id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18791 Crash adding/removing screen chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000206ede0c0 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 58) {""app_name"":""ChimeraX"",""timestamp"":""2025-09-15 16:33:57.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.6.1 (24G90)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""D8877FFD-4296-4FBA-BD64-95006A1EB105""} { ""uptime"" : 290000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 20777, ""osVersion"" : { ""train"" : ""macOS 15.6.1"", ""build"" : ""24G90"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-09-15 16:25:58.4168 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""D8877FFD-4296-4FBA-BD64-95006A1EB105"", ""pid"" : 70773, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-09-15 11:14:03.7551 +0200"", ""procStartAbsTime"" : 6704722841860, ""procExitAbsTime"" : 7064666746523, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""FC77DEA8-EFEC-53B8-9DCD-DE68212CBB52"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D44B6B49-C8F1-50A4-92F9-95517B6FFFA5"", ""appleIntelligenceStatus"" : {""reasons"":[""selectedLanguageDoesNotMatchSelectedSiriLanguage""],""state"":""unavailable""}, ""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"" : ""5A388A98-9F64-4059-8DE6-4EFB88EF0C3D"", ""wakeTime"" : 28, ""sleepWakeUUID"" : ""264931FD-25BC-4C11-8BD2-DC7EA08B4B6E"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x298c76d39ef8 is not in any region. 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bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /Users/leahoffmann/Desktop/MsbA/maps/reference/map Current working directory is: /Users/leahoffmann/Desktop/MsbA/maps/reference/map > open *.mrc Opened A18_wide.mrc as #1.1, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.164, step 1, values float32 Opened A18_wider.mrc as #1.2, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.132, step 1, values float32 Opened A835_narrow.mrc as #1.3, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0969, step 1, values float32 Opened A835_wide.mrc as #1.4, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0851, step 1, values float32 Opened A835_wider.mrc as #1.5, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.0942, step 1, values float32 Opened DDM.mrc as #1.6, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.319, step 1, values float32 Opened GDN_narrow.mrc as #1.7, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.147, step 1, values float32 Opened GDN_wide.mrc as #1.8, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.16, step 1, values float32 Opened LMNG_narrow.mrc as #1.9, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.137, step 1, values float32 Opened LMNG_wide.mrc as #1.10, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.156, step 1, values float32 Opened MSP1D1-PC.mrc as #1.11, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.139, step 1, values float32 Opened MSP1D1.mrc as #1.12, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.128, step 1, values float32 Opened MSP1E3D1.mrc as #1.13, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.194, step 1, values float32 Opened MSP2N2_narrow.mrc as #1.14, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.138, step 1, values float32 Opened MSP2N2_wide.mrc as #1.15, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.106, step 1, values float32 Opened Triton_wide.mrc as #1.16, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.107, step 1, values float32 Opened Triton_wider.mrc as #1.17, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.106, step 1, values float32 Opened UDM_narrow.mrc as #1.18, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.217, step 1, values float32 Opened UDM_wide.mrc as #1.19, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.12, step 1, values float32 Opened UDM_wider.mrc as #1.20, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.108, step 1, values float32 Opened peptidisc_narrow.mrc as #1.21, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.13, step 1, values float32 Opened peptidisc_narrower.mrc as #1.22, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.135, step 1, values float32 > cd /Users/leahoffmann/Desktop/MsbA/maps/reference/model Current working directory is: /Users/leahoffmann/Desktop/MsbA/maps/reference/model > open *.pdb Chain information for A18_wide.pdb #2 --- Chain | Description A B | No description available Chain information for A18_wider.pdb #3 --- Chain | Description A B | No description available Chain information for A835_narrow.pdb #4 --- Chain | Description A B | No description available Chain information for A835_wide.pdb #5 --- Chain | Description A B | No description available Chain information for A835_wider.pdb #6 --- Chain | Description A B | No description available Chain information for DDM.pdb #7 --- Chain | Description A B | No description available Chain information for GDN_narrow.pdb #8 --- Chain | Description A B | No description available Chain information for GDN_wide.pdb #9 --- Chain | Description A B | No description available Chain information for LMNG_narrow.pdb #10 --- Chain | Description A B | No description available Chain information for LMNG_wide.pdb #11 --- Chain | Description A B | No description available Chain information for MSP1D1-PC.pdb #12 --- Chain | Description A B | No description available Chain information for MSP1D1.pdb #13 --- Chain | Description A B | No description available Chain information for MSP1E3D1.pdb #14 --- Chain | Description A B | No description available Chain information for MSP2N2_narrow.pdb #15 --- Chain | Description A B | No description available Chain information for MSP2N2_wide.pdb #16 --- Chain | Description A B | No description available Chain information for Triton_wide.pdb #17 --- Chain | Description A B | No description available Chain information for Triton_wider.pdb #18 --- Chain | Description A B | No description available Chain information for UDM_narrow.pdb #19 --- Chain | Description A B | No description available Chain information for UDM_wide.pdb #20 --- Chain | Description A B | No description available Chain information for UDM_wider.pdb #21 --- Chain | Description A B | No description available Chain information for peptidisc_narrow.pdb #22 --- Chain | Description A B | No description available Chain information for peptidisc_narrower.pdb #23 --- Chain | Description A B | No description available > cd /Users/leahoffmann/Desktop/MsbA/maps/reference/environment/ Current working directory is: /Users/leahoffmann/Desktop/MsbA/maps/reference/environment > open *.mrc Opened A18_wide_disc.mrc as #24.1, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0404, step 1, values float32 Opened A18_wider_disc.mrc as #24.2, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.039, step 1, values float32 Opened A835_narrow_disc.mrc as #24.3, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0442, step 1, values float32 Opened A835_wide_disc.mrc as #24.4, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0453, step 1, values float32 Opened A835_wider_disc.mrc as #24.5, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.0423, step 1, values float32 Opened DDM_micelle.mrc as #24.6, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0827, step 1, values float32 Opened GDN_narrow_micelle.mrc as #24.7, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0495, step 1, values float32 Opened GDN_wide_micelle.mrc as #24.8, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0466, step 1, values float32 Opened LMNG_narrow_micelle.mrc as #24.9, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0506, step 1, values float32 Opened LMNG_wide_micelle.mrc as #24.10, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0501, step 1, values float32 Opened MSP1D1-PC_disc.mrc as #24.11, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0537, step 1, values float32 Opened MSP1D1_disc.mrc as #24.12, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0541, step 1, values float32 Opened MSP1E3D1_disc.mrc as #24.13, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0536, step 1, values float32 Opened MSP2N2_narrow_disc.mrc as #24.14, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0379, step 1, values float32 Opened MSP2N2_wide_disc.mrc as #24.15, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0359, step 1, values float32 Opened Triton_wide_micelle.mrc as #24.16, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0367, step 1, values float32 Opened Triton_wider_micelle.mrc as #24.17, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.0384, step 1, values float32 Opened UDM_narrow_micelle.mrc as #24.18, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0511, step 1, values float32 Opened UDM_wide_micelle.mrc as #24.19, grid size 96,88,113, pixel 1.33,1.33,1.33, shown at level 0.0489, step 1, values float32 Opened UDM_wider_micelle.mrc as #24.20, grid size 103,95,109, pixel 1.33,1.33,1.33, shown at level 0.0488, step 1, values float32 Opened peptidisc_narrow_disc.mrc as #24.21, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0504, step 1, values float32 Opened peptidisc_narrower_disc.mrc as #24.22, grid size 83,78,110, pixel 1.33,1.33,1.33, shown at level 0.0506, step 1, values float32 > dssp > turn x 260 > turn y 55 > turn z -9 > windowsize 1500 1500 > volume #1 step 1 > select /A:1-340 55943 atoms, 56850 bonds, 7260 residues, 22 models selected > color sel #8FBC8F > select /A:341-580 40638 atoms, 41100 bonds, 5210 residues, 22 models selected > color sel #779B77 > select /B:1-340 55961 atoms, 56866 bonds, 7260 residues, 22 models selected > color sel #A7CCE1 > select /B:341-580 40638 atoms, 41100 bonds, 5210 residues, 22 models selected > color sel #7994A3 > color #1 #a9a9a91a models > volume #1.1 level 0.09 > volume #1.2 level 0.08 > volume #1.3 level 0.07 > volume #1.4 level 0.06 > volume #1.5 level 0.08 > volume #1.6 level 0.2 > volume #1.7 level 0.075 > volume #1.8 level 0.1 > volume #1.9 level 0.08 > volume #1.10 level 0.085 > volume #1.11 level 0.09 > volume #1.12 level 0.08 > volume #1.13 level 0.11 > volume #1.14 level 0.075 > volume #1.15 level 0.065 > volume #1.16 level 0.07 > volume #1.17 level 0.08 > volume #1.18 level 0.13 > volume #1.19 level 0.09 > volume #1.20 level 0.09 > volume #1.21 level 0.08 > volume #1.22 level 0.08 > select ::name=""3PE""::name=""JSG"" 1569 atoms, 1591 bonds, 13 residues, 9 models selected > delete sel > color zone #1.1 near #2 distance 5 > color zone #1.2 near #3 distance 5 > color zone #1.3 near #4 distance 5 > color zone #1.4 near #5 distance 5 > color zone #1.5 near #6 distance 5 > color zone #1.6 near #7 distance 5 > color zone #1.7 near #8 distance 5 > color zone #1.8 near #9 distance 5 > color zone #1.9 near #10 distance 5 > color zone #1.10 near #11 distance 5 > color zone #1.11 near #12 distance 5 > color zone #1.12 near #13 distance 5 > color zone #1.13 near #14 distance 5 > color zone #1.14 near #15 distance 5 > color zone #1.15 near #16 distance 5 > color zone #1.16 near #17 distance 5 > color zone #1.17 near #18 distance 5 > color zone #1.18 near #19 distance 5 > color zone #1.19 near #20 distance 5 > color zone #1.20 near #21 distance 5 > color zone #1.21 near #22 distance 5 > color zone #1.22 near #23 distance 5 > surface dust #1 > lighting soft shadows true intensity 0.5 > graphics silhouettes true > select subtract all Nothing selected > volume #24.1 level 0.03 > volume #24.2 level 0.02 > volume #24.3 level 0.02 > volume #24.4 level 0.02 > volume #24.5 level 0.025 > volume #24.6 level 0.07 > volume #24.7 level 0.03 > volume #24.8 level 0.04 > volume #24.9 level 0.04 > volume #24.10 level 0.04 > volume #24.11 level 0.03 > volume #24.12 level 0.03 > volume #24.13 level 0.035 > volume #24.14 level 0.022 > volume #24.15 level 0.013 > volume #24.16 level 0.02 > volume #24.17 level 0.02 > volume #24.18 level 0.02 > volume #24.19 level 0.027 > volume #24.20 level 0.03 > volume #24.21 level 0.05 > volume #24.22 level 0.05 > color #24 #ebebeb1a > surface dust #24 > cd /Users/leahoffmann/Desktop/Dissertation/dozen-environments/ Current working directory is: /Users/leahoffmann/Desktop/Dissertation/dozen- environments > view clip false > hide target m > show #1.1 > save A18_wide.png width 1500 height 1500 supersample 6 transparentBackground > true > hide target m > show #1.2 > save A18_wider.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.3 > save A835_narrow.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.4 > save A835_wide.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.5 > save A835_wider.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.6 > save DDM.png width 1500 height 1500 supersample 6 transparentBackground true > hide target m > show #1.7 > save GDN_narrow.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.8 > save GDN_wide.png width 1500 height 1500 supersample 6 transparentBackground > true > hide target m > show #1.9 > save LMNG_narrow.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.10 > save LMNG_wide.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.11 > save MSP1D1-PC.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.12 > save MSP1D1.png width 1500 height 1500 supersample 6 transparentBackground > true > hide target m > show #1.13 > save MSP1E3D1.png width 1500 height 1500 supersample 6 transparentBackground > true > hide target m > show #1.14 > save MSP2N2_narrow.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.15 > save MSP2N2_wide.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.16 > save Triton_wide.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.17 > save Triton_wider.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.18 > save UDM_narrow.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.19 > save UDM_wide.png width 1500 height 1500 supersample 6 transparentBackground > true > hide target m > show #1.20 > save UDM_wider.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.21 > save peptidisc_narrow.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.22 > save peptidisc_narrower.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.1 #24.1 > save A18_wide_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.2 #24.2 > save A18_wider_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.3 #24.3 > save A835_narrow_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.4 #24.4 > save A835_wide_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.5 #24.5 > save A835_wider_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.6 #24.6 > save DDM_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.7 #24.7 > save GDN_narrow_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.8 #24.8 > save GDN_wide_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.9 #24.9 > save LMNG_narrow_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.10 #24.10 > save LMNG_wide_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.11 #24.11 > save MSP1D1-PC_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.12 #24.12 > save MSP1D1_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.13 #24.13 > save MSP1E3D1_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.14 #24.14 > save MSP2N2_narrow_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.15 #24.15 > save MSP2N2_wide_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.16 #24.16 > save Triton_wide_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.17 #24.17 > save Triton_wider_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.18 #24.18 > save UDM_narrow_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.19 #24.19 > save UDM_wide_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.20 #24.20 > save UDM_wider_micelle.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.21 #24.21 > save peptidisc_narrow_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #1.22 #24.22 > save peptidisc_narrower_disc.png width 1500 height 1500 supersample 6 > transparentBackground true > close session > cd /Users/leahoffmann/Desktop/MsbA/maps/reference/model Current working directory is: /Users/leahoffmann/Desktop/MsbA/maps/reference/model > open *.pdb Chain information for A18_wide.pdb #1 --- Chain | Description A B | No description available Chain information for A18_wider.pdb #2 --- Chain | Description A B | No description available Chain information for A835_narrow.pdb #3 --- Chain | Description A B | No description available Chain information for A835_wide.pdb #4 --- Chain | Description A B | No description available Chain information for A835_wider.pdb #5 --- Chain | Description A B | No description available Chain information for DDM.pdb #6 --- Chain | Description A B | No description available Chain information for GDN_narrow.pdb #7 --- Chain | Description A B | No description available Chain information for GDN_wide.pdb #8 --- Chain | Description A B | No description available Chain information for LMNG_narrow.pdb #9 --- Chain | Description A B | No description available Chain information for LMNG_wide.pdb #10 --- Chain | Description A B | No description available Chain information for MSP1D1-PC.pdb #11 --- Chain | Description A B | No description available Chain information for MSP1D1.pdb #12 --- Chain | Description A B | No description available Chain information for MSP1E3D1.pdb #13 --- Chain | Description A B | No description available Chain information for MSP2N2_narrow.pdb #14 --- Chain | Description A B | No description available Chain information for MSP2N2_wide.pdb #15 --- Chain | Description A B | No description available Chain information for Triton_wide.pdb #16 --- Chain | Description A B | No description available Chain information for Triton_wider.pdb #17 --- Chain | Description A B | No description available Chain information for UDM_narrow.pdb #18 --- Chain | Description A B | No description available Chain information for UDM_wide.pdb #19 --- Chain | Description A B | No description available Chain information for UDM_wider.pdb #20 --- Chain | Description A B | No description available Chain information for peptidisc_narrow.pdb #21 --- Chain | Description A B | No description available Chain information for peptidisc_narrower.pdb #22 --- Chain | Description A B | No description available > dssp > turn x 180 > turn y -5 > turn z -40 > windowsize 1500 1500 > select /A:1-340 55943 atoms, 56850 bonds, 7260 residues, 22 models selected > color sel #8FBC8F > select /A:341-580 40638 atoms, 41100 bonds, 5210 residues, 22 models selected > color sel #779B77 > select /B:1-340 55961 atoms, 56866 bonds, 7260 residues, 22 models selected > color sel #A7CCE1 > select /B:341-580 40638 atoms, 41100 bonds, 5210 residues, 22 models selected > color sel #7994A3 > select subtract all Nothing selected > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix default arrows false xsection round width > 1.5 thickness 1.5 > cartoon style nucleic xsection round width 1.6 thickness 1.6 > nucleotides tube/slab shape ellipsoid > graphics silhouettes true > hide atoms > distance #1/A: 506@CA #1/B: 506@CA Distance between A18_wide.pdb #1/A GLU 506 CA and /B GLU 506 CA: 64.610Å > distance #1/A: 512@CA #1/B: 512@CA Distance between A18_wide.pdb #1/A ASP 512 CA and /B ASP 512 CA: 71.958Å > distance #2/A: 506@CA #2/B: 506@CA Distance between A18_wider.pdb #2/A GLU 506 CA and /B GLU 506 CA: 73.959Å > distance #2/A: 512@CA #2/B: 512@CA Distance between A18_wider.pdb #2/A ASP 512 CA and /B ASP 512 CA: 79.069Å > distance #3/A: 506@CA #3/B: 506@CA Distance between A835_narrow.pdb #3/A ARG 506 CA and /B ARG 506 CA: 58.889Å > distance #3/A: 512@CA #3/B: 512@CA Distance between A835_narrow.pdb #3/A LEU 512 CA and /B LEU 512 CA: 57.428Å > distance #4/A: 506@CA #4/B: 506@CA Distance between A835_wide.pdb #4/A GLU 506 CA and /B GLU 506 CA: 60.854Å > distance #4/A: 512@CA #4/B: 512@CA Distance between A835_wide.pdb #4/A ASP 512 CA and /B ASP 512 CA: 71.524Å > distance #5/A: 506@CA #5/B: 506@CA Distance between A835_wider.pdb #5/A GLU 506 CA and /B GLU 506 CA: 70.439Å > distance #5/A: 512@CA #5/B: 512@CA Distance between A835_wider.pdb #5/A ASP 512 CA and /B ASP 512 CA: 80.011Å > distance #6/A: 506@CA #6/B: 506@CA Distance between DDM.pdb #6/A GLU 506 CA and /B GLU 506 CA: 60.799Å > distance #6/A: 512@CA #6/B: 512@CA Distance between DDM.pdb #6/A ASP 512 CA and /B ASP 512 CA: 70.212Å > distance #7/A: 506@CA #7/B: 506@CA Distance between GDN_narrow.pdb #7/A GLU 506 CA and /B GLU 506 CA: 31.450Å > distance #7/A: 512@CA #7/B: 512@CA Distance between GDN_narrow.pdb #7/A ASP 512 CA and /B ASP 512 CA: 40.831Å > distance #8/A: 506@CA #8/B: 506@CA Distance between GDN_wide.pdb #8/A GLU 506 CA and /B GLU 506 CA: 57.758Å > distance #8/A: 512@CA #8/B: 512@CA Distance between GDN_wide.pdb #8/A ASP 512 CA and /B ASP 512 CA: 67.945Å > distance #9/A: 506@CA #9/B: 506@CA Distance between LMNG_narrow.pdb #9/A GLU 506 CA and /B GLU 506 CA: 35.303Å > distance #9/A: 512@CA #9/B: 512@CA Distance between LMNG_narrow.pdb #9/A ASP 512 CA and /B ASP 512 CA: 50.077Å > distance #10/A: 506@CA #10/B: 506@CA Distance between LMNG_wide.pdb #10/A GLU 506 CA and /B GLU 506 CA: 60.541Å > distance #10/A: 512@CA #10/B: 512@CA Distance between LMNG_wide.pdb #10/A ASP 512 CA and /B ASP 512 CA: 68.493Å > distance #11/A: 506@CA #11/B: 506@CA Distance between MSP1D1-PC.pdb #11/A GLU 506 CA and /B GLU 506 CA: 23.109Å > distance #11/A: 512@CA #11/B: 512@CA Distance between MSP1D1-PC.pdb #11/A ASP 512 CA and /B ASP 512 CA: 34.754Å > distance #12/A: 506@CA #12/B: 506@CA Distance between MSP1D1.pdb #12/A GLU 506 CA and /B GLU 506 CA: 29.126Å > distance #12/A: 512@CA #12/B: 512@CA Distance between MSP1D1.pdb #12/A ASP 512 CA and /B ASP 512 CA: 40.395Å > distance #13/A: 506@CA #13/B: 506@CA Distance between MSP1E3D1.pdb #13/A GLU 506 CA and /B GLU 506 CA: 23.800Å > distance #13/A: 512@CA #13/B: 512@CA Distance between MSP1E3D1.pdb #13/A ASP 512 CA and /B ASP 512 CA: 37.784Å > distance #14/A: 506@CA #14/B: 506@CA Distance between MSP2N2_narrow.pdb #14/A GLU 506 CA and /B GLU 506 CA: 23.800Å > distance #14/A: 512@CA #14/B: 512@CA Distance between MSP2N2_narrow.pdb #14/A ASP 512 CA and /B ASP 512 CA: 37.784Å > distance #15/A: 506@CA #15/B: 506@CA Distance between MSP2N2_wide.pdb #15/A GLU 506 CA and /B GLU 506 CA: 57.758Å > distance #15/A: 512@CA #15/B: 512@CA Distance between MSP2N2_wide.pdb #15/A ASP 512 CA and /B ASP 512 CA: 67.945Å > distance #16/A: 506@CA #16/B: 506@CA Distance between Triton_wide.pdb #16/A GLU 506 CA and /B GLU 506 CA: 58.295Å > distance #16/A: 512@CA #16/B: 512@CA Distance between Triton_wide.pdb #16/A ASP 512 CA and /B ASP 512 CA: 66.921Å > distance #17/A: 506@CA #17/B: 506@CA Distance between Triton_wider.pdb #17/A GLU 506 CA and /B GLU 506 CA: 68.420Å > distance #17/A: 512@CA #17/B: 512@CA Distance between Triton_wider.pdb #17/A ASP 512 CA and /B ASP 512 CA: 77.844Å > distance #18/A: 506@CA #18/B: 506@CA Distance between UDM_narrow.pdb #18/A ARG 506 CA and /B ARG 506 CA: 53.126Å > distance #18/A: 512@CA #18/B: 512@CA Distance between UDM_narrow.pdb #18/A LEU 512 CA and /B LEU 512 CA: 52.744Å > distance #19/A: 506@CA #19/B: 506@CA Distance between UDM_wide.pdb #19/A GLU 506 CA and /B GLU 506 CA: 57.902Å > distance #19/A: 512@CA #19/B: 512@CA Distance between UDM_wide.pdb #19/A ASP 512 CA and /B ASP 512 CA: 68.515Å > distance #20/A: 506@CA #20/B: 506@CA Distance between UDM_wider.pdb #20/A GLU 506 CA and /B GLU 506 CA: 67.918Å > distance #20/A: 512@CA #20/B: 512@CA Distance between UDM_wider.pdb #20/A ASP 512 CA and /B ASP 512 CA: 78.702Å > distance #21/A: 506@CA #21/B: 506@CA Distance between peptidisc_narrow.pdb #21/A GLU 506 CA and /B GLU 506 CA: 35.794Å > distance #21/A: 512@CA #21/B: 512@CA Distance between peptidisc_narrow.pdb #21/A ASP 512 CA and /B ASP 512 CA: 49.480Å > distance #22/A: 506@CA #22/B: 506@CA Distance between peptidisc_narrower.pdb #22/A GLU 506 CA and /B GLU 506 CA: 22.487Å > distance #22/A: 512@CA #22/B: 512@CA Distance between peptidisc_narrower.pdb #22/A ASP 512 CA and /B ASP 512 CA: 31.765Å > select :506 404 atoms, 360 bonds, 22 pseudobonds, 44 residues, 23 models selected > color sel #941751ff > show sel & #1-22 atoms > style sel & #1-22 sphere Changed 404 atom styles > select :512 352 atoms, 308 bonds, 22 pseudobonds, 44 residues, 23 models selected > color sel orange > show sel & #1-22 atoms > style sel & #1-22 sphere Changed 352 atom styles > distance style decimalPlaces 2 > distance style decimalPlaces 2 > hide #23.1 > distance style color black > distance style color black > distance style radius 0.25 > distance style radius 0.25 > cd /Users/leahoffmann/Desktop/Dissertation/dozen-environments/ Current working directory is: /Users/leahoffmann/Desktop/Dissertation/dozen- environments > view clip false > set bgColor white > set bgColor #ffffff00 > ui tool show ""Side View"" > select subtract all Nothing selected > ui tool show ""Side View"" > hide target m > show #1 models > show #!23 models > save A18_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #2 models > show #!23 models > save A18_wider_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #3 models > show #!23 models > save A835_narrow_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #4 models > show #!23 models > save A835_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #5 models > show #!23 models > save A835_wider_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #6 models > show #!23 models > save DDM_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #7 models > show #!23 models > save GDN_narrow_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #8 models > show #!23 models > save GDN_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #9 models > show #!23 models > save LMNG_narrow_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #10 models > show #!23 models > save LMNG_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #11 models > show #!23 models > save MSP1D1-PC_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #12 models > show #!23 models > save MSP1D1_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #13 models > show #!23 models > save MSP1E3D1_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #14 models > show #!23 models > save MSP2N2_narrow_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #15 models > show #!23 models > save MSP2N2_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #16 models > show #!23 models > save Triton_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #17 models > show #!23 models > save Triton_wider_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #18 models > show #!23 models > save UDM_narrow_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #19 models > show #!23 models > save UDM_wide_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #20 models > show #!23 models > save UDM_wider_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #21 models > show #!23 models > save peptidisc_narrow_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > hide target m > show #22 models > show #!23 models > save peptidisc_narrower_distance.png width 1500 height 1500 supersample 6 > transparentBackground true > show #19 models > hide #19 models > open /Users/leahoffmann/Downloads/step3_packing.pdb Summary of feedback from opening /Users/leahoffmann/Downloads/step3_packing.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08. 2025. JOB Ignored bad PDB record found on line 2 REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE Ignored bad PDB record found on line 3 REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui Chain information for step3_packing.pdb #24 --- Chain | Description ? | No description available > close #1-23 > hide #!24 models > show #!24 models > view clip false > select ::name=""ADDM"" 300 atoms, 300 residues, 1 model selected > molmap ::name=""ADDM"" Missing or invalid ""resolution"" argument: Expected a number > molmap ::name=""ADDM"" 8 Opened step3_packing.pdb map 8 as #1, grid size 49,49,32, pixel 2.67, shown at level 0.00567, step 1, values float32 > molmap ::name=""ADDM"" 10 Opened step3_packing.pdb map 10 as #1, grid size 43,43,29, pixel 3.33, shown at level 0.00446, step 1, values float32 > hide #!1 models > show #!1 models > color #1 #941751ff models > color #1 #941100ff models > color #1 #945200ff models > color #1 #ff2600ff models > color #1 #9437ffff models > color #1 #942193ff models > color #1 #941751ff models > color #1 #531b93ff models > color #1 #011993ff models > color #1 #941751ff models > color #1 #771242ff models > color #1 #801447ff models > color #1 #802d52ff models > color #1 #80435eff models > color #1 #803044ff models > color #1 #803354ff models > color #1 #803650ff models > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #2 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #2 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > hide #!24 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #!24 models > show #2 models > hide #!1 models > select add #2 9224 atoms, 9050 bonds, 1440 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #24,1,0,0,-1.9936,0,1,0,-1.2847,0,0,1,-19.876,#2,1,0,0,-1.9936,0,1,0,-1.2847,0,0,1,-19.876 > select add #24 27538 atoms, 27498 bonds, 1 pseudobond, 2604 residues, 3 models selected > select subtract #24 8924 atoms, 9050 bonds, 1140 residues, 1 model selected > view matrix models #2,1,0,0,-120.47,0,1,0,3.4772,0,0,1,-209.38 > view matrix models #2,1,0,0,-185.23,0,1,0,-105.88,0,0,1,-175.33 > view matrix models #2,1,0,0,-140.29,0,1,0,-120.24,0,0,1,-174.46 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > mmaker #2 to #24 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 step3_packing.pdb, chain (blank) (#24) with 9fuq, chain A (#2), sequence alignment score = 2812.6 RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs: 0.000) > show #!1 models > hide #!1 models > close #24 > open /Users/leahoffmann/Downloads/step3_packing.pdb Summary of feedback from opening /Users/leahoffmann/Downloads/step3_packing.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08. 2025. JOB Ignored bad PDB record found on line 2 REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE Ignored bad PDB record found on line 3 REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui Chain information for step3_packing.pdb #3 --- Chain | Description ? | No description available > mmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker step3_packing.pdb, chain (blank) (#3) with 9fuq, chain A (#2), sequence alignment score = 2812.6 RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs: 0.000) > show #!1 models > close #3 > select /A: 1-340 2535 atoms, 2576 bonds, 329 residues, 1 model selected > color sel #8FBC8F > select /A:341-580 1876 atoms, 1898 bonds, 240 residues, 1 model selected > color sel #779B77 > select /B: 1-340 2535 atoms, 2576 bonds, 329 residues, 1 model selected > color sel #A7CCE1 > select /B:341-580 1876 atoms, 1898 bonds, 240 residues, 1 model selected > color sel #7994A3 > hide #2 models > show #2 models > surface resolution 10 2 Gaussian surfaces, threshold level 0.049 - 0.051 > color #1 #cc6689ff models > color #1 #e9749cff models > color #1 #bd5e7fff models > color #1 #b05877ff models > color #1 #b05d73ff models > hide #2.1 models > hide #2.2 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > select add #2 8924 atoms, 9050 bonds, 1140 residues, 3 models selected > select subtract #2 Nothing selected > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #3 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #3 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #4 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #4 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #5 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #5 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > select add #3 8924 atoms, 9050 bonds, 1140 residues, 1 model selected > select add #4 17848 atoms, 18100 bonds, 2280 residues, 2 models selected > select add #5 26772 atoms, 27150 bonds, 3420 residues, 3 models selected > view matrix models > #3,1,0,0,-109.27,0,1,0,17.656,0,0,1,-167.28,#4,1,0,0,-109.27,0,1,0,17.656,0,0,1,-167.28,#5,1,0,0,-109.27,0,1,0,17.656,0,0,1,-167.28 > view matrix models > #3,1,0,0,-186.34,0,1,0,-102.3,0,0,1,-140.03,#4,1,0,0,-186.34,0,1,0,-102.3,0,0,1,-140.03,#5,1,0,0,-186.34,0,1,0,-102.3,0,0,1,-140.03 > view matrix models > #3,1,0,0,-152.69,0,1,0,-135.8,0,0,1,-153.07,#4,1,0,0,-152.69,0,1,0,-135.8,0,0,1,-153.07,#5,1,0,0,-152.69,0,1,0,-135.8,0,0,1,-153.07 > view matrix models > #3,1,0,0,-149.77,0,1,0,-135.88,0,0,1,-145.63,#4,1,0,0,-149.77,0,1,0,-135.88,0,0,1,-145.63,#5,1,0,0,-149.77,0,1,0,-135.88,0,0,1,-145.63 > mmaker #3 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 9fuq, chain A (#2) with 9fuq, chain A (#3), sequence alignment score = 2869.3 RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs: 0.000) > mmaker #4 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 9fuq, chain A (#2) with 9fuq, chain A (#4), sequence alignment score = 2869.3 RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs: 0.000) > mmaker #5 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 9fuq, chain A (#2) with 9fuq, chain A (#5), sequence alignment score = 2869.3 RMSD between 569 pruned atom pairs is 0.000 angstroms; (across all 569 pairs: 0.000) > close #2.2 > close #2.1 > select #2:341-580 3752 atoms, 3796 bonds, 480 residues, 1 model selected > delete sel > select #2/B: 1-340 2535 atoms, 2576 bonds, 329 residues, 1 model selected > delete sel > color #2 #8FBC8F > select #3:1-340 5070 atoms, 5152 bonds, 658 residues, 1 model selected > delete sel > select #3/B:341-580 1876 atoms, 1898 bonds, 240 residues, 1 model selected > delete sel > color #3 #779B77 > select #4:341-580 3752 atoms, 3796 bonds, 480 residues, 1 model selected > delete sel > select #4/A: 1-340 2535 atoms, 2576 bonds, 329 residues, 1 model selected > delete sel > color #4 #A7CCE1 > select #5:1-340 5070 atoms, 5152 bonds, 658 residues, 1 model selected > delete sel > select #5/A:341-580 1876 atoms, 1898 bonds, 240 residues, 1 model selected > delete sel > color #5 #7994A3 > surface resolution 10 4 Gaussian surfaces, threshold level 0.049 - 0.052 > view clp false Expected an objects specifier or a view name or a keyword > view clip false > color #1 #4541bfff models > color #1 #7c64bfff models > color #1 #866bceff models > color #1 #a296ceff models > color #1 #9587ceff models > color #1 #a296ceff models > color #1 #968bbfff models > open /Users/leahoffmann/Downloads/step3_packing.pdb Summary of feedback from opening /Users/leahoffmann/Downloads/step3_packing.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08. 2025. JOB Ignored bad PDB record found on line 2 REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE Ignored bad PDB record found on line 3 REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui Chain information for step3_packing.pdb #6 --- Chain | Description ? | No description available > hide #!5 models > hide #!4 models > hide #!3 models > hide #2.1 models > hide #!2 models > hide #!1 models > select ::name=""ADDM"" 300 atoms, 300 residues, 1 model selected > molmap ::name=""ADDM"" 6 Opened step3_packing.pdb map 6 as #7, grid size 59,59,37, pixel 2, shown at level 0.0078, step 1, values float32 > molmap ::name=""ADDM"" 7 Opened step3_packing.pdb map 7 as #7, grid size 53,53,34, pixel 2.33, shown at level 0.00665, step 1, values float32 > molmap ::name=""ADDM"" 5 Opened step3_packing.pdb map 5 as #7, grid size 67,67,40, pixel 1.67, shown at level 0.00976, step 1, values float32 > hide #!6 models > show #!5 models > show #!4 models > show #!3 models > show #2.1 models > color #7 #968bbfff models > set bgColor black > set bgColor transparent > open /Users/leahoffmann/Desktop/MsbA/Deposition/DDM/DDM_sharpend_map.mrc Opened DDM_sharpend_map.mrc as #8, grid size 320,320,320, pixel 0.837, shown at level 0.078, step 2, values float32 > select add #6 18614 atoms, 18448 bonds, 1 pseudobond, 1464 residues, 2 models selected > select subtract #6 Nothing selected > select add #8 2 models selected > view matrix models #8,1,0,0,-69.899,0,1,0,31.03,0,0,1,-135.76 > view matrix models #8,1,0,0,-154.44,0,1,0,-137.59,0,0,1,-148.43 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.9945,-0.018818,-0.10303,-139.54,0.044029,0.9677,0.24824,-167.53,0.095033,-0.25142,0.9632,-124.37 > view matrix models > #8,0.94804,-0.31725,-0.023887,-102.47,0.31814,0.94572,0.066328,-182.62,0.0015478,-0.070481,0.99751,-139.04 > view matrix models > #8,0.94059,-0.32699,-0.091441,-92.503,0.33702,0.93185,0.13445,-191.13,0.041247,-0.15728,0.98669,-131.92 > view matrix models > #8,0.76168,-0.64794,0.0048864,-35.766,0.64375,0.75757,0.10806,-208.21,-0.073716,-0.079159,0.99413,-126.93 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.76168,-0.64794,0.0048864,-22.034,0.64375,0.75757,0.10806,-207.41,-0.073716,-0.079159,0.99413,-125.77 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 4 atomic models, 2 maps. > hide #!5 models > hide #!4 models > hide #!3 models > hide #2.1 models > hide #!2 models > fitmap #8 inMap #7 Fit map DDM_sharpend_map.mrc in map step3_packing.pdb map 5 using 40842 points correlation = 0.1209, correlation about mean = -0.1382, overlap = 28.57 steps = 128, shift = 5.41, angle = 7.89 degrees Position of DDM_sharpend_map.mrc (#8) relative to step3_packing.pdb map 5 (#7) coordinates: Matrix rotation and translation 0.75031647 -0.64980357 0.12157516 -34.60487664 0.65085976 0.75832925 0.03630890 -194.13565813 -0.11578765 0.05188521 0.99191791 -138.00080275 Axis 0.01178028 0.17951618 0.98368448 Axis point 203.45852639 -128.33202085 0.00000000 Rotation angle (degrees) 41.38520479 Shift along axis -171.00739632 > show #!5 models > hide #!7 models > fitmap #5 inMap #8 Fit molecule 9fuq (#5) to map DDM_sharpend_map.mrc (#8) using 1978 atoms average map value = 0.2004, steps = 128 shifted from previous position = 8.14 rotated from previous position = 13.4 degrees atoms outside contour = 239, contour level = 0.07797 Position of 9fuq (#5) relative to DDM_sharpend_map.mrc (#8) coordinates: Matrix rotation and translation -0.97842157 -0.00579002 -0.20653742 300.24428007 -0.00548330 -0.99852759 0.05396832 257.30895941 -0.20654579 0.05393627 0.97694918 24.36417708 Axis -0.10387115 0.02713334 0.99422058 Axis point 151.38488281 128.33366335 0.00000000 Rotation angle (degrees) 179.99116189 Shift along axis 0.01829874 > undo > volume #8 step 1 > volume #8 level 0.09733 > close #8 > show #!4 models > show #!3 models > show #2.1 models > hide #5.1 models > show #5.1 models > hide #5.1 models > hide #4.1 models > close #4.1 > close #5.1 > close #3.1 > close #1 > close #2.1 > close #5 > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #1 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #1 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > select add #7 2 models selected > select subtract #7 Nothing selected > select add #1 8924 atoms, 9050 bonds, 1140 residues, 1 model selected > view matrix models #1,1,0,0,-94.286,0,1,0,39.428,0,0,1,-132.64 > view matrix models #1,1,0,0,-141.83,0,1,0,-122.59,0,0,1,-160.02 > view matrix models #1,1,0,0,-152.6,0,1,0,-133.26,0,0,1,-149.6 > view matrix models #1,1,0,0,-147.66,0,1,0,-140.96,0,0,1,-148.23 > mmaker #1 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 9fuq, chain A (#2) with 9fuq, chain A (#1), sequence alignment score = 2514.1 RMSD between 329 pruned atom pairs is 0.000 angstroms; (across all 329 pairs: 0.000) > select #1: 1-395 5916 atoms, 6014 bonds, 768 residues, 1 model selected > delete sel > select #1/A: 396-680 1504 atoms, 1517 bonds, 186 residues, 1 model selected > delete sel > color #1 #A7CCE1 > close #1-4#6-7 > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #1 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #1 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #2 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #2 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #3 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #3 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > open 9FUQ 9fuq title: MsbA in DDM inward-facing wide open [more info...] Chain information for 9fuq #4 --- Chain | Description | UniProt A B | ATP-dependent lipid A-core flippase | MSBA_ECOLI 1-582 Non-standard residues in 9fuq #4 --- 3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn- phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine) > select #1:341-580 3752 atoms, 3796 bonds, 480 residues, 1 model selected > delete sel > select #1/B: 1-340 2535 atoms, 2576 bonds, 329 residues, 1 model selected > delete sel > color #1 #8FBC8F > select #2:1-340 5070 atoms, 5152 bonds, 658 residues, 1 model selected > delete sel > select #2/B:341-580 1876 atoms, 1898 bonds, 240 residues, 1 model selected > delete sel > color #2 #779B77 > select #3:341-580 3752 atoms, 3796 bonds, 480 residues, 1 model selected > delete sel > select #3/A: 1-340 2535 atoms, 2576 bonds, 329 residues, 1 model selected > delete sel > color #3 #A7CCE1 > select #4:1-340 5070 atoms, 5152 bonds, 658 residues, 1 model selected > delete sel > select #4/A:341-580 1876 atoms, 1898 bonds, 240 residues, 1 model selected > delete sel > color #4 #7994A3 > surface resolution 10 4 Gaussian surfaces, threshold level 0.049 - 0.052 > select ::name=""3PE"" 408 atoms, 400 bonds, 8 residues, 4 models selected > delete sel > open /Users/leahoffmann/Downloads/step3_packing.pdb Summary of feedback from opening /Users/leahoffmann/Downloads/step3_packing.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 08. 2025. JOB Ignored bad PDB record found on line 2 REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE Ignored bad PDB record found on line 3 REMARK DATE: 9/ 8/25 9:12:41 CREATED BY USER: charmm-gui Chain information for step3_packing.pdb #5 --- Chain | Description ? | No description available > select add #5 18614 atoms, 18448 bonds, 1 pseudobond, 1464 residues, 2 models selected > view matrix models #5,1,0,0,3.2874,0,1,0,-5.1725,0,0,1,150.4 > view matrix models #5,1,0,0,119.99,0,1,0,140.27,0,0,1,145.11 > view matrix models #5,1,0,0,128.35,0,1,0,118.47,0,0,1,151.79 > mmaker #5 to #1 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 9fuq, chain A (#1) with step3_packing.pdb, chain (blank) (#5), sequence alignment score = 2457.4 RMSD between 329 pruned atom pairs is 0.001 angstroms; (across all 329 pairs: 0.001) > select subtract #5 Nothing selected > hide #!5 models > select ::name=""ADDM"" 300 atoms, 300 residues, 1 model selected > molmap ::name=""ADDM"" 5 Opened step3_packing.pdb map 5 as #6, grid size 67,67,40, pixel 1.67, shown at level 0.00976, step 1, values float32 > color #6 #968bbfff models > view clip false > save /Users/leahoffmann/Desktop/Dissertation/Figures/Detergent-DDM300.png > width 4000 height 4000 supersample 6 transparentBackground true > open > /Users/leahoffmann/Desktop/MsbA/Deposition/peptidisc_narrow/peptidisc_narrow_sharpend_map.mrc Opened peptidisc_narrow_sharpend_map.mrc as #7, grid size 320,320,320, pixel 0.837, shown at level 0.0269, step 2, values float32 > select add #5 18614 atoms, 18448 bonds, 1 pseudobond, 1464 residues, 2 models selected > select subtract #5 Nothing selected > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > hide #!6 models > volume #7 step 1 > volume #7 level 0.0676 > ui mousemode right ""pick blobs"" > measure blob #!7.1 triangleNumber 275348 color #0000ccff outline true Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob: volume = 68531 area = 68331 size = 118.89 86.668 65.492 > volume #7 level 0.09007 > measure blob #!7.1 triangleNumber 140767 color #c7129fff Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob: volume = 269.15 area = 403.39 size = 23.478 9.9367 7.2338 > measure blob #!7.1 triangleNumber 142347 color #c7129fff Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob: volume = 268.79 area = 403.39 size = 23.478 9.9267 7.1826 > measure blob #!7.1 triangleNumber 172491 color #c7129fff Surface peptidisc_narrow_sharpend_map.mrc #7.1 blob: volume = 214.78 area = 329.65 size = 23.192 9.908 5.0399 > open /Users/leahoffmann/Downloads/7NMN.cif 7NMN.cif title: Rabbit HCN4 stabilised in amphipol A8-35 [more info...] Chain information for 7NMN.cif #8 --- Chain | Description | UniProt A B C D | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4,Rabbit HCN4 | HCN4_RABIT 1-721 > close #8 > open /Users/leahoffmann/Downloads/step3_packing-2.pdb Summary of feedback from opening /Users/leahoffmann/Downloads/step3_packing-2.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 15. 2025. JOB Ignored bad PDB record found on line 2 REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE Ignored bad PDB record found on line 3 REMARK DATE: 9/15/25 8:56: 6 CREATED BY USER: charmm-gui Chain information for step3_packing-2.pdb #8 --- Chain | Description ? | No description available > hide #!7 models > show #!6 models > show #!5 models > show #!4 models > hide #!4 models > mmaker #8 to #5 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 step3_packing.pdb, chain (blank) (#5) with step3_packing-2.pdb, chain (blank) (#8), sequence alignment score = 5654 RMSD between 1164 pruned atom pairs is 0.001 angstroms; (across all 1164 pairs: 0.001) > molmap ::name=""ADDM"" 5 Opened map 5 as #9, grid size 122,123,91, pixel 1.67, shown at level 0.00827, step 1, values float32 > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > close #9 > close #8 > open /Users/leahoffmann/Downloads/step3_packing-3.pdb Summary of feedback from opening /Users/leahoffmann/Downloads/step3_packing-3.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON SEP, 15. 2025. JOB Ignored bad PDB record found on line 2 REMARK GENERATES DETERGENT PACKING USING A BIG SPHERE Ignored bad PDB record found on line 3 REMARK DATE: 9/15/25 9:12:51 CREATED BY USER: charmm-gui Chain information for step3_packing-3.pdb #8 --- Chain | Description ? | No description available > mmaker #9 to #5 No molecules/chains to match specified > mmaker #8 to #5 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 step3_packing.pdb, chain (blank) (#5) with step3_packing-3.pdb, chain (blank) (#8), sequence alignment score = 5661.2 RMSD between 1164 pruned atom pairs is 0.000 angstroms; (across all 1164 pairs: 0.000) > molmap ::name=""ADDM"" 5 Opened map 5 as #9, grid size 67,67,40, pixel 1.67, shown at level 0.0205, step 1, values float32 > show #!6 models > hide #!9 models > show #!9 models > hide #!6 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > hide #!8 models > hide #!5 models > color #9 #968bbfff models > view clip false > save /Users/leahoffmann/Desktop/Dissertation/Figures/Detergent-DDM350.png > width 4000 height 4000 supersample 6 transparentBackground true > select ::name=""ADDM"" 650 atoms, 650 residues, 2 models selected > show #!1-4 atoms > show #!1-4 cartoons > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > hide #!9 models > show #!8 models > show #!5 models > close #8 > close #5 > show #!9 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!4 models > show #!6 models > hide #!4 models > hide #!9 models > hide #!6 models > show #!9 models > hide #!9 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYD82D/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 20 days, 23 hours, 22 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PA278CV: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal PA278CV: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX