id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19854 Crash in QDockWidget::event() in Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 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 0x0000000206a0ec40 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PIL._imaging, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 53) {""app_name"":""ChimeraX"",""timestamp"":""2026-02-15 16:35:15.00 -0800"",""app_version"":""1.11.1"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.2 (25C56)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""4464DF08-EA84-4AD2-89A9-66EEA47A08D8""} { ""uptime"" : 54000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac16,5"", ""coalitionID"" : 4482, ""osVersion"" : { ""train"" : ""macOS 26.2"", ""build"" : ""25C56"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-02-15 16:35:12.7031 -0800"", ""codeSigningMonitor"" : 2, ""incident"" : ""4464DF08-EA84-4AD2-89A9-66EEA47A08D8"", ""pid"" : 14787, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procLaunch"" : ""2026-02-15 13:13:46.4670 -0800"", ""procStartAbsTime"" : 1122131334319, ""procExitAbsTime"" : 1311321997619, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.1"",""CFBundleVersion"":""1.11.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""3DB91261-B876-5522-8C0C-C59B6D2AB51A"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""3D03C990-9D81-B6B4-6E53-68C3212D14D9"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""siriAssetIsNotReady"",""notOptedIn"",""assetIsNotReady""]}, ""developerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""4EF509EA-843E-402C-843E-2B271E789FC6"", ""wakeTime"" : 1682, ""sleepWakeUUID"" : ""06A7E93A-3E02-4ED8-9897-657BEE1BD318"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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], ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000012 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_Apo/ctpolII_Apo_DNA_fix_isolde1.pdb Chain information for ctpolII_Apo_DNA_fix_isolde1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > set bgColor white > hide atoms > show cartoons > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb Chain information for ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide atoms > show cartoons > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb Chain information for ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide atoms > show cartoons > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_30s/ctpolii_30s_job063_DNA_fixed_isolde1.pdb Chain information for ctpolii_30s_job063_DNA_fixed_isolde1.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide atoms > show cartoons > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_apo_maps/CTpol2EC-3p06A.mrc Opened CTpol2EC-3p06A.mrc as #5, grid size 384,384,384, pixel 0.852, shown at level 0.00838, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s_job162_2p9A.mrc Opened CTpol2EC10s_job162_2p9A.mrc as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 2, values float32 > open > ""/Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_20s_maps/ctpolii20s_2EM_sessions_comb_data > /job271_20s_3A.mrc"" Opened job271_20s_3A.mrc as #7, grid size 384,384,384, pixel 0.852, shown at level 0.00825, step 2, values float32 > ui tool show ""Hide Dust"" > surface dust #5 size 5.11 > surface dust #6 size 5.11 > surface dust #7 size 5.11 > ui tool show ""Fit in Map"" > fitmap #2 inMap #5 Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) to map CTpol2EC-3p06A.mrc (#5) using 66716 atoms average map value = 0.02021, steps = 56 shifted from previous position = 0.829 rotated from previous position = 1.02 degrees atoms outside contour = 25439, contour level = 0.0083837 Position of ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 0.99986131 -0.01547426 0.00615642 1.89582458 0.01543631 0.99986185 0.00616471 -2.76155326 -0.00625096 -0.00606883 0.99996205 2.22505371 Axis -0.34476888 0.34966793 0.87112959 Axis point 187.27243115 127.94508301 0.00000000 Rotation angle (degrees) 1.01657540 Shift along axis 0.31906218 > fitmap #3 inMap #5 Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) to map CTpol2EC-3p06A.mrc (#5) using 66702 atoms average map value = 0.02022, steps = 56 shifted from previous position = 0.828 rotated from previous position = 1.01 degrees atoms outside contour = 25372, contour level = 0.0083837 Position of ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 0.99986429 -0.01533800 0.00601159 1.92306830 0.01530101 0.99986401 0.00615130 -2.75091578 -0.00610512 -0.00605849 0.99996301 2.20639659 Axis -0.34748625 0.34483720 0.87197512 Axis point 187.86821803 130.67379040 0.00000000 Rotation angle (degrees) 1.00666643 Shift along axis 0.30706504 > fitmap #6 inMap #5 Fit map CTpol2EC10s_job162_2p9A.mrc in map CTpol2EC-3p06A.mrc using 70684 points correlation = 0.8971, correlation about mean = 0.8337, overlap = 51.68 steps = 56, shift = 0.928, angle = 0.987 degrees Position of CTpol2EC10s_job162_2p9A.mrc (#6) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 0.99986626 -0.01501576 0.00647951 1.80457066 0.01498051 0.99987291 0.00545466 -2.56359734 -0.00656059 -0.00535686 0.99996413 2.23957619 Axis -0.31384447 0.37853744 0.87075315 Axis point 182.65255824 127.19097287 0.00000000 Rotation angle (degrees) 0.98693015 Shift along axis 0.41334593 > fitmap #7 inMap #5 Fit map job271_20s_3A.mrc in map CTpol2EC-3p06A.mrc using 70685 points correlation = 0.9359, correlation about mean = 0.8973, overlap = 44.03 steps = 60, shift = 0.657, angle = 0.855 degrees Position of job271_20s_3A.mrc (#7) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 0.99996307 -0.00857487 -0.00057312 0.98820547 0.00858122 0.99988882 0.01219473 -3.03505590 0.00046849 -0.01219919 0.99992548 1.92257939 Axis -0.81746585 -0.03490543 0.57491842 Axis point 0.00000000 137.06467626 248.97748847 Rotation angle (degrees) 0.85491071 Shift along axis 0.40344200 > fitmap #1 inMap #5 Fit molecule ctpolII_Apo_DNA_fix_isolde1.pdb (#1) to map CTpol2EC-3p06A.mrc (#5) using 66643 atoms average map value = 0.02038, steps = 60 shifted from previous position = 0.0242 rotated from previous position = 0.0105 degrees atoms outside contour = 25101, contour level = 0.0083837 Position of ctpolII_Apo_DNA_fix_isolde1.pdb (#1) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 1.00000000 0.00003529 -0.00009020 0.02577092 -0.00003530 0.99999999 -0.00015559 0.01884098 0.00009020 0.00015560 0.99999998 -0.02905343 Axis 0.84894345 -0.49214361 -0.19258684 Axis point 0.00000000 164.21253901 178.64619962 Rotation angle (degrees) 0.01050128 Shift along axis 0.01820089 > fitmap #2 inMap #6 Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) to map CTpol2EC10s_job162_2p9A.mrc (#6) using 66716 atoms average map value = 0.0244, steps = 40 shifted from previous position = 0.0499 rotated from previous position = 0.0106 degrees atoms outside contour = 24742, contour level = 0.010466 Position of ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) relative to CTpol2EC10s_job162_2p9A.mrc (#6) coordinates: Matrix rotation and translation 0.99999981 -0.00058608 -0.00018800 0.10929979 0.00058620 0.99999960 0.00067820 -0.22563901 0.00018761 -0.00067831 0.99999975 0.04381637 Axis -0.74054039 -0.20505172 0.63996384 Axis point 0.00000000 70.73121231 334.74828781 Rotation angle (degrees) 0.05247701 Shift along axis -0.00663235 > fitmap #2 inMap #7 Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) to map job271_20s_3A.mrc (#7) using 66716 atoms average map value = 0.0197, steps = 28 shifted from previous position = 0.0401 rotated from previous position = 0.0259 degrees atoms outside contour = 23737, contour level = 0.0082471 Position of ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) relative to job271_20s_3A.mrc (#7) coordinates: Matrix rotation and translation 0.99995062 -0.00743215 0.00659750 1.01000832 0.00747256 0.99995334 -0.00612135 0.16001861 -0.00655170 0.00617035 0.99995950 0.29873535 Axis 0.52596970 0.56266274 0.63778250 Axis point 40.20009438 78.17945122 0.00000000 Rotation angle (degrees) 0.66950469 Shift along axis 0.81179846 > fitmap #3 inMap #7 Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) to map job271_20s_3A.mrc (#7) using 66702 atoms average map value = 0.0197, steps = 40 shifted from previous position = 0.0308 rotated from previous position = 0.0361 degrees atoms outside contour = 23772, contour level = 0.0082471 Position of ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) relative to job271_20s_3A.mrc (#7) coordinates: Matrix rotation and translation 0.99995114 -0.00738075 0.00657657 1.01733162 0.00742148 0.99995330 -0.00619033 0.16848102 -0.00653057 0.00623883 0.99995921 0.29446777 Axis 0.53221754 0.56124885 0.63383295 Axis point 40.00302882 78.25091969 0.00000000 Rotation angle (degrees) 0.66904463 Shift along axis 0.82264489 > fitmap #3 inMap #6 Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) to map CTpol2EC10s_job162_2p9A.mrc (#6) using 66702 atoms average map value = 0.02442, steps = 48 shifted from previous position = 0.0438 rotated from previous position = 0.0364 degrees atoms outside contour = 24689, contour level = 0.010466 Position of ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) relative to CTpol2EC10s_job162_2p9A.mrc (#6) coordinates: Matrix rotation and translation 0.99999990 -0.00031274 -0.00030372 0.09766814 0.00031293 0.99999976 0.00062599 -0.17241600 0.00030352 -0.00062609 0.99999976 0.02387472 Axis -0.82063412 -0.39799225 0.41007537 Axis point 0.00000000 39.16527983 276.54848584 Rotation angle (degrees) 0.04370955 Shift along axis -0.00173915 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_30s_maps/30s_job063_2p75A.mrc Opened 30s_job063_2p75A.mrc as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0097, step 2, values float32 > fitmap #8 inMap #5 Fit map 30s_job063_2p75A.mrc in map CTpol2EC-3p06A.mrc using 70718 points correlation = 0.1967, correlation about mean = 0.06918, overlap = 6.835 steps = 220, shift = 1.38, angle = 5.6 degrees Position of 30s_job063_2p75A.mrc (#8) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 0.99938720 -0.00948291 -0.03369426 7.18323430 0.01251544 0.99577566 0.09096264 -17.71968653 0.03268933 -0.09132859 0.99528413 10.02756392 Axis -0.93365143 -0.34000063 0.11267024 Axis point 0.00000000 99.03411964 197.72692499 Rotation angle (degrees) 5.60229390 Shift along axis 0.44787576 > fitmap #4 inMap #8 Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map 30s_job063_2p75A.mrc (#8) using 66609 atoms average map value = 0.02436, steps = 92 shifted from previous position = 1.7 rotated from previous position = 5.59 degrees atoms outside contour = 23763, contour level = 0.009695 Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to 30s_job063_2p75A.mrc (#8) coordinates: Matrix rotation and translation 0.99999999 -0.00011596 0.00011784 -0.00740255 0.00011598 0.99999998 -0.00014736 0.01792982 -0.00011783 0.00014737 0.99999998 -0.00318123 Axis 0.66538620 0.53204118 0.52363479 Axis point 0.00000000 32.07406570 111.02517673 Rotation angle (degrees) 0.01268970 Shift along axis 0.00294804 > fitmap #4 inMap #8 Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map 30s_job063_2p75A.mrc (#8) using 66609 atoms average map value = 0.02436, steps = 48 shifted from previous position = 0.00943 rotated from previous position = 0.00303 degrees atoms outside contour = 23771, contour level = 0.009695 Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to 30s_job063_2p75A.mrc (#8) coordinates: Matrix rotation and translation 0.99999998 -0.00016839 0.00011748 -0.00514021 0.00016840 0.99999998 -0.00014062 0.00201391 -0.00011746 0.00014064 0.99999998 -0.00321989 Axis 0.56509324 0.47202106 0.67665777 Axis point -23.54544239 -16.65382247 0.00000000 Rotation angle (degrees) 0.01425871 Shift along axis -0.00413285 > ui tool show ""Hide Dust"" > surface dust #8 size 5.11 > volume #5 level 0.01 > volume #6 level 0.01 > volume #7 level 0.01 > volume #8 level 0.01 > select add #8 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.89436,-0.31964,0.31297,22.989,0.31173,0.94709,0.076473,-53.397,-0.32086,0.029168,0.94668,51.552 > fitmap #8 inMap #5 Fit map 30s_job063_2p75A.mrc in map CTpol2EC-3p06A.mrc using 66815 points correlation = 0.9136, correlation about mean = 0.8532, overlap = 50.1 steps = 180, shift = 3.06, angle = 8.01 degrees Position of 30s_job063_2p75A.mrc (#8) relative to CTpol2EC-3p06A.mrc (#5) coordinates: Matrix rotation and translation 0.89301937 -0.37916200 0.24238931 47.11723403 0.33817191 0.92077843 0.19443980 -73.34180389 -0.29691103 -0.09166925 0.95049492 69.06399216 Axis -0.30374099 0.57253561 0.76154080 Axis point 224.19750968 58.03962552 0.00000000 Rotation angle (degrees) 28.09762834 Shift along axis -3.70718149 > fitmap #4 inMap #8 Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map 30s_job063_2p75A.mrc (#8) using 66609 atoms average map value = 0.004249, steps = 160 shifted from previous position = 3.69 rotated from previous position = 6.81 degrees atoms outside contour = 52860, contour level = 0.01 Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to 30s_job063_2p75A.mrc (#8) coordinates: Matrix rotation and translation 0.92596607 0.24404116 -0.28815057 11.08182215 -0.25957613 0.96558393 -0.01636806 48.40576528 0.27423908 0.08995327 0.95744521 -51.56776457 Axis 0.13946054 -0.73768045 -0.66058937 Axis point 186.80160412 0.00000000 -9.48897099 Rotation angle (degrees) 22.40728031 Shift along axis -0.09739243 > hide #!7 models > hide #!6 models > hide #!5 models > hide #4 models > show #4 models > hide #3 models > hide #2 models > hide #1 models > select clear > select add #4 66609 atoms, 67346 bonds, 4164 residues, 1 model selected > view matrix models > #4,0.92961,-0.33513,0.15335,45.859,0.30893,0.93547,0.17163,-69.35,-0.20098,-0.11217,0.97315,55.565 > view matrix models > #4,0.92794,-0.32835,0.1764,41.201,0.30667,0.94156,0.13937,-64.923,-0.21185,-0.075225,0.9744,50.396 > fitmap #4 inMap #8 Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map 30s_job063_2p75A.mrc (#8) using 66609 atoms average map value = 0.02436, steps = 112 shifted from previous position = 3.87 rotated from previous position = 5.83 degrees atoms outside contour = 24534, contour level = 0.01 Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to 30s_job063_2p75A.mrc (#8) coordinates: Matrix rotation and translation 1.00000000 -0.00005134 0.00006600 -0.00639488 0.00005135 0.99999999 -0.00013776 0.02829433 -0.00006599 0.00013776 0.99999999 -0.01188972 Axis 0.85486196 0.40951528 0.31860361 Axis point 0.00000000 91.71488336 198.44717971 Rotation angle (degrees) 0.00923333 Shift along axis 0.00233212 > fitmap #4 inMap #8 Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map 30s_job063_2p75A.mrc (#8) using 66609 atoms average map value = 0.02436, steps = 48 shifted from previous position = 0.00333 rotated from previous position = 0.00413 degrees atoms outside contour = 24538, contour level = 0.01 Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to 30s_job063_2p75A.mrc (#8) coordinates: Matrix rotation and translation 0.99999999 -0.00011244 0.00009957 -0.00073965 0.00011246 0.99999998 -0.00015613 0.02189135 -0.00009956 0.00015614 0.99999998 -0.00652214 Axis 0.72069292 0.45957287 0.51903227 Axis point 0.00000000 62.20177250 122.12353066 Rotation angle (degrees) 0.01241304 Shift along axis 0.00614241 > show #!5 models > hide #!5 models > hide #!8 models > select clear > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > hide #4 models > show #1 models > select #1/R 297 atoms, 321 bonds, 9 residues, 1 model selected > color sel red > style sel ball Changed 297 atom styles > show sel target ab > select #1/A:51 24 atoms, 23 bonds, 1 residue, 1 model selected > select #1/T:15-28 440 atoms, 472 bonds, 14 residues, 1 model selected > color sel cyan > style sel ball Changed 440 atom styles > show sel target ab > select clear > show #!5 models > volume #5 step 1 > volume #6 step 1 > volume #7 step 1 > volume #8 step 1 > hide #!5 models > show #!6 models > volume #5 level 0.03 > show #4 models > hide #!6 models > show #!5 models > volume #5 level 0.02 > volume #5 level 0.015 > volume #5 level 0.013 > volume #5 level 0.014 > show #!6 models > select #1/T:15-28 440 atoms, 472 bonds, 14 residues, 1 model selected > volume #6 level 0.014 > show #!7 models > hide #!6 models > hide #!5 models > volume #7 level 0.014 > show #!8 models > volume #8 level 0.014 > hide #!8 models > hide #!7 models > hide #4 models > select clear > dssp > volume zone #5 nearAtoms #1/T:16-22 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #9, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/R:7-9 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #10, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #11, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #12, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #13, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > select ~#1/R:7-9 #1/T:16-22 #1/A:838-860 #1/A:1083-1123 #1/A:493-501 265247 atoms, 268172 bonds, 16580 residues, 22 models selected > select subtract #13 265247 atoms, 268172 bonds, 16580 residues, 20 models selected > select subtract #12 265247 atoms, 268172 bonds, 16580 residues, 18 models selected > select subtract #11 265247 atoms, 268172 bonds, 16580 residues, 16 models selected > select subtract #10 265247 atoms, 268172 bonds, 16580 residues, 14 models selected > select subtract #9 265247 atoms, 268172 bonds, 16580 residues, 12 models selected > select subtract #8 265247 atoms, 268172 bonds, 16580 residues, 10 models selected > select subtract #7 265247 atoms, 268172 bonds, 16580 residues, 8 models selected > select subtract #6 265247 atoms, 268172 bonds, 16580 residues, 6 models selected > select subtract #5 265247 atoms, 268172 bonds, 16580 residues, 4 models selected > select subtract #4 198638 atoms, 200826 bonds, 12416 residues, 3 models selected > select subtract #3 131936 atoms, 133381 bonds, 8249 residues, 2 models selected > select subtract #2 65220 atoms, 65923 bonds, 4082 residues, 1 model selected > cartoon hide sel > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > select #1/R:1-5 161 atoms, 173 bonds, 5 residues, 1 model selected > hide sel target a > select #1/T:23-28 189 atoms, 202 bonds, 6 residues, 1 model selected > hide sel target a > hide #!13 models > show #!13 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > rename #9 ""CTpol2EC-3p06A_tDNA.mrc zone"" > select add #10 189 atoms, 202 bonds, 6 residues, 3 models selected > select subtract #10 189 atoms, 202 bonds, 6 residues, 1 model selected > hide #!10 models > show #!10 models > rename #10 ""CTpol2EC-3p06A_RNA.mrc zone"" > volume zone #5 nearAtoms #1/T:16-22 range 3 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #14, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/R:7-9 range 3 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #15, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/A:493-501 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #16, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/A:837-861 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #17, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #5 nearAtoms #1/A:1083-1123 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #18, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!18 models > show #!18 models > hide #!18 models > show #!17 models > hide #!17 models > show #!16 models > hide #!16 models > show #!15 models > hide #!15 models > show #!14 models > hide #!14 models > show #!13 models > hide #!13 models > show #!9 models > close #9-13 > show #!14 models > rename #14 ""CTpol2EC-3p06A_tDNA.mrc zone"" > hide #!14 models > show #!15 models > rename #15 ""CTpol2EC-3p06A_RNA.mrc zone"" > hide #!15 models > show #!16 models > rename #16 ""CTpol2EC-3p06A_AS.mrc zone"" > hide #!16 models > show #!16 models > hide #!16 models > show #!17 models > rename #17 ""CTpol2EC-3p06A_BH.mrc zone"" > hide #!17 models > show #!18 models > rename #18 ""CTpol2EC-3p06A_TL.mrc zone"" > select #1/R:6 34 atoms, 36 bonds, 1 residue, 1 model selected > hide sel target a > show #!17 models > show #!16 models > show #!15 models > show #!14 models > surface dust #14 size 5.11 > surface dust #15 size 5.11 > surface dust #16 size 5.11 > surface dust #17 size 5.11 > surface dust #18 size 5.11 > select add #14 34 atoms, 36 bonds, 1 residue, 3 models selected > color (#1 & sel) cyan > select clear > select add #14 2 models selected > color #14.1 cyan > select subtract #14 Nothing selected > select add #15 2 models selected > color #15.1 red > select subtract #15 Nothing selected > select add #16 2 models selected > color #16.1 purple > select subtract #16 Nothing selected > select add #17 2 models selected > color #17.1 forest green > select subtract #17 Nothing selected > select add #18 2 models selected > color #18.1 orange > select clear > select #1/T:15 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel target a > cartoon hide sel > select #1/T:15 32 atoms, 34 bonds, 1 residue, 1 model selected > hide #!14 models > hide #!15 models > hide #!16 models > hide #!17 models > show #!17 models > select #1/A:2000 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > show sel target ab > color sel magenta > select clear > select #1/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > cartoon hide sel > select add #14 123 atoms, 124 bonds, 9 residues, 3 models selected > select add #15 123 atoms, 124 bonds, 9 residues, 5 models selected > select add #16 123 atoms, 124 bonds, 9 residues, 7 models selected > select add #17 123 atoms, 124 bonds, 9 residues, 9 models selected > select add #18 123 atoms, 124 bonds, 9 residues, 11 models selected > show #!16 models > show #!15 models > show #!14 models > transparency (#1 & sel) 80 > select clear > select add #14 2 models selected > transparency #14.1 80 > transparency #14.1 70 > select clear > select add #15 2 models selected > transparency #15.1 70 > select clear > select add #17 2 models selected > transparency #17.1 70 > select subtract #17 Nothing selected > select add #18 2 models selected > transparency #18.1 70 > select clear > select #1/A:838-860 366 atoms, 366 bonds, 23 residues, 1 model selected > color sel forest green > select clear > select #1/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > hide #!18 models > show #!18 models > hide #!17 models > show #!17 models > hide #!15 models > show #!15 models > hide #!16 models > cd /Volumes/Rayees_T7/PolII_Manuscript Current working directory is: /Volumes/Rayees_T7/PolII_Manuscript > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig3/Apo_10s_20s_30s_initial_maps_vol_zones.cxs > includeMaps true > rename #2 id #19 > rename #3 id #20 > rename #4 id #21 > rename #5 id #22 > rename #6 id #23 > rename #7 id #24 > rename #8 id #25 > rename #22 id #2 > rename #14 id #3 > rename #15 id #4 > rename #16 id #5 > rename #17 id #6 > rename #18 id #7 > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!6 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig3/Apo_10s_20s_30s_initial_maps_vol_zones.cxs > includeMaps true > hide #1 models > hide #!7 models > show #19 models > hide #19 models > show #20 models > hide #20 models > show #20 models > hide #20 models > show #1 models > hide #1 models > show #20 models > select #20/R 358 atoms, 386 bonds, 11 residues, 1 model selected > color sel red > select clear > show #1 models > hide #1 models > select #20/R:9-12 129 atoms, 138 bonds, 4 residues, 1 model selected > style sel ball Changed 129 atom styles > show sel target ab > select clear > select #20/T:13-20 254 atoms, 274 bonds, 8 residues, 1 model selected > color sel cyan > style sel ball Changed 254 atom styles > show sel target ab > select clear > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > select #20/T:13 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel target a > select clear > hide #1 models > select ~#20/R:9-12 #20/T:14-20 #20/A:493-501 #20/A:838-860 #20/A:1083-1123 265217 atoms, 268139 bonds, 16579 residues, 22 models selected > select subtract #19 198501 atoms, 200681 bonds, 12412 residues, 21 models selected > select subtract #7 198501 atoms, 200681 bonds, 12412 residues, 19 models selected > select subtract #6 198501 atoms, 200681 bonds, 12412 residues, 17 models selected > select subtract #5 198501 atoms, 200681 bonds, 12412 residues, 15 models selected > select subtract #4 198501 atoms, 200681 bonds, 12412 residues, 13 models selected > select subtract #3 198501 atoms, 200681 bonds, 12412 residues, 11 models selected > select subtract #2 198501 atoms, 200681 bonds, 12412 residues, 9 models selected > select subtract #1 131858 atoms, 133298 bonds, 8247 residues, 8 models selected > select subtract #21 65249 atoms, 65952 bonds, 4083 residues, 7 models selected > select subtract #23 65249 atoms, 65952 bonds, 4083 residues, 5 models selected > select subtract #24 65249 atoms, 65952 bonds, 4083 residues, 3 models selected > select subtract #25 65249 atoms, 65952 bonds, 4083 residues, 1 model selected > cartoon hide sel > select clear > select #20/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > color sel purple > select clear > select #20/A:838-860 366 atoms, 366 bonds, 23 residues, 1 model selected > color sel forest green > select #20/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > volume zone #23 nearAtoms #20/T:14-20 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #23 nearAtoms #20/R:9-12 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #9, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #23 nearAtoms #20/A:493-501 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #10, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #23 nearAtoms #20/A:837-861 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #11, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #23 nearAtoms #20/A:1083-1123 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #12, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!8 models > show #!8 models > rename #8 ""CTpol2EC10s_job162_2p9A_tDNA.mrc zone"" > rename #9 ""CTpol2EC10s_job162_2p9A_RNA.mrc zone"" > hide #!9 models > show #!9 models > hide #!10 models > show #!10 models > rename #10 ""CTpol2EC10s_job162_2p9A_AS.mrc zone"" > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!11 models > show #!11 models > rename #11 ""CTpol2EC10s_job162_2p9A_BH.mrc zone"" > hide #!12 models > show #!12 models > rename #12 ""CTpol2EC10s_job162_2p9A_TL.mrc zone"" > surface dust #8 size 5.11 > surface dust #9 size 5.11 > surface dust #10 size 5.11 > surface dust #11 size 5.11 > surface dust #12 size 5.11 > hide #!8 models > show #!8 models > select add #8 2 models selected > color #8.1 cyan > select subtract #8 Nothing selected > select add #9 2 models selected > color #9.1 red > hide #20 models > show #21 models > hide #21 models > select subtract #9 Nothing selected > select add #10 2 models selected > color #10.1 purple > select subtract #10 Nothing selected > select add #11 2 models selected > color #11.1 forest green > select subtract #11 Nothing selected > select add #12 2 models selected > color #12.1 orange > select #8 2 models selected > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > show #20 models > show #!8 models > show #!9 models > show #!10 models > hide #!10 models > show #!11 models > show #!12 models > show #19 models > hide #19 models > select clear > select add #8 2 models selected > select add #9 4 models selected > select add #10 6 models selected > select add #11 8 models selected > select add #12 10 models selected > transparency #8.1#9.1#11.1#12.1 70 > select clear > select #20/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > cartoon hide sel > select clear > select #20/A:2000 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > show sel target ab > color sel magenta > select clear > rename #8 id #26 > rename #10 id #27 > rename #12 id #28 > rename #9 id #29 > rename #11 id #30 > rename #19 id #31 > rename #20 id #8 > rename #23 id #9 > rename #26 id #10 > rename #27 id #11 > rename #28 id #12 > rename #10 id #32 > rename #11 id #33 > rename #32 id #10 > rename #29 id #11 > rename #12 id #34 > rename #33 id #12 > rename #30 id #13 > rename #34 id #14 > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig3/Apo_10s_20s_30s_initial_maps_vol_zones.cxs > includeMaps true > show #!12 models > hide #!12 models > show #31 models > hide #31 models > hide #!14 models > hide #!13 models > hide #!11 models > hide #!10 models > hide #8 models > show #8 models > show #31 models > hide #31 models > show #31 models > hide #8 models > show #8 models > hide #8 models > show #8 models > select #31/T:14-20 #31/R:911 #31/A:493-501 #31/A:838-860 #31/A:1083-1123 1324 atoms, 1346 bonds, 80 residues, 1 model selected > select ~#31/T:14-20 #31/R:911 #31/A:493-501 #31/A:838-860 #31/A:1083-1123 265346 atoms, 268278 bonds, 16583 residues, 32 models selected > select subtract #25 265346 atoms, 268278 bonds, 16583 residues, 30 models selected > select subtract #24 265346 atoms, 268278 bonds, 16583 residues, 28 models selected > select subtract #21 198737 atoms, 200932 bonds, 12419 residues, 27 models selected > select subtract #14 198737 atoms, 200932 bonds, 12419 residues, 25 models selected > select subtract #13 198737 atoms, 200932 bonds, 12419 residues, 23 models selected > select subtract #12 198737 atoms, 200932 bonds, 12419 residues, 21 models selected > select subtract #11 198737 atoms, 200932 bonds, 12419 residues, 19 models selected > select subtract #10 198737 atoms, 200932 bonds, 12419 residues, 17 models selected > select subtract #9 198737 atoms, 200932 bonds, 12419 residues, 15 models selected > select subtract #8 132035 atoms, 133487 bonds, 8252 residues, 14 models selected > select subtract #7 132035 atoms, 133487 bonds, 8252 residues, 12 models selected > select subtract #6 132035 atoms, 133487 bonds, 8252 residues, 10 models selected > select subtract #5 132035 atoms, 133487 bonds, 8252 residues, 8 models selected > select subtract #4 132035 atoms, 133487 bonds, 8252 residues, 6 models selected > select subtract #3 132035 atoms, 133487 bonds, 8252 residues, 4 models selected > select subtract #2 132035 atoms, 133487 bonds, 8252 residues, 2 models selected > select subtract #1 65392 atoms, 66104 bonds, 4087 residues, 1 model selected > cartoon hide sel > select clear > hide #8 models > select #31/R:9-11 98 atoms, 105 bonds, 3 residues, 1 model selected > cartoon sel > select #31/A:2000 Nothing selected > style #31 sphere Changed 66716 atom styles > show #31 target ab > undo > style #31 sphere Changed 66716 atom styles > show #31 target ab > undo > select #31/A:2000 Nothing selected > show metals Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show ions > select #31/M 1 atom, 1 residue, 1 model selected > changechains #32/M A No residues specified > changechains #32/M:2000 A:2000 No residues specified > changechains #32/M:2000 #32/A:2000 Missing or invalid ""fromIds"" argument: Expected a text string > changechains #31/M:2000 #31/A:2000 Missing or invalid ""fromIds"" argument: Expected a text string > changechains #31/M:2000 A:2000 Chain IDs of 1 residues changed > hide ions > select 31/A:2000 Expected an objects specifier or a keyword > select #31/A:2000 Nothing selected > style #31 sphere Changed 66716 atom styles > show #31 target ab > undo > show ions #31 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show ions > select #31/A:2000 Nothing selected > sequence chain A #31 Missing or invalid ""chains"" argument: invalid chains specifier > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > select clear > select #31//chain_id='A:2000':2000@MG Nothing selected > select clear Drag select of 1 atoms > color sel magenta > select clear > select #31/A:2000 Nothing selected > select #31/A:2000 Nothing selected > select #31/3 4 atoms, 4 residues, 1 model selected > hide sel target a > select #31/T:14-20 222 atoms, 239 bonds, 7 residues, 1 model selected > color sel cyan > style sel ball Changed 222 atom styles > show sel target ab > select #31/R:9-11 98 atoms, 105 bonds, 3 residues, 1 model selected > color sel red > style sel ball Changed 98 atom styles > show sel target ab > select #31/U:1 45 atoms, 46 bonds, 1 residue, 1 model selected > style sel ball Changed 45 atom styles > show sel target ab > select clear > select #31/U:1 45 atoms, 46 bonds, 1 residue, 1 model selected > color sel orange red > select clear > select #31/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > color sel purple > select clear > select #31/A:838-860 366 atoms, 366 bonds, 23 residues, 1 model selected > color sel forest green > select #31/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > show #!10 models > show #!11 models > show #!12 models > hide #!12 models > show #!13 models > show #!14 models > show #!24 models > hide #!14 models > hide #!13 models > hide #!11 models > hide #!10 models > hide #!24 models > show #!24 models > ui tool show ""Volume Viewer"" > volume #24 level 0.01789 > volume #24 level 0.01322 > show #8 models > hide #8 models > show #8 models > hide #8 models > hide #!24 models > hide #31 models > show #31 models > show #8 models > hide #31 models > hide ions > show #8/A:2000 > select clear > show #!24 models > volume zone #24 nearAtoms #8/T:14-20 range 3 invert false minimalBounds > false newMap true Opened job271_20s_3A.mrc zone as #15, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #24 nearAtoms #8/R:9-12 range 3 invert false minimalBounds false > newMap true Opened job271_20s_3A.mrc zone as #16, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #24 nearAtoms #8/A:493-501 range 3 invert false minimalBounds > false newMap true Opened job271_20s_3A.mrc zone as #17, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #24 nearAtoms #8/A:837-861 range 3 invert false minimalBounds > false newMap true Opened job271_20s_3A.mrc zone as #18, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #24 nearAtoms #8/A:1083-1123 range 3 invert false minimalBounds > false newMap true Opened job271_20s_3A.mrc zone as #19, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > surface dust #15 size 5.11 > surface dust #16 size 5.11 > surface dust #17 size 5.11 > surface dust #18 size 5.11 > surface dust #19 size 5.11 > select add #15 2 models selected > color #15.1 cyan > select subtract #15 Nothing selected > select add #16 2 models selected > rename #15 ""job271_20s_3A_tDNA.mrc zone"" > hide #!16 models > show #!16 models > rename #16 ""job271_20s_3A_RNA.mrc zone"" > select add #17 4 models selected > rename #17 ""job271_20s_3A_AS.mrc zone"" > select subtract #17 2 models selected > select subtract #16 Nothing selected > select add #18 2 models selected > select subtract #18 Nothing selected > rename #18 ""job271_20s_3A_BH.mrc zone"" > select add #18 2 models selected > color #18.1 forest green > select clear > select add #16 2 models selected > color #16.1 red > select add #19 4 models selected > select subtract #19 2 models selected > rename #19 ""job271_20s_3A_TL.mrc zone"" > select add #19 4 models selected > color #16.1#19.1 orange > undo > select subtract #16 2 models selected > color #19.1 orange > select clear > ui tool show ""Volume Viewer"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,5 Model Number: Z1FW00077LL/A Chip: Apple M4 Max Total Number of Cores: 16 (12 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 1 day, 2 hours, 19 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal SyncMaster: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX