_Trimmed.pdb #5 to 'G' Remapping chain ID 'A' in copy of Rhom_Model_Trimmed.pdb #8 to 'H' Remapping chain ID 'A' in copy of copy of Rhom_Model_Trimmed.pdb #9 to 'I' Remapping chain ID 'A' in copy of copy of Rhom_Model_Trimmed.pdb #10 to 'J' Remapping chain ID 'A' in copy of copy of Rhom_Model_Trimmed.pdb #11 to 'K' Remapping chain ID 'A' in copy of copy of copy of Rhom_Model_Trimmed.pdb #12 to 'L' Remapping chain ID 'A' in copy of copy of copy of Rhom_Model_Trimmed.pdb #13 to 'M' Remapping chain ID 'A' in copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #14 to 'N' Remapping chain ID 'A' in copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #15 to 'O' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #16 to 'P' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #17 to 'Q' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #18 to 'R' Remapping chain ID 'A' in copy of copy of Rhom_Model_Trimmed.pdb #19 to 'S' Remapping chain ID 'A' in copy of copy of copy of Rhom_Model_Trimmed.pdb #20 to 'T' Remapping chain ID 'A' in copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #21 to 'U' Remapping chain ID 'A' in copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #22 to 'V' Remapping chain ID 'A' in copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #23 to 'W' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #24 to 'X' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #25 to 'Y' > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > hide #!26 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!6 models > hide #!5 models > show #!6 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!26 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!26 models > show #!26 models > show #!14 models > hide #!14 models > hide #!26 models > show #!6 models > show #!20 models > show #!21 models > show #!22 models > show #!23 models > show #!25 models > show #!24 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > hide #!19 models > show #!19 models > hide #!20 models > hide #!19 models > show #!19 models > hide #!19 models > show #!19 models > hide #!19 models > hide #!21 models > hide #!23 models > hide #!14 models > hide #!22 models > hide #!6 models > show #!6 models > combine #15-18,24-25 name 6Flagellin_Representative Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #16 to 'B' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #17 to 'C' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #18 to 'D' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #24 to 'E' Remapping chain ID 'A' in copy of copy of copy of copy of copy of copy of Rhom_Model_Trimmed.pdb #25 to 'F' > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > hide #!24 models > hide #!25 models > hide #!27 models > show #!27 models > hide #!6 models > show #!6 models > hide #!6 models > molmap #27 radius 3 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution 3 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution 5 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution 2 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution 2 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution5 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution 5 Missing or invalid ""resolution"" argument: Expected a number > molmap #27 resolution 2 Missing or invalid ""resolution"" argument: Expected a number > hide #!27 models > show #!27 models > select add #27 12516 atoms, 12588 bonds, 6 pseudobonds, 1638 residues, 2 models selected > select subtract #27 Nothing selected > molmap #27 resolution 5 Missing or invalid ""resolution"" argument: Expected a number > save ""/Users/mbell/sshfs/c0140_4_MotionCor2/Chimera projects/Rhom > fitting/Rhom_2Ring_Trimmed.pdb"" models #26 > save ""/Users/mbell/sshfs/c0140_4_MotionCor2/Chimera projects/Rhom > fitting/Rhom_MaskMaking/6_Flagellin_Selection_ForMask.pdb"" models #27 > save ""/Users/mbell/sshfs/c0140_4_MotionCor2/Chimera projects/Rhom > fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs"" ——— End of log from Wed Aug 2 16:13:43 2023 ——— opened ChimeraX session > hide #!27 models > show #!27 models > save > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs ——— End of log from Thu Aug 10 13:03:26 2023 ——— opened ChimeraX session > show #!26 models > hide #!27 models > show #!27 models > hide #!27 models > show #!1 models > hide #!1 models > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > show #7 models > hide #7 models > lighting soft > lighting full > lighting soft > lighting full > set bgColor white > hide #!6 models > show #!6 models > color #6 #e1ffe478 models > color #6 #fffefa78 models > color #6 #b3b3b078 models > color #6 #a7adb378 models > color #6 #a9b3af78 models > color #6 #f0fff978 models > color #6 #7af4ff78 models > save /Users/mbell/Desktop/image1.png supersample 3 > ui tool show ""Side View"" > view > select add #26 52150 atoms, 52450 bonds, 25 pseudobonds, 6825 residues, 2 models selected > view orient > ui tool show ""Side View"" > view sel > ui tool show ""Side View"" > select clear > save /Users/mbell/Desktop/image2.png supersample 3 > open > /Users/mbell/sshfs/R_inulinivorans/InitialModel/job010/initial_model.mrc Opened initial_model.mrc as #28, grid size 384,384,384, pixel 0.94, shown at level 0.0168, step 2, values float32 > close #28 > save > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs > hide #!26 models > show #!26 models > show #!27 models > hide #!26 models > show #!26 models > close session > open > /Users/mbell/sshfs/R_inulinivorans/InitialModel/job010/initial_model.mrc > format mrc Opened initial_model.mrc as #1, grid size 384,384,384, pixel 0.94, shown at level 0.0168, step 2, values float32 > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs > format session No such file/path: /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs > format session No such file/path: /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_fitting/Rhom_MaskMaking/RH_TrimmedModelFitting_and_MaskSelection.cxs > format session Opened RHom Model.pdb map 3 as #4, grid size 51,73,158, pixel 1, shown at level 0.115, step 1, values float32 Opened Rhom_Flagella_Map_2RingMasked.mrc as #6, grid size 200,201,275, pixel 0.94,0.94,0.94, shown at level 0.024, step 1, values float32 opened ChimeraX session > hide #!27 models > show #!26 models > open > /Users/mbell/sshfs/c0140_4_MotionCor2/Chimera_projects/Rhom_ISOLDE/Current.cxs > format session Opened RHom Model.pdb map 3 as #4, grid size 51,73,158, pixel 1, shown at level 0.115, step 1, values float32 Opened Rhom_Flagella_Map_2RingMasked.mrc as #6, grid size 200,201,275, pixel 0.94,0.94,0.94, shown at level 0.024, step 1, values float32 opened ChimeraX session > set bgColor black > close session > open > /Users/mbell/sshfs/R_inulinivorans/InitialModel/job011/initial_model.mrc Opened initial_model.mrc as #1, grid size 384,384,384, pixel 0.94, shown at level 0.016, step 2, values float32 > open > /Users/mbell/sshfs/R_inulinivorans/InitialModel/job010/initial_model.mrc Opened initial_model.mrc as #2, grid size 384,384,384, pixel 0.94, shown at level 0.0168, step 2, values float32 Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-20.6.1 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0) OS Loader Version: 577~170 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 5 days, 22 hours, 11 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2415: 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: 7MT0197I2H9S Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX