id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17474 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000002067acc00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-23 23:16:18.00 -0500"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""07A4A8C8-E380-48FA-AC4E-D3E350D31C92""} { ""uptime"" : 20000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,7"", ""coalitionID"" : 739, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-23 23:15:56.6980 -0500"", ""codeSigningMonitor"" : 1, ""incident"" : ""07A4A8C8-E380-48FA-AC4E-D3E350D31C92"", ""pid"" : 3695, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-23 18:56:34.6218 -0500"", ""procStartAbsTime"" : 160812905774, ""procExitAbsTime"" : 500545871031, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""4FE1FF3F-D256-597B-8D28-2D9970CD1179"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""7CBB956D-EE73-7D9F-180F-A2ECC121435D"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 24, ""sleepWakeUUID"" : ""C03A97A2-FCE9-478A-8833-6D8D138DD593"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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(2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/lianqi/Files/Postdoc/VEGF/Figures/b1.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00311, step 2, values float32 opened ChimeraX session > show #!1 models > volume step 1 > surface dust #1 size 10.8 > color zone #1 near #3 distance 6.48 > volume style surface > volume hide > volume show > transparency 50 > volume style surface > volume show > volume style surface > transparency 0 > volume style mesh > volume style surface > color zone #1 near #3 distance 6.48 > volume #1 color silver > volume #1 color #ebebeb > hide surfaces > show cartoons > volume hide > select add #3.3 2290 atoms, 146 residues, 1 model selected > color #3.3 #0096ffff > ui tool show ""Color Actions"" > color (#!3 & sel) #0096ffff > color (#!3 & sel) #76d6ffff > select add #3.4 4580 atoms, 292 residues, 2 models selected > select subtract #3.3 2290 atoms, 146 residues, 3 models selected > select add #3.5 11692 atoms, 750 residues, 2 models selected > select subtract #3.4 9402 atoms, 604 residues, 3 models selected > select add #3.6 18804 atoms, 1208 residues, 2 models selected > select subtract #3.5 9402 atoms, 604 residues, 3 models selected > select add #3.5 18804 atoms, 1208 residues, 2 models selected > select subtract #3.6 9402 atoms, 604 residues, 3 models selected > color #3.5 #ff2f92ff > color #3.5 #ff8ad8ff > select subtract #3.5 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > select add #3.6 18804 atoms, 1208 residues, 2 models selected > select subtract #3.6 9402 atoms, 604 residues, 3 models selected > select subtract #3.5 1 model selected > select add #3.7 8330 atoms, 537 residues, 1 model selected > color #3.7 #73fcd6ff > color #3.7 #00f900ff > color #3.7 #73fa79ff > hide #3.7 models > show #3.7 models > ui tool show ""Color Actions"" > color (#!3 & sel) #00f900ff > color (#!3 & sel) #73fa79ff > color (#!3 & sel) #00f900ff > color (#!3 & sel) #73fa79ff > select subtract #3.7 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #009051ff > color (#!3 & sel) #009193ff > color (#!3 & sel) #009051ff > color (#!3 & sel) #008f00ff > color (#!3 & sel) #009051ff > select subtract #3.8 1 model selected > select add #3.3 2290 atoms, 146 residues, 1 model selected > select subtract #3.3 1 model selected > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > show surfaces > hide surfaces > turn y 90 > show surfaces > color #3.5 #ff2f92ff > color #3.5 #ff8ad8ff > color #3.5 #ff85ffff > color #3.5 #ff40ffff > color #3.5 #941751ff > color #3.5 #ff2600ff > color #3.5 #ff7e79ff > color #3.6 #ff40ffff > color #3.6 #ff85ffff > color #3.6 #9437ffff > color #3.6 #ff85ffff > color #3.6 #ff7e79ff > color #3.6 #ffd479ff > color #3.6 #ff2600ff > color #3.6 #941100ff > color #3.6 #945200ff > color #3.6 #ff9300ff > color #3.6 #ff2f92ff > color #3.6 #ff8ad8ff > color #3.5 #ff85ffff > color #3.5 #9437ffff > color #3.5 #ff40ffff > color #3.5 #d783ffff > color #3.5 #ff40ffff > turn y 90 > color #3.5 #ff7e79ff > color #3.5 #ff2600ff > color #3.5 #ff9300ff > color #3.5 #ff7e79ff > color #3.5 #d783ffff > color #3.5 #ff85ffff > color #3.5 #ff8ad8ff > color #3.5 #ff85ffff > color #3.5 #ff40ffff > color #3.5 #ff2f92ff > color #3.5 #9437ffff > color #3.5 #941751ff > color #3.5 #942193ff > color #3.5 #531b93ff > color #3.5 #ff9300ff > color #3.5 #945200ff > color #3.5 #ff2600ff > color #3.5 #ff7e79ff > color #3.5 #ff85ffff > color #3.5 #ff9300ff > color #3.5 #ff7e79ff > color #3.5 #ff2600ff > color #3.5 #941100ff > color #3.5 #ff2600ff > color #3.5 #ff7e79ff Unsupported scale factor (0.000000) detected on Display1 > open ""/Users/lianqi/Files/Postdoc/VEGF/model colored.cxs"" opened ChimeraX session > open /Users/lianqi/Files/Postdoc/VEGF/Figures/b1.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00311, step 2, values float32 opened ChimeraX session > hide surfaces > show cartoons > select add #3.3 2290 atoms, 146 residues, 1 model selected > select add #3.2 2290 atoms, 12 pseudobonds, 146 residues, 3 models selected > select subtract #3.3 11 pseudobonds, 2 models selected > select add #3.3 2290 atoms, 11 pseudobonds, 146 residues, 2 models selected > select add #3.2 2290 atoms, 12 pseudobonds, 146 residues, 3 models selected > select subtract #3.2 2290 atoms, 146 residues, 2 models selected > select add #3.4 4580 atoms, 292 residues, 2 models selected > select subtract #3.3 2290 atoms, 146 residues, 3 models selected > select add #3.5 11692 atoms, 750 residues, 2 models selected > select subtract #3.4 9402 atoms, 604 residues, 3 models selected > cartoon style (#!3 & sel) xsection oval modeHelix default > hide #!3 models > show #!3 models > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 4 models selected > select subtract #3 6 models selected > hide #!3 models > show #!3 models > hide #3.1 models > hide #!3 models > show #!3 models > show #3.1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected > select subtract #3 6 models selected > hide #!3 models > hide #3.1 models > show #3.1 models > hide #3.8 models > hide #3.7 models > show #3.7 models > hide #3.7 models > hide #3.6 models > hide #3.5 models > hide #3.4 models > hide #3.3 models > hide #3.2 models > show #3.2 models > hide #3.1 models > hide #!3 models > show #3.1 models > hide #3.2 models > show #3.2 models > hide #3.1 models > show #3.1 models > hide #3.2 models > hide #3.1 models > show #3.1 models > hide #3.1 models > select add #3.3 2290 atoms, 146 residues, 1 model selected > show #3.3 models > hide #3.3 models > show sel cartoons > ui tool show ""Color Actions"" > color (#!3 & sel) #76d6ffff > select add #3.4 4580 atoms, 292 residues, 2 models selected > select subtract #3.3 2290 atoms, 146 residues, 3 models selected > ui tool show ""Color Actions"" > color (#!3 & sel) #76d6ffff > color (#!3 & sel) #0096ffff > select add #3.5 11692 atoms, 750 residues, 2 models selected > select subtract #3.4 9402 atoms, 604 residues, 3 models selected > color (#!3 & sel) #ff8ad8ff > color (#!3 & sel) #ff557fff > select add #3.6 18804 atoms, 1208 residues, 2 models selected > select subtract #3.5 9402 atoms, 604 residues, 3 models selected > color (#!3 & sel) #ffaaffff > select add #3.7 17732 atoms, 1141 residues, 2 models selected > select subtract #3.6 8330 atoms, 537 residues, 3 models selected > color (#!3 & sel) #76d6ffff > color (#!3 & sel) #73fa79ff > select add #3.8 16660 atoms, 1074 residues, 2 models selected > select subtract #3.7 8330 atoms, 537 residues, 3 models selected > color (#!3 & sel) #009051ff > select subtract #3.8 1 model selected > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > graphics silhouettes false > lighting soft > lighting full > lighting flat > graphics silhouettes false > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > ui tool show ""Side View"" > turn y 90 > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > show #!1 models > transparency #1.1 50 > volume step 1 > surface dust #1 size 10.8 > volume style surface > volume hide > volume show > volume #1 level 0.003198 > color zone #1 near #3 distance 6.48 > volume #1 level 0.003554 > hide #!3 models > turn y 90 > volume style surface > show #3.2 models > hide #3.2 models > select ::name=""CA""::name=""NAG"" 88 atoms, 84 bonds, 10 residues, 1 model selected > color sel white > volume #1 color #ebebeb > transparency #1.1 50 > volume style surface > volume #1 color #d6d6d6 > volume #1 color darkgrey > volume #1 color silver > volume #1 color #d6d6d6 > transparency #1.1 50 > volume #1 color silver > transparency #1.1 50 > volume #1 color #ebebeb > color zone #1 near sel & #3 distance 6.48 > hide #!3 models > show #!3 models > color zone #1 near sel & #3 distance 6.48 > hide #!1 models > show #!1 models > volume style surface > volume style mesh > volume style image > volume style surface > volume hide > volume show > color zone #1 near sel & #3 distance 6.48 > select ::name=""NAG"" 84 atoms, 84 bonds, 6 residues, 1 model selected > show sel atoms > hide #!1 models > color sel gray > select ::name=""NAG"" 84 atoms, 84 bonds, 6 residues, 1 model selected > select ::name=""CA"" 4 atoms, 4 residues, 1 model selected > show sel cartoons > show sel surfaces > hide sel surfaces > show sel surfaces > color (#!3 & sel) dark gray > show #!1 models > color zone #1 near sel & #3 distance 6.48 > hide #!3 models > show #!3 models > show #3.1 models > hide #!3 models > show #!3 models > show #3.8 models > show #3.7 models > show #3.6 models > show #3.5 models > show #3.4 models > show #3.3 models > show #3.2 models > select subtract #3.10 2 atoms, 2 residues, 3 models selected > select subtract #3.9 1 model selected > select add #1 3 models selected > color zone #1 near #3 distance 6.48 > select add #1 3 models selected > select add #1 3 models selected > ui mousemode right select > select clear > hide #!3 models > volume #1 change image level -0.0006805,0 level 0.003109,0.8 level 0.03586,1 > volume #1 level 0.003732 > volume #1 level 0.003643 > volume #1 level 0.003732 > volume #1 level 0.003376 > volume #1 level 0.003198 > color zone #1 near #3 distance 7 > color zone #1 near #3 distance 8 > color zone #1 near #3 distance 10 > color zone #1 near #3 distance 11 > volume #1 level 0.003554 > volume #1 level 0.0036 > volume #1 level 0.00355 > show #!3 models > hide #!3 models > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > lighting soft > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > turn y 45 > turn y 30 > turn y 90 > turn y 30 > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs"" > turn y 90 > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a2.cxs"" > open /Users/lianqi/Files/Postdoc/VEGF/Figures/b1.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00311, step 2, values float32 opened ChimeraX session > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs"" format > session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00355, step 1, values float32 opened ChimeraX session > save /Users/lianqi/Desktop/image1.png supersample 3 > turn y 90 > save /Users/lianqi/Desktop/image2.png supersample 3 > show #!3 models > hide #!1 models > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs"" format > session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00355, step 1, values float32 opened ChimeraX session > show #!3 models > hide #!1 models > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > save /Users/lianqi/Desktop/image3.png supersample 3 > turn y 90 > save /Users/lianqi/Desktop/image4.png supersample 3 > show #!1 models > hide #!1 models > hide #!3 models > show #!3 models > turn y 90 > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected > select clear > select /F:54 10 atoms, 9 bonds, 1 residue, 1 model selected > select clear > select /F:26 22 atoms, 21 bonds, 1 residue, 1 model selected > select clear > select /F:26 22 atoms, 21 bonds, 1 residue, 1 model selected > select add /F:265 41 atoms, 39 bonds, 2 residues, 2 models selected > select add /F:266 58 atoms, 55 bonds, 3 residues, 2 models selected Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 238 of 296 triangles, 42 atoms, 575 residues, 2 pseudobonds, 42 bonds > select clear > select /F:266 17 atoms, 16 bonds, 1 residue, 1 model selected > select clear > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected > color (#!3 & sel) gray > color (#!3 & sel) light gray > select clear > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 3 models selected > color (#!3 & sel) gray > select clear > select /F:26-266 3710 atoms, 3775 bonds, 241 residues, 1 model selected > color (#!3 & sel) #009051ff > color (#!3 & sel) #009193ff > color (#!3 & sel) #00fa92ff > color (#!3 & sel) #008f00ff > color (#!3 & sel) #009051ff > select /C:330-420 1396 atoms, 1411 bonds, 91 residues, 1 model selected > color (#!3 & sel) #ff85ffff > color (#!3 & sel) #ff557fff > show #!1 models > hide #!1 models > show #!1 models > color zone #1 near sel & #3 distance 6.48 > select add #3.8 9726 atoms, 1411 bonds, 628 residues, 2 models selected > color zone #1 near sel & #3 distance 6.48 > select add #1 9726 atoms, 1411 bonds, 628 residues, 6 models selected > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 8 models selected > color zone #1 near sel & #3 distance 6.48 > select clear > transparency 50 > view > view orient > turn z 90 > turn x 90 > view > hide #!3 models > transparency #1.1 0 > color #3 #ebebebff > select add #1 3 models selected > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 6 models selected > show #!3 models > hide #!3 models > show #!3 models > color zone #1 near sel & #3 distance 6.48 > transparency sel 50 > select clear > volume #1 color #d6d6d6 > volume #1 color #ebebeb > volume #1 color darkgrey > volume #1 color silver > volume #1 color #ebebeb > volume #1 color #d6d6d6 > transparency 0 > lighting soft > lighting flat > lighting soft > volume #1 color white > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > view > transparency 50 > volume style surface > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > volume #1 color #ebebeb > volume #1 color #d6d6d6 > transparency 0 > transparency 50 > volume style surface > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > view orient > turn x 90 > view > select /F:26-266 3710 atoms, 3775 bonds, 241 residues, 1 model selected > color (#!3 & sel) #d6d6d6ff > color (#!3 & sel) #009051ff > select /C330-420 Nothing selected > color #3#1.1#!1 #ff557fff > undo > select /C330-420 Nothing selected > select /C:330-420 1396 atoms, 1411 bonds, 91 residues, 1 model selected > select clear > select /C:330-420 1396 atoms, 1411 bonds, 91 residues, 1 model selected > color (#!3 & sel) #ffaaffff > color (#!3 & sel) #ff557fff > select clear > volume #1 level 0.003461 > volume #1 level 0.00355 > hide #!3 models > select /C:330-420 1396 atoms, 1411 bonds, 91 residues, 1 model selected > show #!3 models > hide #3.1 models > show #3.1 models > hide #3.4 models > hide #3.2 models > hide #3.3 models > hide #3.1 models > hide #3.6 models > hide #3.7 models > hide #3.8 models > hide #3.9 models > hide #3.10 models > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 4 models selected > select subtract #3 8 models selected > hide #!3 models > show #!3 models > hide #!3 models > hide #3.5 models > show #3.5 models > hide #3.5 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select /A 2290 atoms, 2319 bonds, 1 pseudobond, 146 residues, 2 models selected > hide sel cartoons > select /B 2290 atoms, 2319 bonds, 1 pseudobond, 146 residues, 2 models selected > hide sel cartoons > select subtract #3.4 1 model selected > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > show #3.4 models > hide #3.4 models > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > hide sel cartoons > select add #3.6 18804 atoms, 1208 residues, 2 models selected > select add #3.7 27134 atoms, 1745 residues, 3 models selected > select add #3.8 35464 atoms, 2282 residues, 4 models selected > select add #3.9 35466 atoms, 2284 residues, 5 models selected > select add #3.10 35468 atoms, 2286 residues, 6 models selected > hide sel cartoons > select subtract #3.5 26066 atoms, 1682 residues, 7 models selected > select subtract #3.6 16664 atoms, 1078 residues, 6 models selected > select subtract #3.7 8334 atoms, 541 residues, 5 models selected > select subtract #3.8 4 atoms, 4 residues, 4 models selected > select subtract #3.9 2 atoms, 2 residues, 3 models selected > select subtract #3.10 1 model selected > select add #3.2 12 pseudobonds, 1 model selected > hide atoms > select subtract #3.2 Nothing selected > select add #3.1 26 pseudobonds, 1 model selected > show atoms > hide atoms > show cartoons > hide cartoons > select subtract #3.1 Nothing selected > select /C:330-420 1396 atoms, 1411 bonds, 91 residues, 1 model selected > show sel cartoons > select /F:26-266 3710 atoms, 3775 bonds, 241 residues, 1 model selected > show sel cartoons > show sel surfaces > hide sel surfaces > select clear > hide #!3 models > show #!3 models > show #3.1 models > hide #3.1 models > show #3.3 models > hide #3.3 models > view orient > view > view orient > turn x 180 > turn z 90 > turn y 90 > turn x 90 > view > turn y 30 > color zone #1 near #3 distance 6.48 > undo > turn y 30 > color zone #1 near #3 distance 6.48 > turn y 30 > transparency #1.1#3.8 0 > transparency #1.1#3.8 50 > transparency #1.1#3.8 0 > volume style surface > transparency #1.1#3.8 50 > transparency #1.1#3.8 0 > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > turn y 30 > turn y 10 > save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a1.cxs > select /C:330-420 1396 atoms, 1411 bonds, 91 residues, 1 model selected > show sel cartoons > hide #!1 models > select clear > undo > open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a1.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00355, step 1, values float32 opened ChimeraX session > hide #!1 models Drag select of 332 residues > volume zone #1 nearAtoms sel range 3 > show #!1 models > select clear > volume zone #1 nearAtoms sel range 4 no atoms specified for zone Drag select of 332 residues, 1 postprocess_b20_3.3A.mrc > volume zone #1 nearAtoms sel range 4 > volume zone #1 nearAtoms sel range 5 > volume zone #1 nearAtoms sel range 4 > surface dust #1 size 10.8 > volume zone #1 nearAtoms sel range 4 > transparency sel & #1.1#3.8 50 > select clear > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a2.cxs > select clear > graphics silhouettes false > graphics silhouettes true > lighting soft Drag select of 6 residues, 1 postprocess_b20_3.3A.mrc > select clear > ui mousemode right translate > volume #1 level 0.004439 > volume #1 level 0.006396 > volume #1 level 0.007107 > ui mousemode right select > select #1 3 models selected > select clear > view orient > view > turn x 90 > select /F:38 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 21 atom styles > color sel byhetero > Hide H Unknown command: Hide H > Hide atom H Unknown command: Hide atom H > ~hbonds > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier Alignment identifier is 3/F > hbonds sel reveal true 2 hydrogen bonds found > undo > select /F:137@CD 1 atom, 1 residue, 1 model selected > hide sel atoms > select /F:137@NH1 1 atom, 1 residue, 1 model selected > select /F:137@HD3 1 atom, 1 residue, 1 model selected Drag select of 22 atoms, 20 residues, 1 pseudobonds, 1 postprocess_b20_3.3A.mrc > select clear > select /F:137@NH1 1 atom, 1 residue, 1 model selected > select /F:137@HD3 1 atom, 1 residue, 1 model selected > hide sel atoms > select /F:137 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel atoms > select clear Drag select of 22 atoms, 329 residues, 1 pseudobonds, 1 postprocess_b20_3.3A.mrc > hide sel atoms > select clear > select /F:38 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 21 atom styles > style sel sphere Changed 21 atom styles > style sel stick Changed 21 atom styles > style sel ball Changed 21 atom styles > style sel stick Changed 21 atom styles > select clear > hide h Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide h atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide atoms H Expected ',' or a keyword > hide atoms h Expected ',' or a keyword > hide atoms hydrogen Expected ',' or a keyword > select #1 3 models selected > select /F:38 21 atoms, 21 bonds, 1 residue, 1 model selected > hide sel & @H > hide sel atoms > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel surfaces > show sel surfaces > hide sel surfaces > color sel byhetero > hide (#!3 & sel) target a > show sel atoms > select clear > select #1 3 models selected > select clear > hide sel & @H > select clear > hide H > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 22 atom styles > style sel sphere Changed 22 atom styles > style sel stick Changed 22 atom styles > hide sel cartoons > show sel cartoons > select clear > hide H > select ::name=""CA"" 4 atoms, 4 residues, 1 model selected > style sel sphere Changed 4 atom styles > show sel surfaces > color (#!3 & sel) dark gray > color (#!3 & sel) cornflower blue > select clear > select /H:3@CA 1 atom, 1 residue, 1 model selected > hide sel surfaces > select /H:2@CA 1 atom, 1 residue, 1 model selected > hide sel surfaces > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 15 atoms, 332 residues, 14 bonds, 1 postprocess_b20_3.3A.mrc > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select clear > select #1 3 models selected > select clear > view orient > view > turn x 90 > volume #1 level 0.009508 > volume #1 level 0.01013 > ui tool show ""Side View"" > view > turn x 90 > view > turn x 90 > view > turn x 90 > view > turn x 90 > view > turn x 90 > view orient Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 15 atoms, 332 residues, 14 bonds, 1 postprocess_b20_3.3A.mrc > hide sel atoms > select clear > save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b1.cxs > turn x 90 > turn y 10 > turn y -10 > save /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b2.cxs > turn x 90 > turn y 10 Drag select of 87 residues, 1 postprocess_b20_3.3A.mrc > view sel > undo > select clear > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > view > undo > view > view orient > open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b2.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > turn y 10 > ui tool show ""Side View"" > turn y 10 > turn y -5 > turn y 5 > turn y -5 > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide H > select /C:410@NZ 1 atom, 1 residue, 1 model selected > show sel | contacts Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show sel contacts Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > contacts sel restrict otherAtoms distance 4 make true Invalid ""restrict"" argument: Expected one of 'any', 'both', or 'cross' or an atoms specifier > contacts sel restrict other Atoms distance 4 make true Invalid ""restrict"" argument: Expected one of 'any', 'both', or 'cross' or an atoms specifier > contacts sel restrict any atoms distance 4 make true Expected a keyword > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > ui tool show Contacts > contacts distanceOnly 4.0 ignoreHiddenModels true 146479 distances > undo > close #3.12 > select add #3.11 2 pseudobonds, 1 model selected > select subtract #3.11 Nothing selected > hide #3.11 models > select /C:410@NZ 1 atom, 1 residue, 1 model selected > hide #!1 models Drag select of 1 atoms, 88 residues > select clear Drag select of 6 atoms, 94 residues, 5 bonds > select clear Drag select of 3 atoms, 91 residues, 3 bonds > color (#!3 & sel) #ffaaffff > color (#!3 & sel) #ff557fff > color (#!3 & sel) #ff557ff1 > color (#!3 & sel) #ff557fe4 > color (#!3 & sel) #ff557fdc > color (#!3 & sel) #ff557fd4 > color (#!3 & sel) #ff557fd0 > color (#!3 & sel) #ff557fcb > color (#!3 & sel) #ff557fc2 > color (#!3 & sel) #ff557fbf > color (#!3 & sel) #ff557fb9 > color (#!3 & sel) #ff557fb2 > color (#!3 & sel) #ff557fab > color (#!3 & sel) #ff557fa3 > color (#!3 & sel) #ff557f9f > color (#!3 & sel) #ff557f9b > color (#!3 & sel) #ff557f98 > color (#!3 & sel) #ff557f97 > color (#!3 & sel) #ff557f94 > color (#!3 & sel) #ff557f8e > color (#!3 & sel) #ff557f8b > color (#!3 & sel) #ff557f8a > color (#!3 & sel) #ff557f8e > color (#!3 & sel) #ff557f94 > color (#!3 & sel) #ff557f95 > color (#!3 & sel) #ff557f9a > color (#!3 & sel) #ff557f9d > color (#!3 & sel) #ff557f97 > color (#!3 & sel) #ff557f90 > color (#!3 & sel) #ff557f8d > color (#!3 & sel) #ff557f89 > color (#!3 & sel) #ff557f87 > color (#!3 & sel) #ff557f86 > color (#!3 & sel) #ff557f84 > color (#!3 & sel) #ff557f83 > color (#!3 & sel) #ff557f81 > color (#!3 & sel) #ff557f80 > select clear > select /C:410@CD 1 atom, 1 residue, 1 model selected > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > color (#!3 & sel) #ff557f80 > color (#!3 & sel) #ff557f81 > color (#!3 & sel) #ff557f88 > color (#!3 & sel) #ff557f97 > color (#!3 & sel) #ff557fa4 > color (#!3 & sel) #ff557fb3 > color (#!3 & sel) #ff557fb8 > color (#!3 & sel) #ff557fc3 > color (#!3 & sel) #ff557fc6 > color (#!3 & sel) #ff557fcc > color (#!3 & sel) #ff557fd2 > color (#!3 & sel) #ff557fde > color (#!3 & sel) #ff557fe3 > color (#!3 & sel) #ff557fe8 > color (#!3 & sel) #ff557fed > color (#!3 & sel) #ff557ff1 > color (#!3 & sel) #ff557ff6 > color (#!3 & sel) #ff557ff9 > color (#!3 & sel) #ff557ffd > color (#!3 & sel) #ff557fff > undo Unknown command: ui undo > reset Unknown command: reset > ui tool show ""Side View"" > view sel > view > open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/a2.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00355, step 1, values float32 opened ChimeraX session > open /Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/b2.cxs format session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > turn y 5 > turn y -5 > turn y 30 > turn y -5 > turn y 5 > turn y -5 > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2.cxs"" > turn y -5 > turn y 5 > turn y -5 > turn y 5 > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1.cxs"" > hide #!1 models Drag select of 89 residues > color (#!3 & sel) #ff557fff > color (#!3 & sel) #ff557ffd > color (#!3 & sel) #ff557ff0 > color (#!3 & sel) #ff557fe3 > color (#!3 & sel) #ff557fdb > color (#!3 & sel) #ff557fd4 > color (#!3 & sel) #ff557fce > color (#!3 & sel) #ff557fc5 > color (#!3 & sel) #ff557fbe > color (#!3 & sel) #ff557fba > color (#!3 & sel) #ff557fb9 > color (#!3 & sel) #ff557fb7 > color (#!3 & sel) #ff557fb6 > color (#!3 & sel) #ff557fab > color (#!3 & sel) #ff557f99 > color (#!3 & sel) #ff557f82 > color (#!3 & sel) #ff557f7c > color (#!3 & sel) #ff557f74 > color (#!3 & sel) #ff557f6e > color (#!3 & sel) #ff557f6a > color (#!3 & sel) #ff557f68 > color (#!3 & sel) #ff557f65 > color (#!3 & sel) #ff557f63 > color (#!3 & sel) #ff557f62 > color (#!3 & sel) #ff557f5f > color (#!3 & sel) #ff557f5e > color (#!3 & sel) #ff557f5c > color (#!3 & sel) #ff557f5b > color (#!3 & sel) #ff557f59 > color (#!3 & sel) #ff557f58 > color (#!3 & sel) #ff557f56 > color (#!3 & sel) #ff557f55 > color (#!3 & sel) #ff557f54 > color (#!3 & sel) #ff557f52 > color (#!3 & sel) #ff557f51 > color (#!3 & sel) #ff557f50 > color (#!3 & sel) #ff557f4f > color (#!3 & sel) #ff557f4e > color (#!3 & sel) #ff557f4c > color (#!3 & sel) #ff557f4b > select clear Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 116 residues > select clear > graphics silhouettes false > graphics silhouettes true > select add #3 40132 atoms, 40646 bonds, 40 pseudobonds, 2584 residues, 6 models selected > select subtract #3 8 models selected > select /F:53 22 atoms, 21 bonds, 1 residue, 1 model selected > select /F:53 22 atoms, 21 bonds, 1 residue, 1 model selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > select add #3.9 8332 atoms, 539 residues, 4 models selected > select subtract #3.9 8330 atoms, 537 residues, 3 models selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #ff557f4d > color (#!3 & sel) #0090514d > select clear > show atoms > style stick Changed 40132 atom styles > color byhetero > select clear > hide H > select clear > ui mousemode right translate > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1.cxs"" format > session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > select add #1 5 models selected > select subtract #1 Nothing selected > hide #!1 models > ui mousemode right select > select /C:402 19 atoms, 18 bonds, 1 residue, 1 model selected > select /C:402 19 atoms, 18 bonds, 1 residue, 1 model selected > select /C:400 16 atoms, 15 bonds, 1 residue, 1 model selected Drag select of 91 residues > select clear Drag select of 89 residues > select subtract #3.5 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > color (#!3 & sel) #ff557f4d > select subtract #3.5 1 model selected > select /F:69 19 atoms, 18 bonds, 1 residue, 1 model selected > select /F:69 19 atoms, 18 bonds, 1 residue, 1 model selected > select /F:89 16 atoms, 15 bonds, 1 residue, 1 model selected > select /F:120 20 atoms, 20 bonds, 1 residue, 1 model selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > hide #3.8 models > color (#!3 & sel) #0090514d > select clear > select /F:38 /C:413,334 58 atoms, 58 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 58 atom styles > hide H > color sel byhetero > select clear > select /F:38@CG 1 atom, 1 residue, 1 model selected > select clear > select /F:38@CG 1 atom, 1 residue, 1 model selected > select clear > select /F:38 21 atoms, 21 bonds, 1 residue, 1 model selected > color (#!3 & sel) #0090514d > color (#!3 & sel) #00905184 > color (#!3 & sel) #009051b7 > color (#!3 & sel) #009051ce > color (#!3 & sel) #009051e6 > color (#!3 & sel) #009051f3 > color (#!3 & sel) #009051f9 > color (#!3 & sel) #009051ff > color sel byhetero > select /C:334,413 37 atoms, 37 bonds, 2 residues, 1 model selected > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051f8 > color (#!3 & sel) #009051d2 > color (#!3 & sel) #009051c2 > color (#!3 & sel) #009051c0 > color (#!3 & sel) #009051cd > color (#!3 & sel) #009051df > color (#!3 & sel) #009051e8 > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051f4 > color (#!3 & sel) #009051fd > color (#!3 & sel) #009051ff > color (#!3 & sel) #ff557fff > select clear > turn y 5 > select /F:38@CZ 1 atom, 1 residue, 1 model selected > select /C:334@CA 1 atom, 1 residue, 1 model selected > select /C:413 17 atoms, 17 bonds, 1 residue, 1 model selected > select add /F:38 38 atoms, 38 bonds, 2 residues, 2 models selected > select add /C:334 58 atoms, 58 bonds, 3 residues, 3 models selected > view sel > view > turn y -5 > turn y 5 > select /F:144-266 1868 atoms, 1898 bonds, 123 residues, 1 model selected > hide sel cartoons > select /G:2@CA 1 atom, 1 residue, 1 model selected > hide sel cartoons > hide sel surfaces Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 24 atoms, 209 residues, 24 bonds > select clear > show #!1 models > transparency #1.1#3.9-10 0 > volume style surface > select clear > transparency #1.1#3.9-10 50 > hide #!1 models Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 24 atoms, 209 residues, 24 bonds > volume zone #1 nearAtoms sel range 4 > show #!1 models > select clear > transparency #1.1#3.9-10 0 > volume style surface > transparency #1.1#3.9-10 50 > volume style mesh > volume style surface > transparency #1.1#3.9-10 0 > volume style surface > volume hide > volume show > volume style surface > transparency #1.1#3.9-10 50 > volume style image > volume style mesh > volume style surface > transparency #1.1#3.9-10 0 > transparency #1.1#3.9-10 50 Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 24 atoms, 209 residues, 24 bonds, 1 postprocess_b20_3.3A.mrc > hide #!1 models > show sel cartoons > show sel atoms > hide sel atoms > show sel surfaces > hide sel surfaces > show #!1 models > transparency sel 0 > volume sel style surface > transparency sel 0 > volume #1 color #d6d6d6 > transparency sel 0 > volume sel style surface > volume sel style mesh > volume sel style image > transparency sel & #3.5,8 0 > transparency sel & #3.5,8 50 > volume sel style surface > transparency sel 0 > select clear > transparency #1.1#3.5,8-10 0 > volume style surface > volume style mesh > volume style surface > transparency #1.1#3.5,8-10 50 > transparency #1.1#3.5,8-10 0 > transparency #1.1#3.5,8-10 50 > transparency #1.1#3.5,8-10 0 > transparency #1.1#3.5,8-10 50 > transparency #1.1#3.5,8-10 0 > transparency #1.1#3.5,8-10 50 > transparency #1.1#3.5,8-10 20 > transparency #1.1#3.5,8-10 90 > transparency #1.1#3.5,8-10 0 > transparency #1.1#3.5,8-10 50 > transparency #1 50 > transparency #1 20 > transparency #1 0 > transparency #1 90 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1.cxs"" format > session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > select /F144-266 Nothing selected > hide cartoons > undo > select /F:144-266 1868 atoms, 1898 bonds, 123 residues, 1 model selected > hide sel cartoons > select #1 5 models selected > select clear > hide #!1 models > select /G:2@CA 1 atom, 1 residue, 1 model selected > hide sel cartoons > hide sel surfaces Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 208 residues > select clear > select /F:68 17 atoms, 16 bonds, 1 residue, 1 model selected > select /F:90 19 atoms, 18 bonds, 1 residue, 1 model selected > select /F:89 16 atoms, 15 bonds, 1 residue, 1 model selected > select /F:68 17 atoms, 16 bonds, 1 residue, 1 model selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #d6d6d680 > color (#!3 & sel) #d6d6d68a > color (#!3 & sel) #d6d6d6a3 > color (#!3 & sel) #d6d6d6c3 > color (#!3 & sel) #d6d6d6e8 > color (#!3 & sel) #d6d6d6fd > color (#!3 & sel) #d6d6d6ff > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051db > color (#!3 & sel) #009051c8 > color (#!3 & sel) #009051bc > color (#!3 & sel) #009051b1 > color (#!3 & sel) #009051a5 > color (#!3 & sel) #009051a0 > color (#!3 & sel) #0090519f > color (#!3 & sel) #0090519c > color (#!3 & sel) #00905194 > color (#!3 & sel) #0090518d > color (#!3 & sel) #0090518e > color (#!3 & sel) #0090518f > color (#!3 & sel) #00905190 > color (#!3 & sel) #00905192 > color (#!3 & sel) #0090519d > color (#!3 & sel) #009051a9 > color (#!3 & sel) #009051ab > color (#!3 & sel) #009051b0 > color (#!3 & sel) #009051b8 > color (#!3 & sel) #009051c0 > color (#!3 & sel) #009051c1 > color (#!3 & sel) #009051c0 > color (#!3 & sel) #009051be > color (#!3 & sel) #009051b8 > color (#!3 & sel) #009051b4 > color (#!3 & sel) #009051b1 > color (#!3 & sel) #009051b0 > color (#!3 & sel) #009051b1 > color (#!3 & sel) #009051b4 > color (#!3 & sel) #009051b3 > select /C:400 16 atoms, 15 bonds, 1 residue, 1 model selected > select subtract #3.5 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > color (#!3 & sel) #ff557fb3 > undo > view > view orient > view > view orient > turn y 90 > turn x 90 > turn z 90 > turn y 90 > turn y 10 > select /C:411 17 atoms, 16 bonds, 1 residue, 1 model selected > select subtract #3.5 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > select clear > ui mousemode right zoom > show #!1 models > hide #!1 models > ui mousemode right select Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 209 residues > volume zone #mapID near sel range 4 Missing or invalid ""volumes"" argument: invalid density maps specifier > show #!1 models > volume zone #1 nearAtoms sel range 4 > select clear > transparency #1.1#3.8-10 0 > transparency #1.1#3.8-10 50 > hide #!1 models > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 2.cxs"" > show #!1 models > select add #3.8 8330 atoms, 537 residues, 1 model selected > select add #3.9 8332 atoms, 539 residues, 2 models selected > select subtract #3.8 2 atoms, 2 residues, 3 models selected > select add #3.10 4 atoms, 4 residues, 2 models selected > select subtract #3.9 2 atoms, 2 residues, 3 models selected > select add #3.9 4 atoms, 4 residues, 2 models selected > select subtract #3.10 2 atoms, 2 residues, 3 models selected > select add #3.8 8332 atoms, 539 residues, 2 models selected > select subtract #3.9 8330 atoms, 537 residues, 3 models selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > select add #3.5 17732 atoms, 1141 residues, 2 models selected > show #3.5 models > hide #3.5 models > hide #3.8 models > select subtract #3.5 8330 atoms, 537 residues, 3 models selected > select subtract #3.8 1 model selected > show #3.8 models > hide #3.8 models > color #3.8 #009051b1 > hide #!1 models > show #!1 models > hide #!1 models > show #3.8 models > show #3.5 models > hide #3.5 models > show #3.4 models > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > hide #3.4 models > select add #3.5 9402 atoms, 604 residues, 1 model selected > show #3.5 models > select add #3.8 17732 atoms, 1141 residues, 2 models selected > show #!1 models > hide #!1 models > show #3.7 models > hide #3.7 models > show #3.7 models > show #3.6 models > hide #3.7 models > hide #3.6 models > hide #3.8 models > show #3.8 models > show sel cartoons > hide sel cartoons > hide #3.8 models > hide #3.5 models > show #3.5 models > show #3.8 models > hide #3.8 models > hide #3.5 models > select subtract #3.5 8330 atoms, 537 residues, 3 models selected > select add #3.5 17732 atoms, 1141 residues, 2 models selected > select subtract #3.8 9402 atoms, 604 residues, 3 models selected > select subtract #3.5 1 model selected > hide #3.11 models > show #3.11 models > close #3.11 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 2.cxs"" format > session Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > hide #3.8 models > select add #3.8 8330 atoms, 537 residues, 1 model selected > select add #3.4 10620 atoms, 683 residues, 2 models selected > select subtract #3.4 8330 atoms, 537 residues, 3 models selected > select add #3.5 17732 atoms, 1141 residues, 2 models selected > show #!1 models > hide #!1 models > raise #3 Unknown command: raise #3 > raise #3.8 Unknown command: raise #3.8 > raise #3 Unknown command: raise #3 > select clear > modeldisplay #3 front Unknown command: modeldisplay #3 front > clip auto Expected a keyword > clip off > show #!1 models > hide #!1 models > show #!1 models > volume #1 color #d6d6d680 > volume #1 color #d6d6d6 > volume #1 color #d6d6d680 > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #d6d6d680 > color (#!3 & sel) #d6d6d68c > color (#!3 & sel) #d6d6d69e > color (#!3 & sel) #d6d6d6aa > color (#!3 & sel) #d6d6d6b8 > color (#!3 & sel) #d6d6d6c3 > color (#!3 & sel) #d6d6d6cf > color (#!3 & sel) #d6d6d6d3 > color (#!3 & sel) #d6d6d6d5 > color (#!3 & sel) #d6d6d6d8 > color (#!3 & sel) #d6d6d6dd > color (#!3 & sel) #d6d6d6e0 > color (#!3 & sel) #d6d6d6e3 > color (#!3 & sel) #d6d6d6e6 > color (#!3 & sel) #d6d6d6e7 > color (#!3 & sel) #d6d6d6e8 > color (#!3 & sel) #009051e8 > color (#!3 & sel) #009051f3 > color (#!3 & sel) #009051f8 > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051f5 > color (#!3 & sel) #009051f1 > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051ea > color (#!3 & sel) #009051eb > color (#!3 & sel) #009051ec > color (#!3 & sel) #009051ee > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051f5 > color (#!3 & sel) #009051f6 > color (#!3 & sel) #009051f8 > color (#!3 & sel) #009051fb > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051f6 > color (#!3 & sel) #009051f5 > color (#!3 & sel) #009051f6 > color (#!3 & sel) #009051f9 > color (#!3 & sel) #009051fb > color (#!3 & sel) #009051fd > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051f5 > color (#!3 & sel) #009051ed > color (#!3 & sel) #009051ec > color (#!3 & sel) #009051e7 > color (#!3 & sel) #009051e4 > color (#!3 & sel) #009051e0 > color (#!3 & sel) #009051e7 > color (#!3 & sel) #009051fd > color (#!3 & sel) #009051ff > show #3.8 models > hide #3.8 models > color #3.8 #ebebebff > color #3.8 white > color #3.8 #ebebebff > color #3.8 #ebebeb00 > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > select clear > hide #!1 models > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > select subtract #3.5 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > select subtract #3.8 1 model selected > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #ebebeb00 > color (#!3 & sel) #00905100 > color (#!3 & sel) #00905107 > color (#!3 & sel) #00905116 > color (#!3 & sel) #00905125 > color (#!3 & sel) #00905138 > color (#!3 & sel) #00905148 > color (#!3 & sel) #0090514e > color (#!3 & sel) #00905151 > color (#!3 & sel) #0090515b > color (#!3 & sel) #00905167 > color (#!3 & sel) #0090516a > color (#!3 & sel) #0090516c > color (#!3 & sel) #0090516e > color (#!3 & sel) #00905171 > color (#!3 & sel) #00905177 > color (#!3 & sel) #0090517b > color (#!3 & sel) #00905180 > color (#!3 & sel) #00905189 > color (#!3 & sel) #0090518d > color (#!3 & sel) #0090518e > color (#!3 & sel) #00905191 > color (#!3 & sel) #00905194 > color (#!3 & sel) #0090519a > color (#!3 & sel) #009051a0 > color (#!3 & sel) #009051a6 > color (#!3 & sel) #009051b3 > color (#!3 & sel) #009051b7 > color (#!3 & sel) #009051b8 > color (#!3 & sel) #009051b9 > color (#!3 & sel) #009051bb > color (#!3 & sel) #009051be > color (#!3 & sel) #009051c0 > color (#!3 & sel) #009051c2 > color (#!3 & sel) #009051c3 > color (#!3 & sel) #009051c4 > show #!1 models > color (#!3 & sel) #009051c4 > color (#!3 & sel) #009051c7 > color (#!3 & sel) #009051cf > color (#!3 & sel) #009051d6 > color (#!3 & sel) #009051dd > color (#!3 & sel) #009051e2 > color (#!3 & sel) #009051e6 > color (#!3 & sel) #009051e9 > color (#!3 & sel) #009051eb > color (#!3 & sel) #009051ed > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051f3 > color (#!3 & sel) #009051f4 > color (#!3 & sel) #009051f5 > color (#!3 & sel) #009051f7 > color (#!3 & sel) #009051f9 > color (#!3 & sel) #009051fb > color (#!3 & sel) #009051fd > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051fc > color (#!3 & sel) #009051f8 > color (#!3 & sel) #009051f4 > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051ed > color (#!3 & sel) #009051eb > color (#!3 & sel) #009051ee > color (#!3 & sel) #009051f9 > color (#!3 & sel) #009051fc > color (#!3 & sel) #009051ff > color (#!3 & sel) #009051f7 > color (#!3 & sel) #009051ee > color (#!3 & sel) #009051e8 > color (#!3 & sel) #009051e4 > color (#!3 & sel) #009051ea > color (#!3 & sel) #009051fd > color (#!3 & sel) #009051ff > color #3.8 #ebebebff > color #3.8 #ebebeb80 > select clear > hide #!1 models Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 120 residues > select clear > select /F:26-143 1842 atoms, 1876 bonds, 1 pseudobond, 118 residues, 2 models selected > color (#!3 & sel) #ebebeb80 > color (#!3 & sel) #00905180 > color (#!3 & sel) #00905181 > color (#!3 & sel) #00905186 > color (#!3 & sel) #0090518b > color (#!3 & sel) #00905193 > color (#!3 & sel) #00905198 > color (#!3 & sel) #0090519b > color (#!3 & sel) #0090519d > color (#!3 & sel) #0090519f > color (#!3 & sel) #009051a1 > color (#!3 & sel) #009051a3 > color (#!3 & sel) #009051a4 > color (#!3 & sel) #009051a5 > color (#!3 & sel) #009051a6 > color (#!3 & sel) #009051a7 > color (#!3 & sel) #009051aa > color (#!3 & sel) #009051ae > color (#!3 & sel) #009051af > color (#!3 & sel) #009051b1 > color (#!3 & sel) #009051b2 > show #!1 models > color (#!3 & sel) #009051b2 > color (#!3 & sel) #009051b5 > color (#!3 & sel) #009051b8 > color (#!3 & sel) #009051bc > color (#!3 & sel) #009051bd > color (#!3 & sel) #009051c1 > color (#!3 & sel) #009051c4 > color (#!3 & sel) #009051c6 > color (#!3 & sel) #009051cb > color (#!3 & sel) #009051ce > color (#!3 & sel) #009051d0 > color (#!3 & sel) #009051d3 > color (#!3 & sel) #009051d4 > color (#!3 & sel) #009051d7 > color (#!3 & sel) #009051d9 > color (#!3 & sel) #009051da > color (#!3 & sel) #009051db > color (#!3 & sel) #009051dc > color (#!3 & sel) #009051de > color (#!3 & sel) #009051e1 > color (#!3 & sel) #009051e2 > color (#!3 & sel) #009051e3 > color (#!3 & sel) #009051e4 > color (#!3 & sel) #009051e5 > color (#!3 & sel) #009051e7 > color (#!3 & sel) #009051e8 > color (#!3 & sel) #009051e9 > color (#!3 & sel) #009051eb > color (#!3 & sel) #009051ec > color (#!3 & sel) #009051ee > color (#!3 & sel) #009051f0 > color (#!3 & sel) #009051f2 > color (#!3 & sel) #009051f4 > color (#!3 & sel) #009051f5 > color (#!3 & sel) #009051f6 > color (#!3 & sel) #009051f9 > color (#!3 & sel) #009051fe > color (#!3 & sel) #009051ff > volume #1 color #d6d6d64c > select clear > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #d6d6d64d > color (#!3 & sel) #0090514d > color (#!3 & sel) #0090515d > color (#!3 & sel) #00905189 > color (#!3 & sel) #009051a6 > color (#!3 & sel) #009051cf > color (#!3 & sel) #009051e2 > color (#!3 & sel) #009051ed > color (#!3 & sel) #009051fe > color (#!3 & sel) #009051ff > color (#!3 & sel) #008f00ff > color (#!3 & sel) #00fa92ff > color (#!3 & sel) #73fcd6ff > color (#!3 & sel) #73fa79ff > select subtract #3.8 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > color (#!3 & sel) #73fa79ff > color (#!3 & sel) #ffaaffff > select clear > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 3.cxs"" > select /F:38 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > color (#!3 & sel) #009051ff > ui mousemode right zoom > select /C:413,334 37 atoms, 37 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 37 atom styles > color sel byhetero > color (#!3 & sel) #ff557fff > hide H > select /F:38 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel cartoons > show sel atoms > hide sel atoms > show sel atoms > style sel ball Changed 21 atom styles > style sel sphere Changed 21 atom styles > style sel stick Changed 21 atom styles > hide sel surfaces > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > hide H > color sel byhetero > ui mousemode right select > ui mousemode right zoom > ui mousemode right select > select clear > ui mousemode right zoom > ui mousemode right select > color byhetero > select #1 3 models selected > select clear > select #1 3 models selected > select clear > ui mousemode right zoom > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 4.cxs"" > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > hide #3.8 models > select add #3.8 8330 atoms, 537 residues, 1 model selected > select /F:26-143 1842 atoms, 1876 bonds, 1 pseudobond, 118 residues, 2 models selected > hide sel cartoons > hide #!1 models > ui mousemode right select > select /G:3@CA 1 atom, 1 residue, 1 model selected > hide sel cartoons > hide sel surfaces Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 214 residues > view sel > view > view orient > turn x 90 > select clear > turn y 90 > turn z 90 > turn x 90 > turn y 10 > turn y -5 > select add #3.3 2290 atoms, 146 residues, 1 model selected > select subtract #3.3 1 model selected > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > select add #3.4 2290 atoms, 146 residues, 1 model selected > select subtract #3.4 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > color (#!3 & sel) #ffaaffff > select subtract #3.5 1 model selected > select add #3.5 9402 atoms, 604 residues, 1 model selected > color (#!3 & sel) #ffaaff > select clear > select add #3.8 8330 atoms, 537 residues, 1 model selected > color (#!3 & sel) #73fa79ff > select clear Drag select of Refined_015_edit_glyco_real_space_refined_016.pdb_G SES surface, 148 of 296 triangles, 214 residues > volume zone #1 nearAtoms sel range 4 > show #!1 models > select clear > turn y 5 > turn y -5 > select /C:410 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color (#!3 & sel) #ff557fff > select /F:250,209,195 39 atoms, 36 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 39 atom styles > color sel byhetero > ui tool show ""Color Actions"" > color (#!3 & sel) #009051ff > hide H > select clear > color byhetero > close #3.11 > select add #3.10 2 atoms, 2 residues, 1 model selected > select subtract #3.10 1 model selected > select add #3.9 2 atoms, 2 residues, 1 model selected > color #3.9 #0096ffff > select clear > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 1.cxs"" > turn x 5 > turn x -5 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 1.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > select clear > ui mousemode right zoom > hide #!1 models > ui mousemode right select > select /F:208 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 21 atom styles > hide sel atoms > select clear > show #!1 models > select clear > ui mousemode right zoom > select clear > save ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 2.cxs"" > save /Users/lianqi/Desktop/image5.png supersample 3 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a2 1.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > save /Users/lianqi/Desktop/image6.png supersample 3 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 4.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > save /Users/lianqi/Desktop/image7.png supersample 3 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 3.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > save /Users/lianqi/Desktop/image8.png supersample 3 > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure2/Ig4 a1 2.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.0101, step 1, values float32 opened ChimeraX session > open ""/Users/lianqi/Files/Postdoc/VEGF/Figures/Figure 1/a1.cxs"" Opened postprocess_b20_3.3A.mrc as #1, grid size 330,330,330, pixel 1.08, shown at level 0.00355, step 1, values float32 opened ChimeraX session > open ""/Users/lianqi/Files/Postdoc/VEGF/EM > Data/Cis/relion_locres_filtered_job187.mrc"" > ""/Users/lianqi/Files/Postdoc/VEGF/EM > Data/Cis/tetramer_cis_13-coot-47_isolde_real_space_refined_057.pdb"" Opened relion_locres_filtered_job187.mrc as #2, grid size 400,400,400, pixel 0.936, shown at level 0.0027, step 2, values float32 Chain information for tetramer_cis_13-coot-47_isolde_real_space_refined_057.pdb #4 --- Chain | Description A B G H | No description available C I | No description available D J | No description available E K | No description available F L | No description available > select add #1 3 models selected > select add #2 5 models selected > select subtract #2 3 models selected > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 6 models selected > select subtract #3 11 models selected > select add #3 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 6 models selected > select subtract #1 40132 atoms, 40646 bonds, 38 pseudobonds, 2584 residues, 11 models selected > show #!3 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,7 Model Number: MRW13LL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 3 days, 1 hour, 37 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL E2218HN: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX