id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19766 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.3-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 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 0x00000001f302e240 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 56 in display File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 144 in show_save_file_dialog File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 133 in File ""/Applications/ChimeraX-1.11.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.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.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 59) {""app_name"":""ChimeraX"",""timestamp"":""2026-01-22 15:00:20.00 -0700"",""app_version"":""1.11.0"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.7.3 (24G419)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D791C58D-7C12-4EB0-86D7-89035CF319DB""} { ""uptime"" : 15000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,2"", ""coalitionID"" : 1786, ""osVersion"" : { ""train"" : ""macOS 15.7.3"", ""build"" : ""24G419"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-01-22 14:59:53.7998 -0700"", ""codeSigningMonitor"" : 1, ""incident"" : ""D791C58D-7C12-4EB0-86D7-89035CF319DB"", ""pid"" : 1730, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2026-01-22 08:38:53.9338 -0700"", ""procStartAbsTime"" : 71645756683, ""procExitAbsTime"" : 368638451064, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.0"",""CFBundleVersion"":""1.11.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""19B1409A-0647-5024-A742-D289F8442506"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""090AF90A-6E34-ECA0-0A97-F46B46199692"", ""appleIntelligenceStatus"" : {""state"":""available""}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""293E2FCA-03B0-484B-8504-7236A1A6807C"", ""wakeTime"" : 340, ""sleepWakeUUID"" : ""395E8EE9-D364-4624-8911-5BD18B17C215"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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240000005 }, { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.3, shown at level 0.495, step 1, values float32 Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size 512,512,512, pixel 0.734, shown at level 0.0298, step 2, values float32 Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level 0.00808, step 1, values float32 Log from Tue Jan 20 09:48:17 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/shamiul/Downloads/cryosparc_P1078_J1017_002_volume_map_sharp.mrc Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.3, shown at level 0.239, step 1, values float32 > open ""/Users/shamiul/projects/fks1/Model > Building/Coot/round19_real_space_refined_001-coot-44.pdb"" Summary of feedback from opening /Users/shamiul/projects/fks1/Model Building/Coot/round19_real_space_refined_001-coot-44.pdb --- warnings | Start residue of secondary structure not found: HELIX 9 9 ALA A 236 LYS A 242 1 7 Start residue of secondary structure not found: HELIX 10 10 LYS A 244 MET A 247 1 4 Start residue of secondary structure not found: HELIX 11 11 ALA A 255 ASP A 257 1 3 Start residue of secondary structure not found: HELIX 12 12 ILE A 258 ASN A 260 1 3 End residue of secondary structure not found: HELIX 64 64 ASN A 788 THR A 792 1 5 End residue of secondary structure not found: HELIX 69 69 PRO A 867 GLU A 888 1 22 Start residue of secondary structure not found: HELIX 70 70 ALA A 900 ASP A 906 1 7 Start residue of secondary structure not found: HELIX 71 71 PHE A 910 ILE A 913 1 4 Start residue of secondary structure not found: HELIX 96 96 PHE A 1239 ILE A 1242 1 4 Start residue of secondary structure not found: HELIX 97 97 LEU A 1243 PHE A 1245 1 3 Start residue of secondary structure not found: HELIX 98 98 THR A 1246 GLN A 1256 1 11 End residue of secondary structure not found: HELIX 108 108 SER A 1385 ASP A 1403 1 19 Chain information for round19_real_space_refined_001-coot-44.pdb #2 --- Chain | Description A | No description available > volume #1 level 0.5677 > select add #2 26286 atoms, 26649 bonds, 8 pseudobonds, 1636 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-40.366,0,1,0,75.715,0,0,1,45.059 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.23585,-0.8656,-0.44171,370.28,0.9416,-0.091141,-0.32417,159.44,0.24034,-0.49237,0.83655,114.88 > view matrix models > #2,-0.87113,-0.1611,-0.46386,357.53,0.42268,-0.72682,-0.54136,382.19,-0.24993,-0.66766,0.70126,243.46 > view matrix models > #2,-0.7965,0.49136,0.35236,106.84,-0.5959,-0.73666,-0.31974,510.13,0.10246,-0.46464,0.87955,125.29 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.7965,0.49136,0.35236,147.44,-0.5959,-0.73666,-0.31974,434.86,0.10246,-0.46464,0.87955,75.24 > view matrix models > #2,-0.7965,0.49136,0.35236,156.43,-0.5959,-0.73666,-0.31974,440.13,0.10246,-0.46464,0.87955,75.704 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule round19_real_space_refined_001-coot-44.pdb (#2) to map cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) using 26286 atoms average map value = 0.505, steps = 112 shifted from previous position = 2.31 rotated from previous position = 14.5 degrees atoms outside contour = 16699, contour level = 0.56771 Position of round19_real_space_refined_001-coot-44.pdb (#2) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.66534498 0.63156314 0.39805034 104.96048430 -0.71667873 -0.68964915 -0.10370951 419.37917810 0.20901597 -0.35427681 0.91148246 37.72015838 Axis -0.18100709 0.13655637 -0.97395523 Axis point 135.48156726 190.61539580 0.00000000 Rotation angle (degrees) 136.19963585 Shift along axis 1.53255925 > select clear > volume #1 level 0.4976 > select clear > molmap #2 16 onGrid #1 Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size 256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32 > \ Unknown command: \ > molmap #2 16 onGrid #1 Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size 256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32 > volume #3 level 0.1386 > volume #3 level 0.1278 > volume #3 level 0.1516 > save /Users/shamiul/Desktop/protein1072.mrc models #3 > close #3 > open /Users/shamiul/Downloads/cryosparc_P23_J469_003_volume_map_sharp.mrc Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size 512,512,512, pixel 0.734, shown at level 0.0147, step 2, values float32 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > volume #3 level 0.04773 > view matrix models > #3,-0.079636,0.51981,-0.85056,277.07,-0.97778,-0.20673,-0.03479,415.67,-0.19392,0.82889,0.52472,-22.468 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.079636,0.51981,-0.85056,291.89,-0.97778,-0.20673,-0.03479,408.22,-0.19392,0.82889,0.52472,18.485 > view matrix models > #3,-0.079636,0.51981,-0.85056,307.4,-0.97778,-0.20673,-0.03479,392.49,-0.19392,0.82889,0.52472,9.5176 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.74236,0.66559,-0.076754,248.06,-0.41506,-0.54679,-0.72715,490.4,-0.52595,-0.50796,0.68217,289.63 > view matrix models > #3,0.99436,0.013795,0.10513,7.5729,-0.1047,-0.029291,0.99407,-12.114,0.016792,-0.99948,-0.027681,423.11 > view matrix models > #3,0.98972,0.10493,0.097203,-6.9775,-0.085366,-0.11195,0.99004,0.51616,0.11477,-0.98816,-0.10184,417.62 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.98972,0.10493,0.097203,-72.684,-0.085366,-0.11195,0.99004,-8.2105,0.11477,-0.98816,-0.10184,383.63 > view matrix models > #3,0.98972,0.10493,0.097203,-74.736,-0.085366,-0.11195,0.99004,-5.7417,0.11477,-0.98816,-0.10184,346.72 > view matrix models > #3,0.98972,0.10493,0.097203,-68.072,-0.085366,-0.11195,0.99004,18.491,0.11477,-0.98816,-0.10184,353.16 > view matrix models > #3,0.98972,0.10493,0.097203,-64.416,-0.085366,-0.11195,0.99004,14.455,0.11477,-0.98816,-0.10184,346.38 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.92649,0.020919,0.37573,-93.139,-0.34112,-0.37493,0.86201,137.37,0.15891,-0.92682,-0.34024,374.81 > view matrix models > #3,0.90761,-0.1023,0.40715,-72.932,-0.40588,-0.46162,0.78878,180.49,0.10725,-0.88116,-0.46049,400.25 > view matrix models > #3,0.92552,-0.24841,0.28584,-24.494,-0.37746,-0.54398,0.74941,198.5,-0.030665,-0.80149,-0.59723,438.84 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.92552,-0.24841,0.28584,-19.878,-0.37746,-0.54398,0.74941,201.85,-0.030665,-0.80149,-0.59723,439.42 > view matrix models > #3,0.92552,-0.24841,0.28584,-23.844,-0.37746,-0.54398,0.74941,197.75,-0.030665,-0.80149,-0.59723,433.55 > fitmap #3 inMap #1 Fit map cryosparc_P23_J469_003_volume_map_sharp.mrc in map cryosparc_P1078_J1017_002_volume_map_sharp.mrc using 20242 points correlation = 0.8993, correlation about mean = 0.6277, overlap = 1661 steps = 188, shift = 6.85, angle = 20.8 degrees Position of cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99518294 0.04427809 0.08746640 -46.83296081 -0.04864464 -0.55158245 0.83270073 121.26914196 0.08511534 -0.83294433 -0.54677156 406.40704997 Axis -0.99844649 0.00140931 -0.05570117 Axis point 0.00000000 170.37616190 171.87178256 Rotation angle (degrees) 123.47585517 Shift along axis 24.29376271 > select clear > volume #3 level 0.04242 > volume #1 level 0.5381 > hide #!2 models > show #!2 models > hide #!3 models > color #1 #b2b2b259 models > set bgColor white > color #1 #b2b2b285 models > color #1 #b2b2b2b1 models > volume #1 level 0.4841 > volume #1 level 0.4706 > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > volume #3 level 0.03357 > hide #!2 models > volume #3 level 0.03003 [Repeated 1 time(s)] > surface dust #3 size 7.34 > volume #3 level 0.02472 > show #!2 models > hide #!2 models > show #!2 models > volume #3 level 0.02915 > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > show #!1 models > hide #!2 models > surface dust #1 size 13 > surface dust #3 size 7.34 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.03092 > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.0495 > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > volume #3 level 0.04419 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > volume #1 level 0.4031 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > color #2 black > color #2 #941100ff > color #3 #b2b2ff9d models > color #3 #b2b2ffea models > color #3 #b2b2ffe2 models > color #3 #b2b2ffdc models > color #3 #b2b2ffdb models > volume #3 level 0.03799 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 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 > show #!1 models > hide #!3 models > volume #1 level 0.4638 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > show #!3 models > volume #3 level 0.02915 > hide #!1 models > volume #3 level 0.02472 > volume #3 level 0.03534 > show #!1 models > volume #3 level 0.04242 > volume #1 level 0.4706 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 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 > show #!1 models > volume #1 level 0.4368 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #3 level 0.03711 > hide #!1 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 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.03357 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.04507 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > show #!2 models > color #2 forest green > select #2:1344 24 atoms, 23 bonds, 1 residue, 1 model selected > color sel red > show #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 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 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 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 > show #!1 models > hide #!1 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 > show #!1 models > hide #!1 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 > show #!1 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!1 models > hide #!1 models > select /A:625 20 atoms, 20 bonds, 1 residue, 1 model selected > select /A:624 21 atoms, 21 bonds, 1 residue, 1 model selected > select /A:625 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > select /A:624 21 atoms, 21 bonds, 1 residue, 1 model selected > color sel red > show sel atoms > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > select /A:623 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > show #!3 models > hide #!1 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select /A:629 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > hide #!1 models > select /A:1344 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!1 models > volume #3 level 0.05392 > volume #3 level 0.0495 > select /A:628 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.4031 > hide #!1 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 > show #!1 models > hide #!1 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 > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.04065 > volume #3 level 0.0318 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > select /A:604 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > hide #!1 models > select /A:231 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.04861 > hide #!1 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 > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4571 > hide #!1 models > select /A:603 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > hide #!1 models > select /A:605 24 atoms, 25 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.5381 > volume #1 level 0.7948 > volume #1 level 0.4436 > volume #1 level 0.4706 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.8353 > volume #1 level 0.4706 > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > volume #3 level 0.03357 > show #!1 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > hide #!3 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.02826 > volume #3 level 0.03357 > volume #3 level 0.04065 > show #!1 models > volume #1 level 0.3828 > hide #!1 models > volume #3 level 0.03622 > volume #3 level 0.03357 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4301 > volume #1 level 0.4503 > volume #1 level 0.4436 > show #!3 models > volume #3 level 0.05127 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.04596 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #1 level 0.4031 > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!3 models > open 33154 fromDatabase emdb_fits format ccp4 Summary of feedback from opening 33154 fetched from emdb_fits --- notes | Fetching compressed map 33154 from https://files.wwpdb.org/pub/emdb/structures/EMD-33154/map/emd_33154.map.gz Fetching map header 33154 from https://files.wwpdb.org/pub/emdb/structures/EMD-33154/header/emd-33154.xml Fetching compressed mmCIF 7xe4 from http://files.rcsb.org/download/7xe4.cif Fetching CCD C14 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/C14/C14.cif Fetching CCD D10 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/D10/D10.cif Fetching CCD D12 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/D12/D12.cif Fetching CCD DD9 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/DD9/DD9.cif Fetching CCD HP6 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/HP6/HP6.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif Fetching CCD XKP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XKP/XKP.cif Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level 0.01, step 1, values float32, fit PDB 7xe4 7xe4 title: structure of a membrane-bound glycosyltransferase [more info...] Chain information for 7xe4 #5 --- Chain | Description | UniProt F | 1,3-beta-glucan synthase component FKS1 | FKS1_YEAST 1-1876 Non-standard residues in 7xe4 #5 --- C14 — tetradecane D10 — decane D12 — dodecane DD9 — nonane HP6 — heptane NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) XKP — (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate > select add #5 12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 3 models selected > select add #4 12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 5 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292,#5,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684,#5,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182,#5,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659,#5,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03,#5,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596,#5,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596 > fitmap #4 inMap #1 Fit map emdb 33154 in map cryosparc_P1078_J1017_002_volume_map_sharp.mrc using 104898 points correlation = 0.8147, correlation about mean = 0.471, overlap = 1137 steps = 108, shift = 4.72, angle = 10.5 degrees Position of emdb 33154 (#4) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.77559150 0.44110259 -0.45153775 245.46031073 -0.19104122 0.51774969 0.83392956 51.53255230 0.60163202 0.73305099 -0.31729348 58.39718054 Axis -0.08185163 -0.85452901 -0.51291372 Axis point 118.21635546 0.00000000 61.69084670 Rotation angle (degrees) 141.95878126 Shift along axis -94.08010205 > fitmap #5 inMap #1 Fit molecule 7xe4 (#5) to map cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) using 12529 atoms average map value = 0.5176, steps = 108 shifted from previous position = 4.28 rotated from previous position = 10.4 degrees atoms outside contour = 5925, contour level = 0.40307 Position of 7xe4 (#5) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.77580956 0.44096383 -0.45129860 245.45501288 -0.19028465 0.51843695 0.83367553 51.42373913 0.60159063 0.73264864 -0.31829969 58.48259859 Axis -0.08201767 -0.85477760 -0.51247278 Axis point 118.18885277 0.00000000 61.73225462 Rotation angle (degrees) 141.98375373 Shift along axis -94.05824869 > volume #4 level 0.01035 > surface dust #4 size 9.2 > volume #4 level 0.008252 > volume #4 level 0.009126 > select clear > hide #!2 models > hide #!5 models > show #!1 models > hide #!1 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.007727 > show #!5 models > hide #!3 models > color #4 #ffb2ff7f models > color #4 #ffb2ffa2 models > color #4 #ffb2ffd0 models > color #4 #ffb2ffd1 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > color #5 #941100ff > color #4 #ffb2ffaa models > color #4 #ffb2ffab models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > volume #4 level 0.00965 > volume #4 level 0.006328 > volume #4 level 0.009126 > show #!1 models > hide #!1 models > show #!3 models > volume #3 level 0.0285 > volume #4 level 0.009126 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > show #!1 models > hide #!1 models > show #!3 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > hide #!5 models > hide #!3 models > hide #!4 models > show #!5 models > color #5 #0433ffff > select #5/F:1357 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/F:639 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > select #5/F:619 14 atoms, 15 bonds, 1 residue, 1 model selected > select #5/F:617 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/F:618 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > hide #!1 models > show #!4 models > volume #4 level 0.008601 > fitmap #5 inMap #4 Fit molecule 7xe4 (#5) to map emdb 33154 (#4) using 12529 atoms average map value = 0.0173, steps = 56 shifted from previous position = 0.0796 rotated from previous position = 0.0627 degrees atoms outside contour = 2448, contour level = 0.0086013 Position of 7xe4 (#5) relative to emdb 33154 (#4) coordinates: Matrix rotation and translation 1.00000000 0.00005862 0.00004014 -0.00661266 -0.00005862 1.00000000 -0.00007132 0.02208420 -0.00004015 0.00007131 1.00000000 -0.00293560 Axis 0.70843877 0.39881019 -0.58229283 Axis point 0.00000000 -6.44294241 277.04962384 Rotation angle (degrees) 0.00576774 Shift along axis 0.00583212 > volume #4 level 0.008601 > show #!3 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!4 models > hide #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!1 models > hide #!2 models > show #!4 models > volume #1 level 0.4236 > volume #4 level 0.009126 > volume #1 level 0.4133 > show #!2 models > hide #!2 models > hide #!4 models > hide #!1 models > show #!1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!1 models > show #!2 models > hide #!2 models > volume #4 level 0.008077 > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > hide #!4 models > show #!4 models > show #!1 models > hide #!4 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4031 > volume #1 level 0.4133 > volume #1 level 0.4031 > surface dust #1 size 13 > ui tool show ""Hide Dust"" > surface dust #1 size 1.3 > surface undust #1 > volume #1 level 0.4338 > volume #1 level 0.5363 > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > select #2:1248 Nothing selected > select #2:1209 12 atoms, 11 bonds, 1 residue, 1 model selected > hide #!3 models > show sel atoms > color sel orange red > show #!4 models > hide #!4 models > show #!1 models > volume #1 level 0.3826 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.02985 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.4338 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models Desktop color scheme is light > view matrix models > #2,-0.66534,0.63156,0.39805,104.96,-0.71668,-0.68965,-0.10371,419.38,0.20902,-0.35428,0.91148,37.72 [Repeated 2 time(s)] > show #!1 models > volume #1 level 0.4953 > show #!4 models > show #!2 models > hide #!4 models > hide #!1 models > show #!1 models > save /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs includeMaps true ——— End of log from Tue Jan 20 09:48:17 2026 ——— > view name session-start opened ChimeraX session > open /Users/shamiul/Downloads/cryosparc_P1078_J1041_002_volume_map_sharp.mrc Opened cryosparc_P1078_J1041_002_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.3, shown at level 0.232, step 1, values float32 > volume #6 level 0.5479 > close #1 > hide #!2 models > show #!2 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > volume #6 level 0.4522 > surface dust #6 size 13 > volume #6 level 0.3949 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > color #6 #b2b2b2e6 models > color #6 #b2b2b2d8 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > volume #3 level 0.0285 > volume #3 level 0.03387 > volume #3 level 0.03924 > volume #3 level 0.05536 > hide #!2 models > volume #3 level 0.0379 > select #2: 625-633, 676-686, 1341-1344 440 atoms, 445 bonds, 24 residues, 1 model selected > show #!2 models > select #2: 625-633, 676-686, 1341-1344 col yellow target C Expected a keyword > select #2: 625-633, 676-686, 1341-1344 col yellow target c Expected a keyword > color sel light sea green > color sel hot pink > color #3 #b2b2ffc2 models > select #3 2 models selected > select #2: 625-633, 676-686, 1341-1344 col yellow target c Expected a keyword > select #2: 625-633, 676-686, 1341-1344 440 atoms, 445 bonds, 24 residues, 1 model selected > color sel red > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > volume #6 level 0.4235 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > volume #3 level 0.02985 > hide #!3 models > show #!6 models > volume #6 level 0.3949 > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > volume #3 level 0.02716 > surface dust #3 size 7.34 > volume #3 level 0.0285 > volume #3 level 0.03119 > show #!6 models > volume #6 level 0.3757 > volume #6 level 0.4044 > volume #3 level 0.03656 > volume #6 level 0.4235 > volume #3 level 0.04864 > volume #6 level 0.5192 > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #6 level 0.4427 > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > volume #3 level 0.04327 > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > show #!2 models > select clear > volume #6 level 0.4427 > volume #3 level 0.02582 > volume #6 level 0.3757 > open /Users/shamiul/Downloads/cryosparc_P1078_J1017_002_volume_map_sharp.mrc Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.3, shown at level 0.239, step 1, values float32 > volume #1 level 0.5467 > hide #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.04059 > volume #3 level 0.02447 > volume #3 level 0.02985 > volume #3 level 0.02447 > volume #3 level 0.02716 > show #!6 models > volume #6 level 0.3949 > hide #!2 models > show #!1 models > hide #!1 models > hide #!6 models > show #!6 models > hide #!6 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4471 > surface dust #1 size 13 > volume #1 level 0.3775 > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!6 models > show #!2 models > hide #!2 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!6 models > show #!6 models > volume #6 level 0.4413 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.0389 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > volume #6 level 0.4041 > hide #!3 models > show #!3 models > volume #6 level 0.3949 > show #!2 models > hide #!2 models > open /Users/shamiul/projects/fks1/round18_aligntocaspo-coot-8.pdb Chain information for round18_aligntocaspo-coot-8.pdb #7 --- Chain | Description A | No description available > matchmaker #7 to #2 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 round19_real_space_refined_001-coot-44.pdb, chain A (#2) with round18_aligntocaspo-coot-8.pdb, chain A (#7), sequence alignment score = 6930.2 RMSD between 1423 pruned atom pairs is 0.575 angstroms; (across all 1636 pairs: 4.230) > molmap #7 16 onGrid 6 Invalid ""onGrid"" argument: invalid density map specifier > hide #!3 models > ui tool show ""Fit in Map"" > fitmap #7 inMap #6 Fit molecule round18_aligntocaspo-coot-8.pdb (#7) to map cryosparc_P1078_J1041_002_volume_map_sharp.mrc (#6) using 28257 atoms average map value = 0.4365, steps = 60 shifted from previous position = 0.0995 rotated from previous position = 0.292 degrees atoms outside contour = 15905, contour level = 0.39486 Position of round18_aligntocaspo-coot-8.pdb (#7) relative to cryosparc_P1078_J1041_002_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.99974929 -0.01555337 -0.01610747 359.00321150 -0.02111031 0.41492603 0.90961021 -79.40764228 -0.00746409 0.90972220 -0.41515034 70.51887473 Axis 0.01089752 -0.84110706 -0.54075887 Axis point 178.85260398 0.00000000 61.33327506 Rotation angle (degrees) 179.70560747 Shift along axis 32.56886537 > molmap #7 16 onGrid #6 Opened round18_aligntocaspo-coot-8.pdb map 16 as #8, grid size 256,256,256, pixel 1.3, shown at level 0.0593, step 1, values float32 > hide #7 models > show #7 models > hide #!6 models > volume #8 level 0.06604 > save /Users/shamiul/Desktop/protein1041.mrc models #8 > volume #8 level 0.1571 > hide #7 models > show #!6 models > volume #8 level 0.1651 > hide #!8 models > volume #6 level 0.3949 > show #!8 models > volume #8 level 0.151 > open /Users/shamiul/Downloads/cryosparc_P1078_J1048_003_volume_map_sharp.mrc Opened cryosparc_P1078_J1048_003_volume_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.3, shown at level 0.236, step 1, values float32 > hide #!6 models > show #!6 models > hide #!8 models > volume #9 level 0.5183 > hide #!6 models > surface dust #9 size 13 > volume #9 level 0.3995 > show #!3 models > hide #!3 models > volume #9 level 0.4143 > show #!3 models > hide #!3 models > volume #9 level 0.3921 > color #9 silver models > close #6 > volume #9 level 0.3728 > volume #9 level 0.4017 > show #!3 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > fitmap #9 inMap #3 Fit map cryosparc_P1078_J1048_003_volume_map_sharp.mrc in map cryosparc_P23_J469_003_volume_map_sharp.mrc using 52265 points correlation = 0.8411, correlation about mean = 0.7355, overlap = 2719 steps = 64, shift = 0.137, angle = 0.284 degrees Position of cryosparc_P1078_J1048_003_volume_map_sharp.mrc (#9) relative to cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.99562998 -0.04508186 0.08178364 17.79528418 0.04351058 -0.55095466 -0.83340013 407.68451908 0.08263030 0.83331661 -0.54658544 125.90881048 Axis 0.99859019 -0.00050727 0.05307893 Axis point 0.00000000 170.27130670 172.32267538 Rotation angle (degrees) 123.43255903 Shift along axis 24.24649662 > 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 > hide #!9 models > show #!9 models > volume #3 level 0.02904 > hide #!9 models > show #!9 models > hide #!9 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.00936 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > fitmap #4 inMap #3 Fit map emdb 33154 in map cryosparc_P23_J469_003_volume_map_sharp.mrc using 116253 points correlation = 0.5847, correlation about mean = 0.3523, overlap = 99 steps = 72, shift = 0.181, angle = 0.177 degrees Position of emdb 33154 (#4) relative to cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.71048798 0.47703780 -0.51734105 264.67558202 -0.43239360 -0.87595053 -0.21388416 341.14525553 -0.55519599 0.07173283 0.82862042 157.39209429 Axis 0.29939554 0.03968112 -0.95330358 Axis point 202.77925698 136.32398446 -0.00000000 Rotation angle (degrees) 151.51104117 Shift along axis -57.26273245 > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!9 models > hide #!9 models > show #!9 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > volume #9 level 0.4111 > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > volume #3 level 0.02644 > show #!9 models > volume #9 level 0.4111 > hide #!3 models > show #!3 models > hide #!9 models > volume #3 level 0.02644 > show #!2 models > show #!9 models > hide #!9 models > show #!9 models > hide #!3 models > fitmap #2 inMap #9 Fit molecule round19_real_space_refined_001-coot-44.pdb (#2) to map cryosparc_P1078_J1048_003_volume_map_sharp.mrc (#9) using 26286 atoms average map value = 0.4951, steps = 28 shifted from previous position = 0.0281 rotated from previous position = 0.0329 degrees atoms outside contour = 13242, contour level = 0.41108 Position of round19_real_space_refined_001-coot-44.pdb (#2) relative to cryosparc_P1078_J1048_003_volume_map_sharp.mrc (#9) coordinates: Matrix rotation and translation -0.66233458 0.63252332 0.40153103 103.73969491 -0.71883862 -0.68755706 -0.10264664 419.32753451 0.21114910 -0.35662243 0.91007500 38.03008402 Axis -0.18296144 0.13714910 -0.97350667 Axis point 135.16573018 190.78373405 0.00000000 Rotation angle (degrees) 136.04691145 Shift along axis 1.50749046 > color #9 #c0c0c0ce models > color #9 #c0c0c0cf models > show #!3 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > volume #3 level 0.02644 > hide #!9 models > volume #3 level 0.03109 > volume #3 level 0.04132 > show #!9 models > hide #!9 models > show #!9 models > volume #9 level 0.4378 > hide #!9 models > volume #3 level 0.03202 > volume #3 level 0.03109 > volume #3 level 0.02644 > volume #3 level 0.04039 > volume #3 level 0.02458 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.02551 > volume #3 level 0.02644 > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > volume #3 level 0.03481 > hide #!2 models > hide #!3 models > show #!3 models QPainter::begin: Paint device returned engine == 0, type: 2 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.3, shown at level 0.495, step 1, values float32 Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size 512,512,512, pixel 0.734, shown at level 0.0298, step 2, values float32 Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level 0.00808, step 1, values float32 Log from Tue Jan 20 09:48:17 2026UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/shamiul/Downloads/cryosparc_P1078_J1017_002_volume_map_sharp.mrc Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.3, shown at level 0.239, step 1, values float32 > open ""/Users/shamiul/projects/fks1/Model > Building/Coot/round19_real_space_refined_001-coot-44.pdb"" Summary of feedback from opening /Users/shamiul/projects/fks1/Model Building/Coot/round19_real_space_refined_001-coot-44.pdb --- warnings | Start residue of secondary structure not found: HELIX 9 9 ALA A 236 LYS A 242 1 7 Start residue of secondary structure not found: HELIX 10 10 LYS A 244 MET A 247 1 4 Start residue of secondary structure not found: HELIX 11 11 ALA A 255 ASP A 257 1 3 Start residue of secondary structure not found: HELIX 12 12 ILE A 258 ASN A 260 1 3 End residue of secondary structure not found: HELIX 64 64 ASN A 788 THR A 792 1 5 End residue of secondary structure not found: HELIX 69 69 PRO A 867 GLU A 888 1 22 Start residue of secondary structure not found: HELIX 70 70 ALA A 900 ASP A 906 1 7 Start residue of secondary structure not found: HELIX 71 71 PHE A 910 ILE A 913 1 4 Start residue of secondary structure not found: HELIX 96 96 PHE A 1239 ILE A 1242 1 4 Start residue of secondary structure not found: HELIX 97 97 LEU A 1243 PHE A 1245 1 3 Start residue of secondary structure not found: HELIX 98 98 THR A 1246 GLN A 1256 1 11 End residue of secondary structure not found: HELIX 108 108 SER A 1385 ASP A 1403 1 19 Chain information for round19_real_space_refined_001-coot-44.pdb #2 --- Chain | Description A | No description available > volume #1 level 0.5677 > select add #2 26286 atoms, 26649 bonds, 8 pseudobonds, 1636 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-40.366,0,1,0,75.715,0,0,1,45.059 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.23585,-0.8656,-0.44171,370.28,0.9416,-0.091141,-0.32417,159.44,0.24034,-0.49237,0.83655,114.88 > view matrix models > #2,-0.87113,-0.1611,-0.46386,357.53,0.42268,-0.72682,-0.54136,382.19,-0.24993,-0.66766,0.70126,243.46 > view matrix models > #2,-0.7965,0.49136,0.35236,106.84,-0.5959,-0.73666,-0.31974,510.13,0.10246,-0.46464,0.87955,125.29 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.7965,0.49136,0.35236,147.44,-0.5959,-0.73666,-0.31974,434.86,0.10246,-0.46464,0.87955,75.24 > view matrix models > #2,-0.7965,0.49136,0.35236,156.43,-0.5959,-0.73666,-0.31974,440.13,0.10246,-0.46464,0.87955,75.704 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule round19_real_space_refined_001-coot-44.pdb (#2) to map cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) using 26286 atoms average map value = 0.505, steps = 112 shifted from previous position = 2.31 rotated from previous position = 14.5 degrees atoms outside contour = 16699, contour level = 0.56771 Position of round19_real_space_refined_001-coot-44.pdb (#2) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.66534498 0.63156314 0.39805034 104.96048430 -0.71667873 -0.68964915 -0.10370951 419.37917810 0.20901597 -0.35427681 0.91148246 37.72015838 Axis -0.18100709 0.13655637 -0.97395523 Axis point 135.48156726 190.61539580 0.00000000 Rotation angle (degrees) 136.19963585 Shift along axis 1.53255925 > select clear > volume #1 level 0.4976 > select clear > molmap #2 16 onGrid #1 Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size 256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32 > \ Unknown command: \ > molmap #2 16 onGrid #1 Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size 256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32 > volume #3 level 0.1386 > volume #3 level 0.1278 > volume #3 level 0.1516 > save /Users/shamiul/Desktop/protein1072.mrc models #3 > close #3 > open /Users/shamiul/Downloads/cryosparc_P23_J469_003_volume_map_sharp.mrc Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size 512,512,512, pixel 0.734, shown at level 0.0147, step 2, values float32 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > volume #3 level 0.04773 > view matrix models > #3,-0.079636,0.51981,-0.85056,277.07,-0.97778,-0.20673,-0.03479,415.67,-0.19392,0.82889,0.52472,-22.468 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.079636,0.51981,-0.85056,291.89,-0.97778,-0.20673,-0.03479,408.22,-0.19392,0.82889,0.52472,18.485 > view matrix models > #3,-0.079636,0.51981,-0.85056,307.4,-0.97778,-0.20673,-0.03479,392.49,-0.19392,0.82889,0.52472,9.5176 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.74236,0.66559,-0.076754,248.06,-0.41506,-0.54679,-0.72715,490.4,-0.52595,-0.50796,0.68217,289.63 > view matrix models > #3,0.99436,0.013795,0.10513,7.5729,-0.1047,-0.029291,0.99407,-12.114,0.016792,-0.99948,-0.027681,423.11 > view matrix models > #3,0.98972,0.10493,0.097203,-6.9775,-0.085366,-0.11195,0.99004,0.51616,0.11477,-0.98816,-0.10184,417.62 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.98972,0.10493,0.097203,-72.684,-0.085366,-0.11195,0.99004,-8.2105,0.11477,-0.98816,-0.10184,383.63 > view matrix models > #3,0.98972,0.10493,0.097203,-74.736,-0.085366,-0.11195,0.99004,-5.7417,0.11477,-0.98816,-0.10184,346.72 > view matrix models > #3,0.98972,0.10493,0.097203,-68.072,-0.085366,-0.11195,0.99004,18.491,0.11477,-0.98816,-0.10184,353.16 > view matrix models > #3,0.98972,0.10493,0.097203,-64.416,-0.085366,-0.11195,0.99004,14.455,0.11477,-0.98816,-0.10184,346.38 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.92649,0.020919,0.37573,-93.139,-0.34112,-0.37493,0.86201,137.37,0.15891,-0.92682,-0.34024,374.81 > view matrix models > #3,0.90761,-0.1023,0.40715,-72.932,-0.40588,-0.46162,0.78878,180.49,0.10725,-0.88116,-0.46049,400.25 > view matrix models > #3,0.92552,-0.24841,0.28584,-24.494,-0.37746,-0.54398,0.74941,198.5,-0.030665,-0.80149,-0.59723,438.84 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.92552,-0.24841,0.28584,-19.878,-0.37746,-0.54398,0.74941,201.85,-0.030665,-0.80149,-0.59723,439.42 > view matrix models > #3,0.92552,-0.24841,0.28584,-23.844,-0.37746,-0.54398,0.74941,197.75,-0.030665,-0.80149,-0.59723,433.55 > fitmap #3 inMap #1 Fit map cryosparc_P23_J469_003_volume_map_sharp.mrc in map cryosparc_P1078_J1017_002_volume_map_sharp.mrc using 20242 points correlation = 0.8993, correlation about mean = 0.6277, overlap = 1661 steps = 188, shift = 6.85, angle = 20.8 degrees Position of cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99518294 0.04427809 0.08746640 -46.83296081 -0.04864464 -0.55158245 0.83270073 121.26914196 0.08511534 -0.83294433 -0.54677156 406.40704997 Axis -0.99844649 0.00140931 -0.05570117 Axis point 0.00000000 170.37616190 171.87178256 Rotation angle (degrees) 123.47585517 Shift along axis 24.29376271 > select clear > volume #3 level 0.04242 > volume #1 level 0.5381 > hide #!2 models > show #!2 models > hide #!3 models > color #1 #b2b2b259 models > set bgColor white > color #1 #b2b2b285 models > color #1 #b2b2b2b1 models > volume #1 level 0.4841 > volume #1 level 0.4706 > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > volume #3 level 0.03357 > hide #!2 models > volume #3 level 0.03003 [Repeated 1 time(s)] > surface dust #3 size 7.34 > volume #3 level 0.02472 > show #!2 models > hide #!2 models > show #!2 models > volume #3 level 0.02915 > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > show #!1 models > hide #!2 models > surface dust #1 size 13 > surface dust #3 size 7.34 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.03092 > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.0495 > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > volume #3 level 0.04419 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > volume #1 level 0.4031 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > color #2 black > color #2 #941100ff > color #3 #b2b2ff9d models > color #3 #b2b2ffea models > color #3 #b2b2ffe2 models > color #3 #b2b2ffdc models > color #3 #b2b2ffdb models > volume #3 level 0.03799 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 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 > show #!1 models > hide #!3 models > volume #1 level 0.4638 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!2 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > show #!3 models > volume #3 level 0.02915 > hide #!1 models > volume #3 level 0.02472 > volume #3 level 0.03534 > show #!1 models > volume #3 level 0.04242 > volume #1 level 0.4706 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 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 > show #!1 models > volume #1 level 0.4368 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #3 level 0.03711 > hide #!1 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 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.03357 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.04507 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > show #!2 models > color #2 forest green > select #2:1344 24 atoms, 23 bonds, 1 residue, 1 model selected > color sel red > show #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 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 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 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 > show #!1 models > hide #!1 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 > show #!1 models > hide #!1 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 > show #!1 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!1 models > hide #!1 models > select /A:625 20 atoms, 20 bonds, 1 residue, 1 model selected > select /A:624 21 atoms, 21 bonds, 1 residue, 1 model selected > select /A:625 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > select /A:624 21 atoms, 21 bonds, 1 residue, 1 model selected > color sel red > show sel atoms > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > select /A:623 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > show #!3 models > hide #!1 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select /A:629 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > hide #!1 models > select /A:1344 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!1 models > volume #3 level 0.05392 > volume #3 level 0.0495 > select /A:628 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.4031 > hide #!1 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 > show #!1 models > hide #!1 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 > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.04065 > volume #3 level 0.0318 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > select /A:604 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > hide #!1 models > select /A:231 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.04861 > hide #!1 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 > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4571 > hide #!1 models > select /A:603 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > show #!1 models > hide #!1 models > select /A:605 24 atoms, 25 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.5381 > volume #1 level 0.7948 > volume #1 level 0.4436 > volume #1 level 0.4706 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.8353 > volume #1 level 0.4706 > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > volume #3 level 0.03357 > show #!1 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!3 models > show #!1 models > hide #!1 models > hide #!3 models > show #!1 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.02826 > volume #3 level 0.03357 > volume #3 level 0.04065 > show #!1 models > volume #1 level 0.3828 > hide #!1 models > volume #3 level 0.03622 > volume #3 level 0.03357 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4301 > volume #1 level 0.4503 > volume #1 level 0.4436 > show #!3 models > volume #3 level 0.05127 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > volume #3 level 0.04596 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > volume #1 level 0.4031 > hide #!1 models > show #!1 models > hide #!3 models > hide #!1 models > show #!3 models > open 33154 fromDatabase emdb_fits format ccp4 Summary of feedback from opening 33154 fetched from emdb_fits --- notes | Fetching compressed map 33154 from https://files.wwpdb.org/pub/emdb/structures/EMD-33154/map/emd_33154.map.gz Fetching map header 33154 from https://files.wwpdb.org/pub/emdb/structures/EMD-33154/header/emd-33154.xml Fetching compressed mmCIF 7xe4 from http://files.rcsb.org/download/7xe4.cif Fetching CCD C14 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/C14/C14.cif Fetching CCD D10 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/D10/D10.cif Fetching CCD D12 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/D12/D12.cif Fetching CCD DD9 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/DD9/DD9.cif Fetching CCD HP6 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/HP6/HP6.cif Fetching CCD NAG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif Fetching CCD XKP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XKP/XKP.cif Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level 0.01, step 1, values float32, fit PDB 7xe4 7xe4 title: structure of a membrane-bound glycosyltransferase [more info...] Chain information for 7xe4 #5 --- Chain | Description | UniProt F | 1,3-beta-glucan synthase component FKS1 | FKS1_YEAST 1-1876 Non-standard residues in 7xe4 #5 --- C14 — tetradecane D10 — decane D12 — dodecane DD9 — nonane HP6 — heptane NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) XKP — (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate > select add #5 12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 3 models selected > select add #4 12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 5 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292,#5,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684,#5,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182,#5,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659,#5,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03,#5,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596,#5,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596 > fitmap #4 inMap #1 Fit map emdb 33154 in map cryosparc_P1078_J1017_002_volume_map_sharp.mrc using 104898 points correlation = 0.8147, correlation about mean = 0.471, overlap = 1137 steps = 108, shift = 4.72, angle = 10.5 degrees Position of emdb 33154 (#4) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.77559150 0.44110259 -0.45153775 245.46031073 -0.19104122 0.51774969 0.83392956 51.53255230 0.60163202 0.73305099 -0.31729348 58.39718054 Axis -0.08185163 -0.85452901 -0.51291372 Axis point 118.21635546 0.00000000 61.69084670 Rotation angle (degrees) 141.95878126 Shift along axis -94.08010205 > fitmap #5 inMap #1 Fit molecule 7xe4 (#5) to map cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) using 12529 atoms average map value = 0.5176, steps = 108 shifted from previous position = 4.28 rotated from previous position = 10.4 degrees atoms outside contour = 5925, contour level = 0.40307 Position of 7xe4 (#5) relative to cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.77580956 0.44096383 -0.45129860 245.45501288 -0.19028465 0.51843695 0.83367553 51.42373913 0.60159063 0.73264864 -0.31829969 58.48259859 Axis -0.08201767 -0.85477760 -0.51247278 Axis point 118.18885277 0.00000000 61.73225462 Rotation angle (degrees) 141.98375373 Shift along axis -94.05824869 > volume #4 level 0.01035 > surface dust #4 size 9.2 > volume #4 level 0.008252 > volume #4 level 0.009126 > select clear > hide #!2 models > hide #!5 models > show #!1 models > hide #!1 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.007727 > show #!5 models > hide #!3 models > color #4 #ffb2ff7f models > color #4 #ffb2ffa2 models > color #4 #ffb2ffd0 models > color #4 #ffb2ffd1 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > color #5 #941100ff > color #4 #ffb2ffaa models > color #4 #ffb2ffab models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > volume #4 level 0.00965 > volume #4 level 0.006328 > volume #4 level 0.009126 > show #!1 models > hide #!1 models > show #!3 models > volume #3 level 0.0285 > volume #4 level 0.009126 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > show #!1 models > hide #!1 models > show #!3 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > hide #!5 models > hide #!3 models > hide #!4 models > show #!5 models > color #5 #0433ffff > select #5/F:1357 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5/F:639 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > select #5/F:619 14 atoms, 15 bonds, 1 residue, 1 model selected > select #5/F:617 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/F:618 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!1 models > hide #!1 models > show #!4 models > volume #4 level 0.008601 > fitmap #5 inMap #4 Fit molecule 7xe4 (#5) to map emdb 33154 (#4) using 12529 atoms average map value = 0.0173, steps = 56 shifted from previous position = 0.0796 rotated from previous position = 0.0627 degrees atoms outside contour = 2448, contour level = 0.0086013 Position of 7xe4 (#5) relative to emdb 33154 (#4) coordinates: Matrix rotation and translation 1.00000000 0.00005862 0.00004014 -0.00661266 -0.00005862 1.00000000 -0.00007132 0.02208420 -0.00004015 0.00007131 1.00000000 -0.00293560 Axis 0.70843877 0.39881019 -0.58229283 Axis point 0.00000000 -6.44294241 277.04962384 Rotation angle (degrees) 0.00576774 Shift along axis 0.00583212 > volume #4 level 0.008601 > show #!3 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!4 models > hide #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!1 models > hide #!2 models > show #!4 models > volume #1 level 0.4236 > volume #4 level 0.009126 > volume #1 level 0.4133 > show #!2 models > hide #!2 models > hide #!4 models > hide #!1 models > show #!1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!1 models > show #!2 models > hide #!2 models > volume #4 level 0.008077 > show #!2 models > hide #!2 models > show #!5 models > hide #!5 models > hide #!4 models > show #!4 models > show #!1 models > hide #!4 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > volume #1 level 0.4031 > volume #1 level 0.4133 > volume #1 level 0.4031 > surface dust #1 size 13 > ui tool show ""Hide Dust"" > surface dust #1 size 1.3 > surface undust #1 > volume #1 level 0.4338 > volume #1 level 0.5363 > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > select #2:1248 Nothing selected > select #2:1209 12 atoms, 11 bonds, 1 residue, 1 model selected > hide #!3 models > show sel atoms > color sel orange red > show #!4 models > hide #!4 models > show #!1 models > volume #1 level 0.3826 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > volume #3 level 0.02985 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.4338 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models Desktop color scheme is light > view matrix models > #2,-0.66534,0.63156,0.39805,104.96,-0.71668,-0.68965,-0.10371,419.38,0.20902,-0.35428,0.91148,37.72 [Repeated 2 time(s)] > show #!1 models > volume #1 level 0.4953 > show #!4 models > show #!2 models > hide #!4 models > hide #!1 models > show #!1 models > save /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs includeMaps true ——— End of log from Tue Jan 20 09:48:17 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 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 Air Model Identifier: Mac14,2 Model Number: MLY33LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 13822.61.10 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.3 (24G419) Kernel Version: Darwin 24.6.0 Time since boot: 7 hours, 13 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL E2414H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 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 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: 2.7.11 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: 7.13.0 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: 4.25.1 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: 3.2.5 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 pytz: 2025.2 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: 4.0.0 roman-numerals-py: 4.0.0 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 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: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 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 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 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 can't reproduce all ChimeraX