id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18632 mshMIGPerform crash in NSAccessiblity native Mac APIs chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000038bed3000 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fdb260c0 (most recent call first): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 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, 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""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""b5dac49819004f09fc6a7b2f82a4dadb99eae123"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs Opened cryosparc_P5_J157_008_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.968, shown at level 0.194, step 1, values float32 Opened emd_31442 (1) copy.map as #2, grid size 272,272,272, pixel 0.86, shown at level 0.38, step 2, values float32 Log from Tue Aug 26 15:42:57 2025 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/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/cryosparc_P5_J157_008_volume_map_sharp.mrc Opened cryosparc_P5_J157_008_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.968, shown at level 0.0922, step 1, values float32 > volume #1 level 0.1939 > surface dust #1 size 9.68 > open ""/Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/emd_31442 (1) > copy.map"" Opened emd_31442 (1) copy.map as #2, grid size 272,272,272, pixel 0.86, shown at level 0.201, step 2, values float32 > open /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/7f3x.pdb 7f3x.pdb title: Lysophospholipid acyltransferase LPCAT3 In complex with lysophosphatidylcholine [more info...] Chain information for 7f3x.pdb #3 --- Chain | Description A B | LPCAT3 Non-standard residues in 7f3x.pdb #3 --- LAP — [2-((1-oxododecanoxy-(2-hydroxy-3-propanyl))-phosphonate- oxy)-ethyl]-trimethylammonium (L-ALFA-lysophosphatidylcholine, lauroyl) > open > /Users/s230038/Projects_JieL/mboat1:2/Structure/Prediction/M2/AF-Q6ZWT7-F1-model_v4.pdb AF-Q6ZWT7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for lysophospholipid acyltransferase 2 (Q6ZWT7) [more info...] Chain information for AF-Q6ZWT7-F1-model_v4.pdb #4 --- Chain | Description | UniProt A | lysophospholipid acyltransferase 2 | MBOA2_HUMAN 1-520 > open > /Users/s230038/Projects_JieL/mboat1:2/Structure/Prediction/M2/AF-Q6ZWT7-F1-model_v4.pdb AF-Q6ZWT7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for lysophospholipid acyltransferase 2 (Q6ZWT7) [more info...] Chain information for AF-Q6ZWT7-F1-model_v4.pdb #5 --- Chain | Description | UniProt A | lysophospholipid acyltransferase 2 | MBOA2_HUMAN 1-520 > volume #2 level 0.3799 > vop zflip # 1 > volume zflip # 1 Expected a density maps specifier or a keyword > volume #1 flipNormals z Invalid ""flipNormals"" argument: Expected true or false (or 1 or 0) > turn z 180 models #1 > ui mousemode right ""translate selected models"" > select add #1 2 models selected > view matrix models > #1,-0.6818,-0.3553,0.63947,131.33,-0.3553,-0.60329,-0.71401,302.7,0.63947,-0.71401,0.28509,115.7 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.36783,-0.67338,0.64129,40.467,-0.82616,0.079882,0.55774,115.73,-0.4268,-0.73496,-0.52694,353 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.36783,-0.67338,0.64129,58.135,-0.82616,0.079882,0.55774,141.15,-0.4268,-0.73496,-0.52694,331.91 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.29555,-0.87473,0.38405,197.77,-0.93605,0.34551,0.066612,183.9,-0.19096,-0.3398,-0.92091,303.5 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.29555,-0.87473,0.38405,176.93,-0.93605,0.34551,0.066612,149.88,-0.19096,-0.3398,-0.92091,255.4 > volume #2 color #ffffb252 > view matrix models > #1,-0.29555,-0.87473,0.38405,182.02,-0.93605,0.34551,0.066612,125.72,-0.19096,-0.3398,-0.92091,240.07 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.29555,-0.87473,0.38405,212.25,-0.93605,0.34551,0.066612,187.14,-0.19096,-0.3398,-0.92091,286.3 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.38122,-0.87231,0.30618,232.4,-0.9071,0.41686,0.058243,175.77,-0.17844,-0.25553,-0.95019,278.01 > view matrix models > #1,-0.66657,-0.72243,-0.18379,311.09,-0.68219,0.69057,-0.24026,151.7,0.30049,-0.034774,-0.95315,191.69 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.66657,-0.72243,-0.18379,301.75,-0.68219,0.69057,-0.24026,146.21,0.30049,-0.034774,-0.95315,196.64 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1) copy.map using 35907 points correlation = 0.3988, correlation about mean = 0.02134, overlap = 1727 steps = 100, shift = 3.29, angle = 2.32 degrees Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to emd_31442 (1) copy.map (#2) coordinates: Matrix rotation and translation -0.68712657 -0.69650141 -0.20674354 304.49818345 -0.65813608 0.71724043 -0.22896086 135.33178890 0.30775642 -0.02125974 -0.95122764 193.06643960 Axis 0.37345092 -0.92508159 0.06898166 Axis point 164.77416164 0.00000000 124.87000349 Rotation angle (degrees) 163.85414125 Shift along axis 1.84022591 > view matrix models > #1,-0.68713,-0.6965,-0.20674,305.73,-0.65814,0.71724,-0.22896,136.66,0.30776,-0.02126,-0.95123,192.88 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.67249,-0.57949,-0.46038,321.47,-0.71598,0.66691,0.20639,95.065,0.18743,0.46842,-0.8634,136.02 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.67249,-0.57949,-0.46038,317.24,-0.71598,0.66691,0.20639,99.239,0.18743,0.46842,-0.8634,136.68 > fitmap #1 inMap #2 Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1) copy.map using 35907 points correlation = 0.4155, correlation about mean = 0.04248, overlap = 1789 steps = 100, shift = 2.12, angle = 11.6 degrees Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to emd_31442 (1) copy.map (#2) coordinates: Matrix rotation and translation -0.70239863 -0.64990492 -0.29027533 308.10200003 -0.70241308 0.69884856 0.13500587 103.97346773 0.11511755 0.29872110 -0.94737196 175.64973182 Axis 0.37178907 -0.92062691 -0.11924339 Axis point 164.42846237 0.00000000 99.78879984 Rotation angle (degrees) 167.28085305 Shift along axis -2.11688376 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.65447,-0.71606,-0.24275,304.36,-0.75439,0.6399,0.14636,116.28,0.050531,0.27892,-0.95898,187.57 > view matrix models > #1,-0.52355,-0.82963,-0.19394,296.04,-0.84821,0.48609,0.21037,138.88,-0.080254,0.27465,-0.95819,204.21 > fitmap #1 inMap #2 Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1) copy.map using 35907 points correlation = 0.4072, correlation about mean = 0.07536, overlap = 1800 steps = 284, shift = 6.44, angle = 10.8 degrees Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to emd_31442 (1) copy.map (#2) coordinates: Matrix rotation and translation -0.41639192 -0.90486798 -0.08849704 283.42770145 -0.90679873 0.40627898 0.11248769 165.43159725 -0.06583199 0.12708793 -0.98970439 221.42313198 Axis 0.54015765 -0.83852688 -0.07143096 Axis point 194.10544743 0.00000000 104.81052587 Rotation angle (degrees) 179.22563553 Shift along axis -1.43966854 > hide #4 models > hide #5 models > save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs > hide #3 models > hide #!2 models > show #!2 models > hide #!1 models > show #3 models > show #!1 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.62852,-0.76641,-0.1326,298.13,-0.77614,0.6069,0.1711,116.98,-0.050658,0.21045,-0.97629,207.52 > view matrix models > #1,-0.64368,0.50169,-0.57792,199.15,0.23414,-0.58985,-0.77283,259.33,-0.7286,-0.63276,0.26221,239.53 > view matrix models > #1,-0.45788,0.78674,-0.41399,120.1,0.84628,0.52836,0.068102,-61.294,0.27232,-0.31917,-0.90773,224.46 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.45788,0.78674,-0.41399,137.47,0.84628,0.52836,0.068102,-51.497,0.27232,-0.31917,-0.90773,225.94 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.37089,0.37043,-0.8516,233.55,0.77388,-0.38363,-0.50392,142.73,-0.51337,-0.84594,-0.14439,292.12 > view matrix models > #1,-0.75504,0.48144,-0.44512,216.04,0.4895,-0.037777,-0.87118,181.52,-0.43624,-0.87566,-0.20714,294.17 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.75504,0.48144,-0.44512,212.61,0.4895,-0.037777,-0.87118,176.02,-0.43624,-0.87566,-0.20714,303.94 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.29164,0.64518,-0.70618,167.89,0.9306,0.36212,-0.053478,-31.484,0.22122,-0.67277,-0.70601,260.37 > view matrix models > #1,-0.29894,0.4985,-0.81372,200.55,0.7869,-0.35361,-0.50571,132.13,-0.53983,-0.79149,-0.28657,316.38 > view matrix models > #1,0.57958,0.65328,-0.48714,31.265,-0.73956,0.17061,-0.6511,274.68,-0.34224,0.73764,0.58203,-7.2889 > view matrix models > #1,0.56591,0.61347,-0.55082,45.938,-0.75915,0.12709,-0.63839,280.89,-0.32163,0.77943,0.53763,-9.4118 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #1,0.56591,0.61347,-0.55082,25.765,-0.75915,0.12709,-0.63839,296.07,-0.32163,0.77943,0.53763,-5.6319 > fitmap #1 inMap #2 Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1) copy.map using 35907 points correlation = 0.4291, correlation about mean = 0.05808, overlap = 1413 steps = 80, shift = 1.66, angle = 3.98 degrees Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to emd_31442 (1) copy.map (#2) coordinates: Matrix rotation and translation 0.60314778 0.61485029 -0.50810619 17.09187444 -0.73936907 0.19198720 -0.64534817 286.90572149 -0.29924264 0.76491833 0.57039796 -10.25848893 Axis 0.71721375 -0.10622092 -0.68871007 Axis point 0.00000000 159.76350051 242.70653410 Rotation angle (degrees) 79.46905946 Shift along axis -11.15173722 > view matrix models > #1,0.60315,0.61485,-0.50811,19.64,-0.73937,0.19199,-0.64535,279.66,-0.29924,0.76492,0.5704,-15.967 > view matrix models > #1,0.60315,0.61485,-0.50811,12.419,-0.73937,0.19199,-0.64535,291.15,-0.29924,0.76492,0.5704,-9.9911 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.60315,0.61485,-0.50811,31.422,-0.73937,0.19199,-0.64535,255.82,-0.29924,0.76492,0.5704,-16.34 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.020597,0.24228,-0.96999,208.11,-0.7924,0.59557,0.13193,114.19,0.60966,0.7659,0.20425,-82.817 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.020597,0.24228,-0.96999,207.5,-0.7924,0.59557,0.13193,123.43,0.60966,0.7659,0.20425,-85.938 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.25815,0.13535,-0.95658,253.59,-0.28409,0.93573,0.20907,8.5555,0.92339,0.32573,-0.2031,-18.81 > view matrix models > #1,0.12323,-0.33895,-0.9327,262.08,-0.16763,0.91925,-0.35621,67.581,0.97812,0.20024,0.056458,-42.833 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.12323,-0.33895,-0.9327,256.39,-0.16763,0.91925,-0.35621,70.038,0.97812,0.20024,0.056458,-52.348 > view matrix models > #1,0.12323,-0.33895,-0.9327,237.51,-0.16763,0.91925,-0.35621,148.44,0.97812,0.20024,0.056458,-78.819 > view matrix models > #1,0.12323,-0.33895,-0.9327,232.4,-0.16763,0.91925,-0.35621,167.19,0.97812,0.20024,0.056458,-76.469 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.82535,-0.55581,0.099368,246.41,-0.55358,0.76196,-0.33611,231.96,0.1111,-0.33242,-0.93657,222.4 > volume #1 color #b2b2b29f > set bgColor white > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.91681,-0.38005,0.12257,233.04,-0.39382,0.80969,-0.4351,218.76,0.066111,-0.44717,-0.892,236.56 > view matrix models > #1,-0.94422,0.32386,0.059735,157.16,0.28889,0.72747,0.62236,10.764,0.1581,0.6049,-0.78045,80.724 > view matrix models > #1,-0.54076,0.81634,-0.20289,79.33,0.55171,0.52628,0.64703,0.011378,0.63497,0.23795,-0.73498,61.359 > view matrix models > #1,0.40711,0.58493,0.70151,-123.7,0.91239,-0.22472,-0.34211,173.33,-0.042468,0.77933,-0.62517,64.345 > view matrix models > #1,0.4719,0.88113,0.030238,-83.619,0.75438,-0.3858,-0.5311,236.74,-0.4563,0.27344,-0.84677,206.29 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.4719,0.88113,0.030238,-40.179,0.75438,-0.3858,-0.5311,135.64,-0.4563,0.27344,-0.84677,241.96 > view matrix models > #1,0.4719,0.88113,0.030238,-46.784,0.75438,-0.3858,-0.5311,138.31,-0.4563,0.27344,-0.84677,241.06 > fitmap #1 inMap #2 Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1) copy.map using 35907 points correlation = 0.4112, correlation about mean = 0.05985, overlap = 1821 steps = 112, shift = 2.99, angle = 11.8 degrees Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to emd_31442 (1) copy.map (#2) coordinates: Matrix rotation and translation 0.45951627 0.88101964 0.11246871 -56.63973154 0.84526238 -0.39491411 -0.35996445 104.14962316 -0.27272024 0.26047506 -0.92616218 231.47216333 Axis 0.84856924 0.52681928 -0.04890487 Axis point -0.00000000 43.85689839 125.98886915 Rotation angle (degrees) 158.55673239 Shift along axis -4.51482007 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.42804,0.90371,-0.0095249,-40.139,0.9034,-0.42755,0.032658,51.388,0.025441,-0.022584,-0.99942,238.86 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.42804,0.90371,-0.0095249,-36.614,0.9034,-0.42755,0.032658,47.54,0.025441,-0.022584,-0.99942,237.93 > view matrix models > #1,0.42804,0.90371,-0.0095249,-33.097,0.9034,-0.42755,0.032658,43.517,0.025441,-0.022584,-0.99942,240.7 > view matrix models > #1,0.42804,0.90371,-0.0095249,-31.397,0.9034,-0.42755,0.032658,42.985,0.025441,-0.022584,-0.99942,240.62 > view matrix models > #1,0.42804,0.90371,-0.0095249,-34.097,0.9034,-0.42755,0.032658,44.633,0.025441,-0.022584,-0.99942,239.94 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.47868,0.87783,0.016754,-40.485,0.85481,-0.4616,-0.23713,88.957,-0.20043,0.12783,-0.97133,245.74 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.47868,0.87783,0.016754,-43.136,0.85481,-0.4616,-0.23713,94.909,-0.20043,0.12783,-0.97133,240.71 > fitmap #1 inMap #2 Fit map cryosparc_P5_J157_008_volume_map_sharp.mrc in map emd_31442 (1) copy.map using 35907 points correlation = 0.4149, correlation about mean = 0.05652, overlap = 1773 steps = 136, shift = 3.68, angle = 9.25 degrees Position of cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) relative to emd_31442 (1) copy.map (#2) coordinates: Matrix rotation and translation 0.58959800 0.80561011 0.05802220 -49.50542004 0.80195294 -0.57534064 -0.16079383 106.05933050 -0.09615458 0.14133476 -0.98528106 227.44902909 Axis 0.89067485 0.45451301 -0.01078132 Axis point 0.00000000 54.75316690 118.47463635 Rotation angle (degrees) 170.23505584 Shift along axis 1.65991125 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.5896,0.80561,0.058022,-19.604,0.80195,-0.57534,-0.16079,209.01,-0.096155,0.14133,-0.98528,254.46 > view matrix models > #1,0.5896,0.80561,0.058022,-55.156,0.80195,-0.57534,-0.16079,245.22,-0.096155,0.14133,-0.98528,266.81 > show #4 models > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 4199 atoms average map value = 0, steps = 24 shifted from previous position = 0 rotated from previous position = 0 degrees atoms outside contour = 4199, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.58959799 0.80195292 -0.09615460 -138.48411228 0.80561009 -0.57534063 0.14133479 147.81220800 0.05802219 -0.16079379 -0.98528107 305.51472320 Axis -0.89067482 -0.45451307 0.01078134 Axis point 0.00000000 123.86024254 143.53521853 Rotation angle (degrees) 170.23505596 Shift along axis 59.45558924 > select subtract #1 Nothing selected > select add #4 4199 atoms, 4309 bonds, 520 residues, 1 model selected > view matrix models #4,1,0,0,34.907,0,1,0,293.13,0,0,1,-16.131 > view matrix models #4,1,0,0,148.49,0,1,0,239.83,0,0,1,30.839 > view matrix models #4,1,0,0,149.36,0,1,0,239.33,0,0,1,29.272 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.32401,-0.3039,-0.89591,147.14,0.6647,0.60074,-0.44417,235.4,0.67319,-0.73943,0.007356,22.221 > view matrix models > #4,0.68619,0.41396,0.59814,153.3,0.074378,0.77805,-0.62379,237.02,-0.72361,0.47253,0.5031,33.005 > view matrix models > #4,0.43981,0.89193,0.10501,156.75,0.044019,0.095373,-0.99447,231.43,-0.89701,0.442,0.0026844,32.457 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.43981,0.89193,0.10501,117.1,0.044019,0.095373,-0.99447,317.83,-0.89701,0.442,0.0026844,121.05 > select clear > select #4/A:480 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 126 atoms, 127 bonds, 15 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:488 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 21 atoms, 20 bonds, 3 residues, 1 model selected > select up 261 atoms, 262 bonds, 34 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:466 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 78 atoms, 78 bonds, 9 residues, 1 model selected > delete atoms sel > delete bonds sel > ui mousemode right ""rotate selected models"" > select add #4 3734 atoms, 3839 bonds, 462 residues, 1 model selected > view matrix models > #4,0.43405,0.89787,0.07366,117.05,-0.36089,0.24821,-0.89897,316.05,-0.82544,0.36362,0.43177,121.76 > view matrix models > #4,-0.55307,0.07934,-0.82935,108.63,-0.81339,-0.26687,0.51689,313.99,-0.18032,0.96046,0.21213,126.46 > view matrix models > #4,-0.46087,-0.34196,-0.81894,108.18,-0.789,-0.26458,0.5545,314.17,-0.40629,0.9017,-0.14787,124.66 > view matrix models > #4,-0.43468,-0.32294,-0.84069,108.35,-0.48585,-0.70191,0.52083,314.8,-0.75829,0.63484,0.14821,122.43 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.43468,-0.32294,-0.84069,107.43,-0.48585,-0.70191,0.52083,272.7,-0.75829,0.63484,0.14821,134.16 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.50319,-0.32511,-0.80069,107.1,-0.56202,-0.58071,0.58899,272.64,-0.65646,0.74637,0.10949,134.93 > view matrix models > #4,-0.2983,-0.22446,-0.9277,108.32,-0.7934,-0.482,0.37174,271.33,-0.53059,0.84693,-0.034304,135.7 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.2983,-0.22446,-0.9277,110.42,-0.7934,-0.482,0.37174,253.47,-0.53059,0.84693,-0.034304,138.15 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.40927,0.0086167,-0.91237,110.37,-0.67444,-0.67634,0.29615,253.59,-0.61452,0.73654,0.28262,137.8 > view matrix models > #4,-0.45763,-0.047851,-0.88786,109.99,-0.65112,-0.66196,0.37128,253.84,-0.60549,0.74801,0.27177,137.87 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.45763,-0.047851,-0.88786,110.2,-0.65112,-0.66196,0.37128,271.56,-0.60549,0.74801,0.27177,136.91 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06061, steps = 92 shifted from previous position = 2.82 rotated from previous position = 9.97 degrees atoms outside contour = 3232, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.82226951 -0.52311174 -0.22411366 131.45972009 -0.11201597 0.53487062 -0.83747587 97.22191800 0.55796526 -0.66352661 -0.49840467 131.20998200 Axis 0.19316900 -0.86849126 0.45651797 Axis point 58.62750865 0.00000000 109.13656195 Rotation angle (degrees) 153.24018107 Shift along axis 0.85727183 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.54268,0.083972,-0.83573,133.52,-0.68469,-0.62055,0.38225,324.78,-0.48652,0.77966,0.39425,130.33 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.15664,-0.23047,-0.96039,136.53,-0.96973,-0.2203,-0.10529,323.56,-0.18731,0.94781,-0.258,131.62 > view matrix models > #4,0.34533,0.10698,-0.93236,138.39,-0.52651,-0.80032,-0.28684,324.47,-0.77688,0.58995,-0.22005,127.57 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.34533,0.10698,-0.93236,139.1,-0.52651,-0.80032,-0.28684,274.22,-0.77688,0.58995,-0.22005,151.68 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.34533,0.10698,-0.93236,119.89,-0.52651,-0.80032,-0.28684,254.68,-0.77688,0.58995,-0.22005,128.96 > view matrix models > #4,0.34533,0.10698,-0.93236,122.45,-0.52651,-0.80032,-0.28684,256.94,-0.77688,0.58995,-0.22005,134.39 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.56153,0.08835,-0.82273,123.73,-0.48948,-0.7662,-0.41636,257.08,-0.66716,0.6365,-0.387,134.91 > view matrix models > #4,0.51187,0.026603,-0.85865,123.27,-0.55709,-0.75058,-0.35535,256.81,-0.65394,0.66024,-0.36938,135.06 > view matrix models > #4,0.37292,0.23786,-0.89686,122.95,-0.81519,-0.37767,-0.43913,256.14,-0.44316,0.89487,0.05306,137.26 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.69314,0.50873,-0.51063,125.8,-0.71957,0.52982,-0.44891,258.76,0.042168,0.67859,0.73331,140.24 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.69314,0.50873,-0.51063,129.43,-0.71957,0.52982,-0.44891,264.17,0.042168,0.67859,0.73331,140.79 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06347, steps = 108 shifted from previous position = 2.88 rotated from previous position = 3.61 degrees atoms outside contour = 3159, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.12729822 0.68087217 -0.72125462 138.51587855 0.98900174 0.14234061 -0.04018332 122.05232409 0.07530409 -0.71843734 -0.69150350 131.67605304 Axis -0.62189082 -0.73036434 0.28252387 Axis point -17.36882087 0.00000000 100.13564662 Rotation angle (degrees) 146.95373972 Shift along axis -138.08279054 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.42461,0.80905,-0.40639,131.69,-0.86712,0.23429,-0.43957,263.1,-0.26042,0.53903,0.80102,138.91 > save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs > ui mousemode right ""translate selected models"" > view matrix models > #4,0.42461,0.80905,-0.40639,158.95,-0.86712,0.23429,-0.43957,311.78,-0.26042,0.53903,0.80102,114.79 > matchmaker #4 to #3 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 7f3x.pdb, chain B (#3) with AF-Q6ZWT7-F1-model_v4.pdb, chain A (#4), sequence alignment score = 713 RMSD between 201 pruned atom pairs is 1.242 angstroms; (across all 421 pairs: 5.150) > ui mousemode right ""translate selected models"" > view matrix models > #4,0.7367,0.49979,-0.45549,102.09,-0.27992,-0.38778,-0.87822,314.79,-0.61556,0.77449,-0.14578,104.34 > save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs ——— End of log from Tue Aug 26 15:42:57 2025 ——— > view name session-start opened ChimeraX session > matchmaker #4 to #3 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 7f3x.pdb, chain B (#3) with AF-Q6ZWT7-F1-model_v4.pdb, chain A (#4), sequence alignment score = 713 RMSD between 201 pruned atom pairs is 1.242 angstroms; (across all 421 pairs: 5.150) > hide #3 models > show #3 models > hide #!2 models > ui mousemode right ""translate selected models"" > view matrix models > #4,0.7367,0.49979,-0.45549,126.26,-0.27992,-0.38778,-0.87822,270.01,-0.61556,0.77449,-0.14578,133.59 > ui tool show ""Fit in Map"" > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06537, steps = 96 shifted from previous position = 1.17 rotated from previous position = 6.67 degrees atoms outside contour = 3147, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.25840829 0.02482437 -0.96571677 139.19869591 0.64480116 0.73995737 0.19155817 112.75028801 0.71934456 -0.67219556 0.17520431 138.76375878 Axis -0.43351248 -0.84572152 0.31116239 Axis point -71.37574422 0.00000000 148.43980884 Rotation angle (degrees) 85.02132379 Shift along axis -112.52165385 > view matrix models > #4,0.71355,0.57175,-0.4049,124.85,-0.27942,-0.29773,-0.91284,269.75,-0.64247,0.7645,-0.052694,133.67 > view matrix models > #4,0.71355,0.57175,-0.4049,124.15,-0.27942,-0.29773,-0.91284,269.38,-0.64247,0.7645,-0.052694,133.16 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06537, steps = 56 shifted from previous position = 1.75 rotated from previous position = 0.013 degrees atoms outside contour = 3147, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.25825859 0.02475727 -0.96575854 139.19347255 0.64473164 0.74006336 0.19138265 112.74694351 0.71946063 -0.67208134 0.17516589 138.76394098 Axis -0.43336551 -0.84579770 0.31116006 Axis point -71.34696702 0.00000000 148.44155812 Rotation angle (degrees) 85.02368525 Shift along axis -112.50495910 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.57621,0.6438,-0.50349,125.09,-0.24825,-0.44907,-0.85832,269.56,-0.77869,0.61956,-0.098932,131.5 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.57621,0.6438,-0.50349,131.02,-0.24825,-0.44907,-0.85832,271.8,-0.77869,0.61956,-0.098932,132.33 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.17359,0.7035,-0.68917,128.71,-0.43433,-0.57337,-0.6947,270.67,-0.88387,0.41992,0.20602,131.64 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.17359,0.7035,-0.68917,119.72,-0.43433,-0.57337,-0.6947,271.86,-0.88387,0.41992,0.20602,136.87 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.07018, steps = 120 shifted from previous position = 5.03 rotated from previous position = 16 degrees atoms outside contour = 3046, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.10374815 0.04153714 -0.99373586 138.02925909 0.50330022 0.86395534 -0.01643317 111.55685728 0.85786082 -0.50185243 -0.11053945 129.71772261 Axis -0.24652112 -0.94033700 0.23450729 Axis point -14.72943306 -0.00000000 128.34117281 Rotation angle (degrees) 100.08832600 Shift along axis -108.50841656 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.42814,0.67696,-0.59869,123.79,-0.506,-0.36932,-0.77947,270.92,-0.74877,0.63666,0.18441,141.62 > view matrix models > #4,-0.79961,-0.063497,0.59715,116.65,0.11648,0.95911,0.25796,278.65,-0.58911,0.27583,-0.75952,140.57 > view matrix models > #4,-0.55677,0.52094,0.64701,119.41,0.82855,0.29274,0.47729,281.31,0.059235,0.80183,-0.59461,145.58 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06685, steps = 76 shifted from previous position = 5.91 rotated from previous position = 4.3 degrees atoms outside contour = 3207, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.32235255 0.42335464 0.84667565 143.17677766 -0.90068388 0.41240875 0.13670239 96.82990632 -0.29130282 -0.80665350 0.51424975 122.67574433 Axis -0.47537690 0.57345132 -0.66721090 Axis point 156.09290881 17.64062945 -0.00000000 Rotation angle (degrees) 82.84779842 Shift along axis -94.38628917 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.55244,0.53505,0.63916,126.35,0.82355,0.23194,0.51766,278.24,0.12872,0.81236,-0.56877,144.45 > view matrix models > #4,-0.55244,0.53505,0.63916,113.27,0.82355,0.23194,0.51766,273.27,0.12872,0.81236,-0.56877,144.01 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.81715,0.10823,0.56617,110.73,0.56349,-0.056841,0.82416,271.52,0.12138,0.9925,-0.014541,145.03 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.81715,0.10823,0.56617,114.75,0.56349,-0.056841,0.82416,275.24,0.12138,0.9925,-0.014541,144.27 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06383, steps = 84 shifted from previous position = 5.5 rotated from previous position = 4.89 degrees atoms outside contour = 3140, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.04830002 -0.02580030 0.99849959 136.11761176 -0.97984546 0.19521535 -0.04235349 97.97943271 -0.19382968 -0.98042100 -0.03470919 122.74761427 Axis -0.52342970 0.66530453 -0.53234503 Axis point 146.12202994 0.00000000 54.51989508 Rotation angle (degrees) 116.35278694 Shift along axis -71.40592354 > hide #!1 models > select clear > select #4/A:461 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 91 atoms, 91 bonds, 12 residues, 1 model selected > color sel red > show #!1 models > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.98374,0.17786,-0.025004,109.84,0.031442,0.3076,0.951,276.16,0.17684,0.93475,-0.30819,146.87 > view matrix models > #4,-0.76733,-0.40179,-0.49977,109.15,-0.28152,-0.48918,0.8255,272.44,-0.57615,0.77413,0.26225,142.99 > view matrix models > #4,0.37221,0.20811,-0.90452,116.41,-0.92518,0.0053,-0.37949,268.62,-0.074181,0.97809,0.19451,146.16 > view matrix models > #4,0.23616,-0.094695,-0.96709,114.88,-0.69798,-0.70896,-0.10103,268.55,-0.67606,0.69886,-0.23352,141.68 > view matrix models > #4,0.34209,0.39535,-0.85245,116.74,-0.92915,0.0069926,-0.36963,268.61,-0.14017,0.9185,0.36973,145.86 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06762, steps = 108 shifted from previous position = 1.65 rotated from previous position = 11.8 degrees atoms outside contour = 3121, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.54642107 -0.05423592 -0.83575262 131.60633888 0.73015310 0.45796015 -0.50709854 105.94785777 0.41024432 -0.88731674 -0.21063856 125.52547356 Axis -0.25003858 -0.81939082 0.51582885 Axis point 6.35752857 -0.00000000 129.26118427 Rotation angle (degrees) 130.50766368 Shift along axis -54.96970332 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.40792,0.47102,-0.78214,116.31,-0.79501,-0.23799,-0.55796,269.93,-0.44896,0.84941,0.27739,144.19 > view matrix models > #4,0.78425,0.42754,-0.44963,118.68,-0.43249,-0.14291,-0.89024,271.77,-0.44487,0.89263,0.072829,144.08 > view matrix models > #4,0.94021,0.31453,-0.13066,119.66,-0.20585,0.21913,-0.95373,273.79,-0.27135,0.92361,0.27078,145.34 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.07051, steps = 72 shifted from previous position = 2.88 rotated from previous position = 6.67 degrees atoms outside contour = 3125, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.39787946 0.31561160 -0.86144137 138.45669809 0.87267658 0.15951182 0.46151007 108.37622873 0.28306800 -0.93538511 -0.21196042 127.22430024 Axis -0.73915600 -0.60560805 0.29476652 Axis point 0.00000000 77.25734416 77.08011521 Rotation angle (degrees) 109.10404291 Shift along axis -130.47315170 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.95405,0.26032,-0.14841,121.82,-0.22852,0.31174,-0.92228,276.13,-0.19382,0.91381,0.3569,141.92 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.66312,0.74851,-0.0019277,121.5,-0.0043303,0.001261,-0.99999,276.57,-0.7485,0.66312,0.0040775,137.86 > view matrix models > #4,0.33713,0.50715,-0.79318,118.22,-0.85599,0.51588,-0.033978,274.16,0.39195,0.69041,0.60804,144.95 > view matrix models > #4,-0.27304,0.25381,-0.92792,114.09,-0.9536,-0.19863,0.22627,272.26,-0.12688,0.94664,0.29626,142.3 > view matrix models > #4,0.26572,-0.045243,-0.96299,116.35,-0.90554,-0.35442,-0.23322,271.64,-0.33075,0.93399,-0.13514,140.64 > view matrix models > #4,0.14437,0.32743,-0.93378,116.57,-0.42674,-0.8308,-0.35729,273.05,-0.89278,0.45006,0.019787,136.58 > fitmap #4 inMap #1 Fit molecule AF-Q6ZWT7-F1-model_v4.pdb (#4) to map cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) using 3734 atoms average map value = 0.06965, steps = 68 shifted from previous position = 4.14 rotated from previous position = 7.07 degrees atoms outside contour = 3054, contour level = 0.19392 Position of AF-Q6ZWT7-F1-model_v4.pdb (#4) relative to cryosparc_P5_J157_008_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.20600772 -0.60214270 -0.77135269 138.28257777 0.25753747 0.72710890 -0.63638596 107.29525118 0.94405257 -0.32975269 0.00528426 132.78459885 Axis 0.15780515 -0.88281280 0.44242411 Axis point 16.86859417 0.00000000 155.79423963 Rotation angle (degrees) 103.69818008 Shift along axis -14.15281015 > save /Users/s230038/Projects_JieL/mboat1:2/Structure/CryoEM/250826.cxs > hide #!4 models > show #5 models > ui mousemode right ""translate selected models"" > select add #5 4290 atoms, 4400 bonds, 532 residues, 2 models selected > select add #4 7933 atoms, 8148 bonds, 982 residues, 2 models selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,8 Model Number: MX2F3LL/A Chip: Apple M4 Pro Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 3 days, 19 hours, 47 minutes Graphics/Displays: Apple M4 Pro: Chipset Model: Apple M4 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 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 ED343CUR V: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 100.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Platform duplicate all ChimeraX