Opened 13 months ago
Closed 13 months ago
#15964 closed defect (nonchimerax)
Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics 655
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Graphics | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit 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: Aborted Current thread 0x00007ff84699fdc0 (most recent call first): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback 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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 60) {"app_name":"ChimeraX","timestamp":"2024-09-18 16:20:34.00 +0200","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"C9238B6C-0C10-41CB-927B-9C64F7767EFD"} { "uptime" : 870000, "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro15,2", "coalitionID" : 122465, "osVersion" : { "train" : "macOS 14.6.1", "build" : "23G93", "releaseType" : "User" }, "captureTime" : "2024-09-18 16:20:32.7602 +0200", "codeSigningMonitor" : 0, "incident" : "C9238B6C-0C10-41CB-927B-9C64F7767EFD", "pid" : 19657, "cpuType" : "X86-64", "roots_installed" : 0, "bug_type" : "309", "procLaunch" : "2024-09-18 11:48:25.5600 +0200", "procStartAbsTime" : 856502835302723, "procExitAbsTime" : 872829728241986, "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":"2D1D3C45-E2CD-50DC-B3E4-890A9DF5387C","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "edu.ucsf.cgl.ChimeraX", "crashReporterKey" : "C9E08316-F481-AE51-0088-DBB74F890D4B", "codeSigningID" : "edu.ucsf.cgl.ChimeraX", "codeSigningTeamID" : "LWV8X224YF", "codeSigningFlags" : 570491649, "codeSigningValidationCategory" : 6, "codeSigningTrustLevel" : 4294967295, "wakeTime" : 17015, "bridgeVersion" : {"build":"21P6074","train":"8.6"}, "sleepWakeUUID" : "4E90044D-30F0-461D-949D-8EDEC89765CC", "sip" : "enabled", "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"}, "termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":19657}, "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n", "asi" : {"libsystem_c.dylib":["abort() called"]}, "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"], "extMods" : 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UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/lau/Documentos/Ongoing/COP1/ChimeraX/COP!_open&closed&hy5ed.cxs Log from Tue Sep 17 20:22:45 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/lau/Documentos/Ongoing/COP1/full_data_session.cxs format session Log from Mon Sep 16 20:24:56 2024UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open "/Users/lau/Wigge Lab Dropbox/Wigge Lab's shared workspace/Lab > Info/Manuscripts/COP1/COP1 2024/COP1-HY5 animation/ChimeraX/COP1_closed.cxs" Log from Sat Sep 14 13:54:22 2024 Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif" Chain information for fold_cop1_model_0.cif #1 --- Chain | Description A | . > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif" Chain information for fold_cop1_model_0.cif #2 --- Chain | Description A | . > ui tool show "Show Sequence Viewer" > sequence chain #1/A #2/A Alignment identifier is 1 > select #1/A:10 #2/A:10 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/A:10-11 #2/A:10-11 28 atoms, 28 bonds, 4 residues, 2 models selected . [ID: 1] region 2 chains [10-11] RMSD: 0.000 > color sel red > select #1/A:1 #2/A:1 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/A:1-9 #2/A:1-9 138 atoms, 138 bonds, 18 residues, 2 models selected . [ID: 1] region 2 chains [1-9] RMSD: 0.000 > color sel orange > select #1/A:12 #2/A:12 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/A:12-19 #2/A:12-19 122 atoms, 124 bonds, 16 residues, 2 models selected . [ID: 1] region 2 chains [12-19] RMSD: 0.000 > color sel orange > select #1/A:20 #2/A:20 12 atoms, 10 bonds, 2 residues, 2 models selected > select #1/A:20-675 #2/A:20-675 10396 atoms, 10588 bonds, 1312 residues, 2 models selected . [ID: 1] region 2 chains [20-675] RMSD: 0.000 > color sel medium blue > color sel #8aacffff [Repeated 1 time(s)] > color sel #89abffff > color sel #88aaffff > color sel #86a9ffff > color sel #84a8ffff > color sel #82a8ffff > color sel #81a8ffff > color sel #80a8ffff [Repeated 1 time(s)] > color sel #80a9ffff > color sel #80abffff > color sel #80acffff > color sel #81aeffff > color sel #81afffff > color sel #81b0ffff > color sel #81b1ffff > color sel #82b2ffff > color sel #83b3ffff > color sel #83b4ffff > color sel #84b5ffff > color sel #84b6ffff > color sel #84b7ffff > color sel #85b8ffff [Repeated 1 time(s)] > color sel #86b9ffff > color sel #87baffff > color sel #88bbffff > color sel #88bcffff > color sel #89bdffff > color sel #8bbeffff > color sel #8dbeffff > color sel #8fbfffff > color sel #90c0ffff [Repeated 1 time(s)] > color sel #91c0ffff > color sel #92c0ffff > color sel #92bfffff > color sel #94bfffff [Repeated 1 time(s)] > color sel #95bfffff [Repeated 1 time(s)] > color sel #97c0ffff [Repeated 1 time(s)] > color sel #98c0ffff > color sel #99c0ffff [Repeated 1 time(s)] > color sel #9ac0ffff [Repeated 1 time(s)] > color sel #9bc0ffff > color sel #9cbfffff [Repeated 1 time(s)] > color sel #9dbfffff [Repeated 1 time(s)] > color sel #9ebfffff > color sel #9fbfffff > color sel #a0bfffff [Repeated 1 time(s)] > color sel #a1bfffff [Repeated 1 time(s)] > color sel #a2bfffff > color sel #a3beffff > color sel #a4bdffff [Repeated 1 time(s)] > color sel #a4bcffff > color sel #a7baffff > color sel #acb6ffff > color sel #aeb3ffff > color sel #afb2ffff > color sel #aeb1ffff > color sel #adafffff > color sel #adadffff > color sel #acacffff > color sel #acabffff [Repeated 1 time(s)] > color sel #acaaffff [Repeated 1 time(s)] > color sel #aba9ffff > color sel #aba8ffff [Repeated 1 time(s)] > color sel #aaa7ffff > color sel #aaa6ffff > color sel #a9a4ffff > color sel #a8a2ffff > color sel #a7a1ffff > color sel #a6a0ffff > color sel #a59fffff > color sel #a59effff > color sel #a59dffff > color sel #a49cffff [Repeated 1 time(s)] > color sel #a49bffff > color sel #a49affff > color sel #a39affff [Repeated 2 time(s)] > select clear > set bgColor white > select #1/A:12 #2/A:12 10 atoms, 8 bonds, 2 residues, 2 models selected > select #1/A:12-24 #2/A:12-24 186 atoms, 188 bonds, 26 residues, 2 models selected . [ID: 1] region 2 chains [12-24] RMSD: 0.000 > color sel cornflower blue > select #1/A:1 #2/A:1 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/A:1-39 #2/A:1-39 550 atoms, 558 bonds, 78 residues, 2 models selected . [ID: 1] region 2 chains [1-39] RMSD: 0.000 > select #1/A:40-41 #2/A:40-41 34 atoms, 32 bonds, 4 residues, 2 models selected > select #1/A:8-41 #2/A:8-41 474 atoms, 482 bonds, 68 residues, 2 models selected . [ID: 1] region 2 chains [8-41] RMSD: 0.000 > select #1/A:1 #2/A:1 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/A:1-40 #2/A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected . [ID: 1] region 2 chains [1-40] RMSD: 0.000 > ui tool show "Color Actions" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color sel pink [Repeated 2 time(s)] > select clear > select /A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected > set bgColor black > select clear > select A/:1-40 Expected an objects specifier or a keyword > select /A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected > color sel yellow > select clear > select #1/A:1-40 #2/A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected > select #1/A:10 #2/A:10 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/A:10-11 #2/A:10-11 28 atoms, 28 bonds, 4 residues, 2 models selected . [ID: 1] region 2 chains [10-11] RMSD: 0.000 > color sel red > select clear > surface > transparency 60 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #1.1 models > hide #!2 models > show #!2 models > hide #2.1 models > show #2.1 models > select /A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected > color (#!2 & sel) #f4e90d66 [Repeated 1 time(s)] > color (#!2 & sel) #f4e90e66 > color (#!2 & sel) #f4ea1266 > color (#!2 & sel) #f4ea1566 > color (#!2 & sel) #f4ea1866 > color (#!2 & sel) #f4ea1e66 > color (#!2 & sel) #f4ea2166 > color (#!2 & sel) #f4eb2466 > color (#!2 & sel) #f4ef2d66 > color (#!2 & sel) #f4f43e66 > color (#!2 & sel) #f0f44866 > color (#!2 & sel) #eff44a66 > color (#!2 & sel) #f0f44c66 > color (#!2 & sel) #f0f44d66 > color (#!2 & sel) #eff44f66 > color (#!2 & sel) #ebf45d66 > color (#!2 & sel) #e6f47066 > color (#!2 & sel) #e6f47366 > color (#!2 & sel) #e6f47466 [Repeated 1 time(s)] > color (#!2 & sel) #e7f47666 > color (#!2 & sel) #ebf48366 > color (#!2 & sel) #edf49366 > color (#!2 & sel) #eef49a66 > color (#!2 & sel) #eff49b66 > color (#!2 & sel) #eff49c66 > color (#!2 & sel) #f0f49d66 > color (#!2 & sel) #f0f49e66 > color (#!2 & sel) #f2f4a166 > color (#!2 & sel) #f3f4a366 > color (#!2 & sel) #f4f4a666 > color (#!2 & sel) #f4f3a766 > color (#!2 & sel) #f4f2a966 > color (#!2 & sel) #f4f0ad66 > color (#!2 & sel) #f4efaf66 > color (#!2 & sel) #f4efb066 > color (#!2 & sel) #f4edb266 > color (#!2 & sel) #f4ecb666 > color (#!2 & sel) #f4ebba66 > color (#!2 & sel) #f4ebbb66 [Repeated 1 time(s)] > color (#!2 & sel) #f4e9bd66 > color (#!2 & sel) #f4e9c066 > color (#!2 & sel) #f4e9c166 > color (#!2 & sel) #f4e8c466 > color (#!2 & sel) #f4e9c866 [Repeated 1 time(s)] > color (#!2 & sel) #f4e9c766 > color (#!2 & sel) #f4eac666 > color (#!2 & sel) #f4ebc366 > color (#!2 & sel) #f4e9be66 > color (#!2 & sel) #f4e8b966 > color (#!2 & sel) #f4e7b566 > color (#!2 & sel) #f4e7b366 > color (#!2 & sel) #f4e6b066 > color (#!2 & sel) #f4e7ab66 > color (#!2 & sel) #f4e8a666 > color (#!2 & sel) #f4e89566 > color (#!2 & sel) #f4e57966 > color (#!2 & sel) #f4e46566 > color (#!2 & sel) #f4e46066 [Repeated 1 time(s)] > color (#!2 & sel) #f4e45f66 > color (#!2 & sel) #f4e55f66 > color (#!2 & sel) #f4e65f66 [Repeated 1 time(s)] > color (#!2 & sel) #f4e75f66 [Repeated 1 time(s)] > color (#!2 & sel) #f4e85f66 > color (#!2 & sel) #f4e95f66 > color (#!2 & sel) #f4ea5f66 > color (#!2 & sel) #f4eb5f66 > color (#!2 & sel) #f4ec6066 > color (#!2 & sel) #f4ed6066 > color (#!2 & sel) #f4ed6166 > color (#!2 & sel) #f4ee6166 > color (#!2 & sel) #f4ef6266 > color (#!2 & sel) #f4f06366 > color (#!2 & sel) #f4f16366 > color (#!2 & sel) #f4f06666 > color (#!2 & sel) #f4ef6866 > color (#!2 & sel) #f4ee6a66 > color (#!2 & sel) #f4ed6c66 > color (#!2 & sel) #f4ed6d66 > color (#!2 & sel) #f4ed6f66 > color (#!2 & sel) #f4ee6f66 > color (#!2 & sel) #f4ef7166 > color (#!2 & sel) #f4ef7366 > color (#!2 & sel) #f4ef7466 > color (#!2 & sel) #f4ee7766 > color (#!2 & sel) #f4ee7966 > color (#!2 & sel) #f4ed7c66 > color (#!2 & sel) #f4ee8266 > color (#!2 & sel) #f4ee8666 > color (#!2 & sel) #f4ef8a66 > color (#!2 & sel) #f4ef8b66 > color (#!2 & sel) #f4ef8c66 > color (#!2 & sel) #f4ee8d66 > color (#!2 & sel) #f4ef8e66 [Repeated 1 time(s)] > color (#!2 & sel) #f4ef9066 > color (#!2 & sel) #f4ef9266 [Repeated 1 time(s)] > color (#!2 & sel) #f4f09366 [Repeated 1 time(s)] > color (#!2 & sel) #f4f09466 > color (#!2 & sel) #f4f09566 [Repeated 1 time(s)] > color (#!2 & sel) #f4f19666 [Repeated 1 time(s)] > color (#!2 & sel) #f4f19766 > color (#!2 & sel) #f4f09966 > color (#!2 & sel) #f4f19966 > color (#!2 & sel) #f4f19a66 > color (#!2 & sel) #f4f19b66 > color (#!2 & sel) #f4f19c66 > color (#!2 & sel) #f4f19d66 > color (#!2 & sel) #f4f19e66 > color (#!2 & sel) #f4f19f66 > color (#!2 & sel) #f4f2a166 > color (#!2 & sel) #f4f3a266 > color (#!2 & sel) #f4f3a366 > color (#!2 & sel) #f4f3a466 > color (#!2 & sel) #f4f4a466 > color (#!2 & sel) #f4f4a566 > color (#!2 & sel) #f3f4a566 > color (#!2 & sel) #f2f4a266 > color (#!2 & sel) #f1f4a066 > color (#!2 & sel) #f1f49d66 > color (#!2 & sel) #f1f49c66 > color (#!2 & sel) #f1f49b66 > color (#!2 & sel) #f0f49966 > color (#!2 & sel) #f0f49866 > color (#!2 & sel) #eff49666 > color (#!2 & sel) #edf49366 > color (#!2 & sel) #ecf49166 > color (#!2 & sel) #ecf49066 [Repeated 3 time(s)] > color (#!2 & sel) #ecf48f66 > color (#!2 & sel) #edf48f66 > color (#!2 & sel) #eef48e66 > color (#!2 & sel) #eff48e66 > color (#!2 & sel) #f0f48e66 [Repeated 1 time(s)] > color (#!2 & sel) #f1f48e66 > color (#!2 & sel) #f2f48e66 > color (#!2 & sel) #f3f48e66 > color (#!2 & sel) #f4f48f66 > color (#!2 & sel) #f4f38e66 [Repeated 1 time(s)] > color (#!2 & sel) #f4f28e66 [Repeated 1 time(s)] > color (#!2 & sel) #f4f28f66 > select /A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected > select #1/A:10 #2/A:10 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/A:10-11 #2/A:10-11 28 atoms, 28 bonds, 4 residues, 2 models selected . [ID: 1] region 2 chains [10-11] RMSD: 0.000 > color (#!2 & sel) #f4452d66 [Repeated 1 time(s)] > color (#!2 & sel) #f4472b66 [Repeated 1 time(s)] > color (#!2 & sel) #f4482b66 > color (#!2 & sel) #f44a2b66 > color (#!2 & sel) #f4572e66 > color (#!2 & sel) #f4643166 > color (#!2 & sel) #f4663266 > color (#!2 & sel) #f4673166 > color (#!2 & sel) #f4693066 > color (#!2 & sel) #f4682c66 > color (#!2 & sel) #f4672966 > color (#!2 & sel) #f4662866 > color (#!2 & sel) #f4652766 > color (#!2 & sel) #f4642666 > color (#!2 & sel) #f4632566 > color (#!2 & sel) #f4622466 > color (#!2 & sel) #f4602266 > color (#!2 & sel) #f45f2066 > color (#!2 & sel) #f45e2066 > color (#!2 & sel) #f45d1f66 [Repeated 1 time(s)] > color (#!2 & sel) #f45c1e66 > color (#!2 & sel) #f45b1d66 > select clear > transparency #2 30 > transparency #2 90 > transparency #2 30 > transparency #2 40 > select /A:368-619 4014 atoms, 4106 bonds, 504 residues, 2 models selected > select /A:368-675 4858 atoms, 4968 bonds, 616 residues, 2 models selected > color (#!2 & sel) #f45b1a66 > color (#!2 & sel) #f45c1b66 > color (#!2 & sel) #f4723166 > color (#!2 & sel) #f48f4e66 > color (#!2 & sel) #f4935266 > color (#!2 & sel) #f4945366 > color (#!2 & sel) #f4995e66 > color (#!2 & sel) #f49e6b66 > color (#!2 & sel) #f49d6c66 > color (#!2 & sel) #f49c6d66 > color (#!2 & sel) #f49d7b66 > color (#!2 & sel) #f4a09266 > color (#!2 & sel) #f49d9466 > color (#!2 & sel) #f49b9466 > color (#!2 & sel) #f4999466 > color (#!2 & sel) #f4a3ad66 > color (#!2 & sel) #f4b0e066 > color (#!2 & sel) #f4afe766 > color (#!2 & sel) #f4aee866 > color (#!2 & sel) #f4adea66 > color (#!2 & sel) #e6a4f466 > color (#!2 & sel) #c58ef466 > color (#!2 & sel) #c089f466 > color (#!2 & sel) #bf88f466 > color (#!2 & sel) #be86f466 > color (#!2 & sel) #b07af466 > color (#!2 & sel) #8f60f466 > color (#!2 & sel) #8b5cf466 > color (#!2 & sel) #895af466 > color (#!2 & sel) #885af466 > color (#!2 & sel) #7042f466 > color (#!2 & sel) #6033f466 > color (#!2 & sel) #6032f466 > color (#!2 & sel) #6033f466 > color (#!2 & sel) #6435f466 > color (#!2 & sel) #6637f466 > color (#!2 & sel) #6b39f466 > color (#!2 & sel) #6c3af466 > color (#!2 & sel) #6d3bf466 > color (#!2 & sel) #6e3cf466 > color (#!2 & sel) #6f3cf466 > color (#!2 & sel) #713ff466 > color (#!2 & sel) #7541f466 > color (#!2 & sel) #7943f466 > color (#!2 & sel) #7c44f466 > color (#!2 & sel) #7e44f466 > color (#!2 & sel) #8145f466 > color (#!2 & sel) #8346f466 > color (#!2 & sel) #914ff466 > color (#!2 & sel) #9350f466 > color (#!2 & sel) #9551f466 > color (#!2 & sel) #9751f466 > color (#!2 & sel) #9851f466 > color (#!2 & sel) #9a51f466 > color (#!2 & sel) #9d51f466 > color (#!2 & sel) #9f51f466 > color (#!2 & sel) #a051f466 [Repeated 1 time(s)] > color (#!2 & sel) #9456f466 > color (#!2 & sel) #7a5ef466 > color (#!2 & sel) #5a5af466 > color (#!2 & sel) #4e66f466 > color (#!2 & sel) #3c75f466 > color (#!2 & sel) #307ff466 > color (#!2 & sel) #248cf466 > color (#!2 & sel) #1c95f466 > color (#!2 & sel) #199bf466 > color (#!2 & sel) #1a9df466 > color (#!2 & sel) #1a9ef466 > color (#!2 & sel) #1b9ff466 > color (#!2 & sel) #1f9ff466 > color (#!2 & sel) #229ef466 > color (#!2 & sel) #259af466 > color (#!2 & sel) #2697f466 > color (#!2 & sel) #2794f466 > color (#!2 & sel) #2893f466 > color (#!2 & sel) #2891f466 > color (#!2 & sel) #2990f466 > color (#!2 & sel) #298ff466 > color (#!2 & sel) #298ef466 > color (#!2 & sel) #298cf466 > color (#!2 & sel) #298bf466 > color (#!2 & sel) #298af466 > color (#!2 & sel) #2b89f466 > color (#!2 & sel) #2c87f466 > color (#!2 & sel) #2e86f466 > color (#!2 & sel) #2f85f466 > color (#!2 & sel) #3084f466 > color (#!2 & sel) #3c81f466 > color (#!2 & sel) #4e78f466 > color (#!2 & sel) #586df466 > color (#!2 & sel) #6a63f466 > color (#!2 & sel) #8366f466 > color (#!2 & sel) #8e67f466 > color (#!2 & sel) #9566f466 > color (#!2 & sel) #9666f466 > color (#!2 & sel) #9964f466 > color (#!2 & sel) #9a62f466 > color (#!2 & sel) #9d5ff466 > color (#!2 & sel) #9f5df466 > color (#!2 & sel) #a05bf466 > color (#!2 & sel) #a059f466 > color (#!2 & sel) #a159f466 > color (#!2 & sel) #a158f466 > color (#!2 & sel) #a255f466 [Repeated 1 time(s)] > color (#!2 & sel) #a253f466 > color (#!2 & sel) #a450f466 > color (#!2 & sel) #a64bf466 > color (#!2 & sel) #a848f466 > color (#!2 & sel) #a846f466 > color (#!2 & sel) #a945f466 > color (#!2 & sel) #a944f466 > color (#!2 & sel) #a841f466 > color (#!2 & sel) #a93ff466 > color (#!2 & sel) #aa3df466 > color (#!2 & sel) #aa38f466 > color (#!2 & sel) #ad33f466 > color (#!2 & sel) #ac32f466 [Repeated 1 time(s)] > color (#!2 & sel) #ac31f466 > color (#!2 & sel) #ab30f466 [Repeated 1 time(s)] > color (#!2 & sel) #ab2ff466 > color (#!2 & sel) #aa2ef466 > color (#!2 & sel) #a92df466 [Repeated 1 time(s)] > color (#!2 & sel) #a92cf466 > color (#!2 & sel) #a82bf466 > color (#!2 & sel) #a729f466 > color (#!2 & sel) #a627f466 > color (#!2 & sel) #a525f466 > color (#!2 & sel) #a524f466 > color (#!2 & sel) #a424f466 > color (#!2 & sel) #a222f466 > color (#!2 & sel) #a01ff466 > color (#!2 & sel) #9e1df466 > color (#!2 & sel) #9d1cf466 > color (#!2 & sel) #9b1bf466 > color (#!2 & sel) #9818f466 > color (#!2 & sel) #9617f466 > color (#!2 & sel) #9516f466 > color (#!2 & sel) #9316f466 > color (#!2 & sel) #9214f466 > color (#!2 & sel) #8e13f466 > color (#!2 & sel) #8910f466 > color (#!2 & sel) #870ff466 [Repeated 1 time(s)] > color (#!2 & sel) #860ff466 > color (#!2 & sel) #7f0cf466 > color (#!2 & sel) #7a08f466 > color (#!2 & sel) #7907f466 > color (#!2 & sel) #7502f466 > color (#!2 & sel) #7400f466 > color (#!2 & sel) #7100f466 > color (#!2 & sel) #6e00f466 > color (#!2 & sel) #6500f466 > color (#!2 & sel) #6200f466 > color (#!2 & sel) #5f00f466 > color (#!2 & sel) #5300f466 > color (#!2 & sel) #4700f466 > color (#!2 & sel) #4400f466 > color (#!2 & sel) #4100f466 > color (#!2 & sel) #3e00f466 > color (#!2 & sel) #3b00f466 > color (#!2 & sel) #3800f466 > color (#!2 & sel) #3500f466 > color (#!2 & sel) #3200f466 [Repeated 1 time(s)] > color (#!2 & sel) #3300f466 > color (#!2 & sel) #3400f466 > color (#!2 & sel) #3700f466 > color (#!2 & sel) #3b00f466 > color (#!2 & sel) #3e00f466 > color (#!2 & sel) #4200f466 > color (#!2 & sel) #4700f466 > color (#!2 & sel) #5100f466 > color (#!2 & sel) #5900f466 > color (#!2 & sel) #6201f466 > color (#!2 & sel) #6a02f466 > color (#!2 & sel) #6f02f466 > color (#!2 & sel) #7502f466 > color (#!2 & sel) #7a04f466 > color (#!2 & sel) #7c06f466 > color (#!2 & sel) #7f0af466 > color (#!2 & sel) #850ff466 > color (#!2 & sel) #8a14f466 > color (#!2 & sel) #961df466 > color (#!2 & sel) #9b21f466 > color (#!2 & sel) #9d22f466 > color (#!2 & sel) #9d23f466 > color (#!2 & sel) #9e25f466 > color (#!2 & sel) #a22df466 > color (#!2 & sel) #a32ff466 > color (#!2 & sel) #a532f466 > color (#!2 & sel) #a83af466 > color (#!2 & sel) #ab41f466 > color (#!2 & sel) #ad45f466 > color (#!2 & sel) #b04bf466 > color (#!2 & sel) #b24ef466 > color (#!2 & sel) #b350f466 > color (#!2 & sel) #b656f466 > color (#!2 & sel) #b758f466 > color (#!2 & sel) #b85af466 > color (#!2 & sel) #b95ff466 > color (#!2 & sel) #b860f466 > color (#!2 & sel) #b963f466 > color (#!2 & sel) #b967f466 > color (#!2 & sel) #b96af466 > color (#!2 & sel) #ba6df466 > color (#!2 & sel) #b96ef466 > color (#!2 & sel) #b96ff466 > color (#!2 & sel) #bb72f466 > color (#!2 & sel) #bc75f466 > color (#!2 & sel) #bd76f466 > color (#!2 & sel) #be78f466 > color (#!2 & sel) #bf7bf466 > color (#!2 & sel) #c080f466 > color (#!2 & sel) #c082f466 > color (#!2 & sel) #c185f466 > color (#!2 & sel) #c288f466 > color (#!2 & sel) #c289f466 > color (#!2 & sel) #c28af466 > color (#!2 & sel) #c38cf466 > color (#!2 & sel) #c48ef466 [Repeated 1 time(s)] > color (#!2 & sel) #c58ff466 > color (#!2 & sel) #c691f466 > color (#!2 & sel) #c692f466 > color (#!2 & sel) #c795f466 > color (#!2 & sel) #c798f466 > color (#!2 & sel) #c899f466 [Repeated 1 time(s)] > color (#!2 & sel) #c89bf466 > color (#!2 & sel) #c99ef466 > color (#!2 & sel) #ca9ff466 > color (#!2 & sel) #caa0f466 [Repeated 1 time(s)] > color (#!2 & sel) #caa1f466 > color (#!2 & sel) #cba2f466 > color (#!2 & sel) #cba3f466 > color (#!2 & sel) #cca4f466 > color (#!2 & sel) #cca5f466 > color (#!2 & sel) #cda6f466 > color (#!2 & sel) #cda7f466 > color (#!2 & sel) #cda8f466 > color (#!2 & sel) #cea9f466 [Repeated 1 time(s)] > color (#!2 & sel) #cdaaf466 > color (#!2 & sel) #cbaaf466 > color (#!2 & sel) #cba9f466 > color (#!2 & sel) #c9a9f466 > color (#!2 & sel) #c7a8f466 > color (#!2 & sel) #c5a8f466 > color (#!2 & sel) #c3a8f466 > color (#!2 & sel) #c2a8f466 > color (#!2 & sel) #c0a7f466 > color (#!2 & sel) #bda6f466 > color (#!2 & sel) #bba6f466 > color (#!2 & sel) #b8a5f466 > color (#!2 & sel) #b7a5f466 [Repeated 1 time(s)] > color (#!2 & sel) #b6a4f466 > color (#!2 & sel) #b5a4f466 > color (#!2 & sel) #b4a4f466 > color (#!2 & sel) #b2a4f466 > color (#!2 & sel) #b2a3f466 > color (#!2 & sel) #b1a3f466 > color (#!2 & sel) #b0a3f466 > color (#!2 & sel) #afa3f466 > color (#!2 & sel) #ada2f466 > color (#!2 & sel) #aba2f466 > color (#!2 & sel) #aaa1f466 > color (#!2 & sel) #a8a0f466 > color (#!2 & sel) #a7a0f466 > color (#!2 & sel) #a59ff466 > color (#!2 & sel) #a49ff466 > color (#!2 & sel) #a29ef466 > color (#!2 & sel) #a19ef466 > color (#!2 & sel) #9e9df466 > color (#!2 & sel) #9c9cf466 > color (#!2 & sel) #9b9bf466 > color (#!2 & sel) #999cf466 > color (#!2 & sel) #979cf466 > color (#!2 & sel) #979bf466 > color (#!2 & sel) #969bf466 > color (#!2 & sel) #959cf466 > color (#!2 & sel) #919af466 > color (#!2 & sel) #8e99f466 > color (#!2 & sel) #8c98f466 > color (#!2 & sel) #8a97f466 > color (#!2 & sel) #8897f466 > color (#!2 & sel) #8797f466 > color (#!2 & sel) #8696f466 > color (#!2 & sel) #8596f466 [Repeated 1 time(s)] > color (#!2 & sel) #8495f466 > color (#!2 & sel) #8395f466 > color (#!2 & sel) #8195f466 > color (#!2 & sel) #8094f466 > color (#!2 & sel) #7f94f466 > color (#!2 & sel) #7e94f466 > color (#!2 & sel) #7d94f466 [Repeated 1 time(s)] > color (#!2 & sel) #7b94f466 > color (#!2 & sel) #7a94f466 > color (#!2 & sel) #7994f466 > color (#!2 & sel) #7893f466 > color (#!2 & sel) #7793f466 > color (#!2 & sel) #7693f466 > color (#!2 & sel) #7593f466 [Repeated 2 time(s)] > color (#!2 & sel) #7592f366 > color (#!2 & sel) #7492f266 > color (#!2 & sel) #7491f166 [Repeated 1 time(s)] > color (#!2 & sel) #7391f066 [Repeated 1 time(s)] > color (#!2 & sel) #7390ef66 [Repeated 1 time(s)] > color (#!2 & sel) #7290ee66 > color (#!2 & sel) #728fed66 [Repeated 1 time(s)] > color (#!2 & sel) #728eec66 > color (#!2 & sel) #718eec66 [Repeated 1 time(s)] > color (#!2 & sel) #718eeb66 > color (#!2 & sel) #718deb66 > color (#!2 & sel) #708ce866 > color (#!2 & sel) #6e8be666 > color (#!2 & sel) #6d89e466 > color (#!2 & sel) #6d88e266 > color (#!2 & sel) #6984db66 > color (#!2 & sel) #657fd266 > color (#!2 & sel) #617aca66 > color (#!2 & sel) #5f77c566 > color (#!2 & sel) #5e76c466 > color (#!2 & sel) #5e76c366 > color (#!2 & sel) #5c73bf66 > color (#!2 & sel) #5a71bc66 > color (#!2 & sel) #586eb666 > color (#!2 & sel) #566bb266 > color (#!2 & sel) #556bb266 [Repeated 1 time(s)] > color (#!2 & sel) #566cb366 > color (#!2 & sel) #576eb666 > color (#!2 & sel) #596fb966 > color (#!2 & sel) #5a71bb66 > color (#!2 & sel) #5b72be66 > color (#!2 & sel) #5c73bf66 > color (#!2 & sel) #5d74c166 > color (#!2 & sel) #5d75c266 > color (#!2 & sel) #5e76c566 > color (#!2 & sel) #5f78c666 > color (#!2 & sel) #617aca66 > color (#!2 & sel) #637ccd66 > color (#!2 & sel) #637cce66 > color (#!2 & sel) #647dcf66 > color (#!2 & sel) #6680d466 > color (#!2 & sel) #6782d766 > color (#!2 & sel) #6882d866 [Repeated 1 time(s)] > color (#!2 & sel) #6983da66 > color (#!2 & sel) #6a84dc66 > color (#!2 & sel) #6a85dc66 > color (#!2 & sel) #6b86de66 > color (#!2 & sel) #6b87e066 > color (#!2 & sel) #6c87e066 [Repeated 1 time(s)] > color (#!2 & sel) #6c87e166 > color (#!2 & sel) #6c88e166 > color (#!2 & sel) #6c88e266 > color (#!2 & sel) #6d88e266 > color (#!2 & sel) #6d89e366 > select clear > set bgColor white > hide #!2 cartoons [Repeated 1 time(s)] > show #!2 cartoons > transparency #2 60 > transparency #2 20 > select /A 368-675 Expected a keyword > select /A:368-675 4858 atoms, 4968 bonds, 616 residues, 2 models selected > color (#!2 & sel) #698ae366 [Repeated 1 time(s)] > color (#!2 & sel) #6787e366 > color (#!2 & sel) #6786e366 > color (#!2 & sel) #6785e366 > color (#!2 & sel) #6684e366 > color (#!2 & sel) #6582e366 > color (#!2 & sel) #6079e366 > color (#!2 & sel) #5868e366 > color (#!2 & sel) #545ee366 > color (#!2 & sel) #545de366 > color (#!2 & sel) #545ce366 > color (#!2 & sel) #5356e366 > color (#!2 & sel) #5350e366 [Repeated 1 time(s)] > color (#!2 & sel) #544fe366 > color (#!2 & sel) #534ee366 > color (#!2 & sel) #534de366 > color (#!2 & sel) #554be366 > color (#!2 & sel) #584ae366 > color (#!2 & sel) #5b49e366 > color (#!2 & sel) #5f48e366 > color (#!2 & sel) #6246e366 > color (#!2 & sel) #6444e366 > color (#!2 & sel) #6743e366 > color (#!2 & sel) #6842e366 > color (#!2 & sel) #6941e366 > color (#!2 & sel) #6b3fe366 > color (#!2 & sel) #703de366 > color (#!2 & sel) #723ce366 > color (#!2 & sel) #723be366 > color (#!2 & sel) #713ae366 > color (#!2 & sel) #6d37e366 > color (#!2 & sel) #6a35e366 > color (#!2 & sel) #6432e366 > color (#!2 & sel) #5d2ee366 > color (#!2 & sel) #4c25e366 > color (#!2 & sel) #4321e366 > color (#!2 & sel) #4121e366 > color (#!2 & sel) #3b1fe366 > color (#!2 & sel) #2516e366 > color (#!2 & sel) #1e13e366 > color (#!2 & sel) #1c12e366 > color (#!2 & sel) #1b13e366 > color (#!2 & sel) #1410e366 > color (#!2 & sel) #0b0fe366 > color (#!2 & sel) #0a10e366 > color (#!2 & sel) #0b13e366 > color (#!2 & sel) #0717e366 > color (#!2 & sel) #0518e366 > color (#!2 & sel) #0619e366 > color (#!2 & sel) #061ae366 > color (#!2 & sel) #041ce366 > color (#!2 & sel) #0024e366 > color (#!2 & sel) #0029e366 > color (#!2 & sel) #002be366 > color (#!2 & sel) #002de366 > color (#!2 & sel) #0031e366 > color (#!2 & sel) #0035e366 > color (#!2 & sel) #0038e366 > color (#!2 & sel) #003ce366 > color (#!2 & sel) #003de366 > color (#!2 & sel) #003fe366 > color (#!2 & sel) #0040e366 > color (#!2 & sel) #0041e366 > color (#!2 & sel) #0042e366 > color (#!2 & sel) #0043e366 > color (#!2 & sel) #0545e366 > color (#!2 & sel) #0a47e366 > color (#!2 & sel) #104be366 > color (#!2 & sel) #144de366 > color (#!2 & sel) #1a51e366 > color (#!2 & sel) #2053e366 > color (#!2 & sel) #2a56e366 > color (#!2 & sel) #3259e366 > color (#!2 & sel) #355ae366 [Repeated 1 time(s)] > color (#!2 & sel) #385ae366 > color (#!2 & sel) #3e5ae366 [Repeated 3 time(s)] > color (#!2 & sel) #3e5be366 > color (#!2 & sel) #405de366 > color (#!2 & sel) #425fe366 > color (#!2 & sel) #4360e366 > color (#!2 & sel) #4862e366 > color (#!2 & sel) #4b63e366 > color (#!2 & sel) #4d63e366 [Repeated 1 time(s)] > color (#!2 & sel) #4e63e366 [Repeated 2 time(s)] > color (#!2 & sel) #4f63e366 > color (#!2 & sel) #5062e366 > color (#!2 & sel) #5261e366 > color (#!2 & sel) #5361e366 > color (#!2 & sel) #5461e366 > color (#!2 & sel) #5560e366 > color (#!2 & sel) #5660e366 > color (#!2 & sel) #585fe366 > color (#!2 & sel) #585ee366 > color (#!2 & sel) #595ee366 > color (#!2 & sel) #5a5de366 > color (#!2 & sel) #5b5de366 > color (#!2 & sel) #5c5de366 > color (#!2 & sel) #5d5ce366 > color (#!2 & sel) #635fe366 > color (#!2 & sel) #6560e366 > color (#!2 & sel) #6760e366 > color (#!2 & sel) #6961e366 > color (#!2 & sel) #6b61e366 > color (#!2 & sel) #7063e366 > color (#!2 & sel) #7665e366 > color (#!2 & sel) #7966e366 > color (#!2 & sel) #7a66e366 [Repeated 2 time(s)] > color (#!2 & sel) #847fe366 > color (#!2 & sel) #837fe366 > color (#!2 & sel) #837ee366 [Repeated 1 time(s)] > color (#!2 & sel) #837de366 > color (#!2 & sel) #827ce366 > color (#!2 & sel) #827be366 > color (#!2 & sel) #8279e366 [Repeated 1 time(s)] > color (#!2 & sel) #8378e366 > color (#!2 & sel) #8478e366 > color (#!2 & sel) #8678e366 > color (#!2 & sel) #8777e366 > color (#!2 & sel) #8877e366 > color (#!2 & sel) #8a76e366 > color (#!2 & sel) #8b76e366 > color (#!2 & sel) #8b75e366 > color (#!2 & sel) #8b74e366 > color (#!2 & sel) #8c74e366 > color (#!2 & sel) #8b73e366 > color (#!2 & sel) #8b72e366 > color (#!2 & sel) #8a71e366 > color (#!2 & sel) #8a70e366 > color (#!2 & sel) #8970e366 > color (#!2 & sel) #896fe366 > color (#!2 & sel) #896ee366 > color (#!2 & sel) #886ee366 > color (#!2 & sel) #886de366 > color (#!2 & sel) #886ce366 > color (#!2 & sel) #876ce366 > color (#!2 & sel) #876be366 > color (#!2 & sel) #876ae366 > color (#!2 & sel) #8669e366 [Repeated 1 time(s)] > color (#!2 & sel) #8568e366 > color (#!2 & sel) #8468e366 > color (#!2 & sel) #8368e366 > color (#!2 & sel) #8367e366 > color (#!2 & sel) #8364e366 > color (#!2 & sel) #8363e366 [Repeated 1 time(s)] > color (#!2 & sel) #8261e366 [Repeated 1 time(s)] > color (#!2 & sel) #815fe366 [Repeated 1 time(s)] > color (#!2 & sel) #805de366 > color (#!2 & sel) #7f5ce366 > color (#!2 & sel) #7d5be366 > color (#!2 & sel) #755be366 > color (#!2 & sel) #725ee366 > color (#!2 & sel) #7264e366 > color (#!2 & sel) #7267e366 [Repeated 2 time(s)] > color (#!2 & sel) #6d66e366 > color (#!2 & sel) #6c65e366 > color (#!2 & sel) #6663e366 > color (#!2 & sel) #6362e366 > color (#!2 & sel) #6262e366 > color (#!2 & sel) #5e63e366 > color (#!2 & sel) #5d64e366 > color (#!2 & sel) #5c64e366 [Repeated 1 time(s)] > color (#!2 & sel) #5b65e366 > color (#!2 & sel) #5966e366 > color (#!2 & sel) #5867e366 [Repeated 2 time(s)] > select clear > set bgColor black > set bgColor white > lighting simple > lighting soft > lighting full > lighting simple > lighting full > lighting simple > lighting full > lighting simple > lighting soft > lighting simple > lighting full > select A/:368-675 Expected an objects specifier or a keyword > select /A:368-675 4858 atoms, 4968 bonds, 616 residues, 2 models selected > transparency (#!2 & sel) 40 > lighting soft > lighting simple > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > lighting soft > lighting full > select /A:1:40 34 atoms, 30 bonds, 4 residues, 2 models selected > ui tool show "Color Actions" > color sel gold > select /A:1-40 568 atoms, 576 bonds, 80 residues, 2 models selected > color sel gold > color sel yellow > color sel khaki > color sel goldenrod > color sel green yellow > color sel yellow green > color sel dark khaki > color sel light salmon > color sel sandy brown > color sel wheat > color sel khaki > color sel goldenrod > select #1/A:10 #2/A:10 14 atoms, 12 bonds, 2 residues, 2 models selected > select #1/A:10-11 #2/A:10-11 28 atoms, 28 bonds, 4 residues, 2 models selected . [ID: 1] region 2 chains [10-11] RMSD: 0.000 > color sel red > color sel dark red > color sel maroon > color sel coral > color sel indian red > color sel tomato > select /A:41-675 10116 atoms, 10306 bonds, 1270 residues, 2 models selected > color sel medium purple > select /A:368-675 4858 atoms, 4968 bonds, 616 residues, 2 models selected > color sel royal blue > color sel slate blue > color sel dark slate blue > color sel medium blue > color sel blue violet > color sel dark violet > color sel rebecca purple > color sel dodger blue > color sel cornflower blue > color sel blue > color sel royal blue > color sel medium slate blue > color sel slate blue > color sel dark slate blue > color sel rebecca purple > color sel cornflower blue > color sel slate blue > color sel medium slate blue > color sel royal blue > color sel medium slate blue > color sel royal blue > select clear > ui tool show "Side View" > lighting simple > lighting soft > lighting full > view orient > select A/ Expected an objects specifier or a keyword > select /A 10684 atoms, 10884 bonds, 1350 residues, 2 models selected > show sel & #!2 cartoons [Repeated 3 time(s)] > transparency (#!2 & sel) 40 > select /A:368-675 4858 atoms, 4968 bonds, 616 residues, 2 models selected > show sel & #!2 cartoons [Repeated 2 time(s)] > show sel & #!2 atoms [Repeated 1 time(s)] > show sel & #!2 cartoons > hide sel & #!2 surfaces > hide sel & #!2 atoms > show sel & #!2 surfaces > select clear > save /Users/lau/Desktop/COP1_colored.tif width 1616 height 1023 supersample > 3 transparentBackground true > select all 10684 atoms, 10884 bonds, 1350 residues, 2 models selected > transparency (#!2 & sel) 10 > select A/ Expected an objects specifier or a keyword > select /A 10684 atoms, 10884 bonds, 1350 residues, 2 models selected > transparency (#!2 & sel) 30 > save /Users/lau/Desktop/COP1_colored.tif width 1616 height 1023 supersample > 3 > select clear > save /Users/lau/Desktop/COP1_colored.tif width 1616 height 1023 supersample > 3 > select A/:6-13 Expected an objects specifier or a keyword > select /A:6-13 110 atoms, 112 bonds, 16 residues, 2 models selected > ui tool show "Color Actions" > color sel tomato > select clear > save /Users/lau/Desktop/COP1_colored_2.tif width 1616 height 1023 > supersample 3 > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_hy5/fold_hy5_model_0.cif" Chain information for fold_hy5_model_0.cif #3 --- Chain | Description A | . > close #3 > save "/Users/lau/Wigge Lab Dropbox/Wigge Lab's shared workspace/Lab > Info/Manuscripts/COP1/COP1 2024/COP1-HY5 animation/COP1_closed.cxs" ——— End of log from Sat Sep 14 13:54:22 2024 ——— opened ChimeraX session > close #1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Cell requested for row 0 is out of bounds for table with 2 rows! Resizing table model. > ui tool show Angles/Torsions > select /A: 22 7 atoms, 6 bonds, 1 residue, 1 model selected > cofr sel > ui mousemode right "rotate slab" > ui tool show "Model Panel" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ~hbonds > hbonds sel reveal true 0 hydrogen bonds found Exactly two atoms must be selected! > show sel atoms > hide sel cartoons [Repeated 4 time(s)] > close #2.2 > hide sel surfaces > show sel atoms > hide sel atoms > show sel atoms > distance style symbol false [Repeated 2 time(s)] The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show (#!2 & sel) target ab > style (#!2 & sel) stick Changed 7 atom styles > ui tool show Rotamers The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 3 time(s)] > swapaa interactive sel VAL rotLib Dunbrack /A VAL 22: phi -58.5, psi 130.4 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide sel atoms > show sel cartoons > hide sel surfaces > select /A 5357 atoms, 5454 bonds, 678 residues, 4 models selected > hide sel surfaces > hide sel atoms > select /A: 22 7 atoms, 6 bonds, 1 residue, 1 model selected > swapaa interactive sel VAL rotLib Dynameomics fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa interactive sel VAL rotLib Dynameomics fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa interactive sel VAL rotLib Dynameomics fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa interactive sel VAL rotLib Richardson.mode fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa #!2/A:22 VAL criteria 2 rotLib Dynameomics retain false Using Dynameomics library fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Applying VAL rotamer (chi angles: -72.1) to fold_cop1_model_0.cif #!2/A VAL 22 > swapaa interactive sel VAL rotLib Richardson.mode fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa #!2/A:22 VAL criteria 3 rotLib Dynameomics retain false Using Dynameomics library fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Applying VAL rotamer (chi angles: 60.7) to fold_cop1_model_0.cif #!2/A VAL 22 No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column to the table. > swapaa #!2/A:22 VAL criteria 2 rotLib Dynameomics retain false Using Dynameomics library fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans Applying VAL rotamer (chi angles: -72.1) to fold_cop1_model_0.cif #!2/A VAL 22 > select subtract #2.1 1 model selected > select add #2.2 15 atoms, 12 bonds, 3 residues, 4 models selected > select add #2.6 30 atoms, 24 bonds, 6 residues, 8 models selected > select subtract #2.2 15 atoms, 12 bonds, 3 residues, 4 models selected > swapaa interactive sel VAL rotLib Richardson.mode No amino acid residues specified for swapping > hide #!2.2 models > close #2.2 > close #2.6 > view #2.1 clip false No displayed objects specified. > select /A: 22 7 atoms, 6 bonds, 1 residue, 1 model selected > ui tool show Rotamers The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > select /A: 21 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A: 20 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A: 20 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A: 19 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A: 19 7 atoms, 6 bonds, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show "Show Sequence Viewer" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain /A Alignment identifier is 2/A > select /A:15 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:15 7 atoms, 7 bonds, 1 residue, 1 model selected > swapaa interactive sel THR rotLib Dunbrack /A PRO 15: phi -66.4, psi 131.0 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > hbonds #!2 & ~#!2/A:15 & ~solvent reveal true restrict #2.2 & ~@c,ca,n 0 hydrogen bonds found No rotamers selected > swapaa #!2/A:15 THR criteria 2 rotLib Dunbrack Using Dunbrack library fold_cop1_model_0.cif #!2/A PRO 15: phi -66.4, psi 131.0 trans Applying THR rotamer (chi angles: 58.0) to fold_cop1_model_0.cif #!2/A THR 15 > swapaa interactive sel THR rotLib Dunbrack /A THR 15: phi -66.4, psi 131.0 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa interactive sel THR rotLib Dunbrack fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa interactive sel THR rotLib Dunbrack fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #2.1 models > hide #!2 models > show #!2 models > hide #1 models > close #1 > hide #!2.2 models > show #!2.2 models > hide #!2.3 models > show #!2.3 models > hide #!2.4 models > show #!2.4 models > swapaa #!2/A:15 THR criteria 3 rotLib Dunbrack retain false Using Dunbrack library fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans Applying THR rotamer (chi angles: -177.1) to fold_cop1_model_0.cif #!2/A THR 15 > view #2.3 clip false > ui tool show Rotamers The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > swapaa interactive sel THR rotLib Dunbrack fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans Changed 12 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > swapaa interactive sel CYH rotLib Dunbrack fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans Changed 9 bond radii The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_summary_confidences_0.json" JSON file "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_summary_confidences_0.json" is not AlphaFold predicted aligned error data, expected a top level list > preset "overall look" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > color bfactor sel 4 atoms, 1 residues, 1 surfaces, atom bfactor range 34.6 to 38 > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" Opened AlphaFold PAE with values for 675 residues and atoms The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui windowfill toggle [Repeated 1 time(s)] > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms > alphafold pae #2 colorDomains true > show #2.1 models > show #!2 target m [Repeated 5 time(s)] > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > alphafold pae #2 colorDomains true [Repeated 3 time(s)] > select clear > color /A:27-230 lime > alphafold pae #2 colorDomains true > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae Opened AlphaFold PAE with values for 675 residues and atoms The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view #2.1 clip false No displayed objects specified. > hide #2.1 models > show #2.1 models > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif" Chain information for fold_cop1_model_0.cif #1 --- Chain | Description A | . > color #2/A:40 lime > color #2/A:66 magenta > color #2/A:26-239 lime > color #2/A:178 lime > color #2/A:152 magenta > alphafold pae #2 colorDomains true [Repeated 5 time(s)] > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > select all 10684 atoms, 10883 bonds, 1350 residues, 2 models selected > alphafold pae #2 colorDomains true > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > alphafold pae #2 colorDomains true [Repeated 1 time(s)] > show sel surfaces [Repeated 1 time(s)] > alphafold pae #2 colorDomains true > color #2/A:288-674 lime > color #2/A:1-18 magenta > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > alphafold pae #2 colorDomains true [Repeated 1 time(s)] > color #2/A:2-35 lime > color #2/A:48-675 magenta > alphafold pae #2 colorDomains true [Repeated 4 time(s)] > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > color bfactor #2 palette alphafold 5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8 > preset "molecular surfaces" "atomic coloring (transparent)" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > hide sel surfaces > hide sel atoms > show sel atoms > hide sel cartoons [Repeated 1 time(s)] > hide sel atoms > show sel cartoons > alphafold pae #2 colorDomains true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #1.1 target m > select subtract #1.1 5342 atoms, 5441 bonds, 675 residues, 3 models selected > hide #!1 models > select clear > close #1 > color /A:118 lime > color /A:183 magenta > color /A:42-231 lime > color /A:7-99 lime > color /A:286-669 magenta > color /A:99 lime > color /A:669 magenta > color /A:1-48 lime > color /A:19 lime > color /A:6 magenta > color /A:272-675 lime > color /A:1-26 magenta > color /A:1-20 lime > color /A:286-675 magenta > alphafold pae #2 colorDomains true Alignment identifier is 2/A > select /A:10 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:10-11 14 atoms, 14 bonds, 2 residues, 1 model selected > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_full_data_0.json" Opening an AlphaFold PAE file requires specifying the structure to associate. Did not find an open structure from the same directory. To specify the structure use menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command, for example open /Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_full_data_0.json format pae structure #1 > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif" Chain information for fold_cop1_model_0.cif #1 --- Chain | Description A | . > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_1.cif" Chain information for fold_cop1_model_1.cif #3 --- Chain | Description A | . > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_2.cif" Chain information for fold_cop1_model_2.cif #4 --- Chain | Description A | . > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_3.cif" Chain information for fold_cop1_model_3.cif #5 --- Chain | Description A | . > open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_4.cif" Chain information for fold_cop1_model_4.cif #6 --- Chain | Description A | . > hide #!2 models > hide #2.1 models > show #!2 models > show #2.1 models > hide #1 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #1 models > hide #1 models > show #1 models > hide #!2 models > hide #2.1 models > close #2.1 > hide #1 models > select add #2 5342 atoms, 5441 bonds, 675 residues, 1 model selected > select subtract #2 Nothing selected > show #1 models > close #2 > show #3 models > hide #1 models > show #1 models > hide #1 models > hide #3 models > show #4 models > show #1 models > hide #4 models > show #4 models > hide #4 models > hide #1 models > show #3 models > hide #3 models > show #5 models > hide #5 models > show #6 models > hide #6 models > show #5 models > hide #5 models > show #4 models > hide #4 models > show #3 models > show #1 models > select /1 Nothing selected > select /A 26710 atoms, 27210 bonds, 3375 residues, 5 models selected > show #4 models > show #5 models > show #6 models > select subtract #3 21368 atoms, 21768 bonds, 2700 residues, 4 models selected > select subtract #4 16026 atoms, 16326 bonds, 2025 residues, 3 models selected > select subtract #5 10684 atoms, 10884 bonds, 1350 residues, 2 models selected > select subtract #6 5342 atoms, 5442 bonds, 675 residues, 1 model selected > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #3 models > select subtract #1 Nothing selected > select add #3 5342 atoms, 5442 bonds, 675 residues, 1 model selected > hide #1 models > show #1 models > ui mousemode right "translate selected models" > ui mousemode right rotate > select subtract #3 Nothing selected > select 1/ Expected an objects specifier or a keyword > select /1:A Nothing selected > select /1 Nothing selected > show #4 models > show #5 models > show #6 models > select add #1 5342 atoms, 5442 bonds, 675 residues, 1 model selected > select add #3 10684 atoms, 10884 bonds, 1350 residues, 2 models selected > select add #4 16026 atoms, 16326 bonds, 2025 residues, 3 models selected > select add #5 21368 atoms, 21768 bonds, 2700 residues, 4 models selected > select add #6 26710 atoms, 27210 bonds, 3375 residues, 5 models selected > ui tool show "Modeller Comparative" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. No alignments chosen for modeling > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #3-6 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 fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif, chain A (#3), sequence alignment score = 3505.1 RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs: 5.895) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif, chain A (#4), sequence alignment score = 3502.7 RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs: 4.976) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif, chain A (#5), sequence alignment score = 3506.3 RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs: 7.536) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif, chain A (#6), sequence alignment score = 3498.5 RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs: 8.497) > select subtract #1 21368 atoms, 21768 bonds, 2700 residues, 4 models selected > select subtract #3 16026 atoms, 16326 bonds, 2025 residues, 3 models selected > select subtract #4 10684 atoms, 10884 bonds, 1350 residues, 2 models selected > select subtract #5 5342 atoms, 5442 bonds, 675 residues, 1 model selected > select subtract #6 Nothing selected > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #3 models > hide #3 models > show #4 models > show #3 models > hide #1 models > show #5 models > hide #4 models > hide #3 models > hide #5 models > show #1 models > show #5 models > hide #1 models > show #6 models > hide #5 models > show #5 models > show #4 models > show #3 models > show #1 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > show #6 models > hide #6 models > show #3 models > show #4 models > show #5 models > show #6 models > ui mousemode right "play coordinates" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/lau/Documentos/Ongoing/COP1/COP1_alone.cxs > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_0.cif" Chain information for fold_cop1_hy5_complex_model_0.cif #2 --- Chain | Description A | . B | . > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_1.cif" Chain information for fold_cop1_hy5_complex_model_1.cif #7 --- Chain | Description A | . B | . > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_2.cif" Chain information for fold_cop1_hy5_complex_model_2.cif #8 --- Chain | Description A | . B | . > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_3.cif" Chain information for fold_cop1_hy5_complex_model_3.cif #9 --- Chain | Description A | . B | . > open "/Volumes/LAU_32GB/COP1-HY5 > Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_4.cif" Chain information for fold_cop1_hy5_complex_model_4.cif #10 --- Chain | Description A | . B | . > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2 to #8/A pairing bs Parameters --- Chain pairing | bs 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 fold_cop1_hy5_complex_model_2.cif, chain A (#8) with fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score = 3442.1 RMSD between 451 pruned atom pairs is 0.580 angstroms; (across all 675 pairs: 14.410) > hide #1 models > hide #2 models > hide #3 models > hide #4 models > hide #5 models > hide #6 models > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 1 time(s)] > matchmaker #2,8-10 & sel to #7/A & sel pairing bs No 'to' chains specified Traceback (most recent call last): File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh self._items_change() File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change item_names = self._item_names() ^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names values = [v for v in self.list_func() if self.filter_func(v)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py", line 47, in values = [v for v in self.list_func() if self.filter_func(v)] ^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_chooser.py", line 22, in filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and isinstance(x, cf) ^^^^^ File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models ref_structures = [ref_value.structure] ^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'structure' AttributeError: 'NoneType' object has no attribute 'structure' File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models ref_structures = [ref_value.structure] ^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > matchmaker #2-10 & sel to #1 & sel No 'to' model specified > matchmaker #2-10 & sel to #1 & sel No 'to' model specified > matchmaker #3-10 & sel to #2 & sel No 'to' model specified > hide #7 models > hide #8 models > hide #9 models > hide #10 models > show #9 models > hide #9 models > show #8 models > hide #8 models > show #7 models > hide #7 models > show #6 models > show #7 models > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2-10 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 fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score = 3442.7 RMSD between 431 pruned atom pairs is 0.644 angstroms; (across all 675 pairs: 20.990) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif, chain A (#3), sequence alignment score = 3505.1 RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs: 5.895) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif, chain A (#4), sequence alignment score = 3502.7 RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs: 4.976) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif, chain A (#5), sequence alignment score = 3506.3 RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs: 7.536) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif, chain A (#6), sequence alignment score = 3498.5 RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs: 8.497) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_1.cif, chain A (#7), sequence alignment score = 3452.9 RMSD between 413 pruned atom pairs is 0.685 angstroms; (across all 675 pairs: 21.616) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_2.cif, chain A (#8), sequence alignment score = 3432.5 RMSD between 452 pruned atom pairs is 0.784 angstroms; (across all 675 pairs: 21.495) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_3.cif, chain A (#9), sequence alignment score = 3462.5 RMSD between 455 pruned atom pairs is 0.601 angstroms; (across all 675 pairs: 22.545) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_4.cif, chain A (#10), sequence alignment score = 3448.1 RMSD between 460 pruned atom pairs is 0.796 angstroms; (across all 675 pairs: 22.634) > hide #6 models > show #1 models > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select /1 Nothing selected > matchmaker #2-10 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 fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score = 3442.7 RMSD between 431 pruned atom pairs is 0.644 angstroms; (across all 675 pairs: 20.990) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif, chain A (#3), sequence alignment score = 3505.1 RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs: 5.895) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif, chain A (#4), sequence alignment score = 3502.7 RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs: 4.976) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif, chain A (#5), sequence alignment score = 3506.3 RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs: 7.536) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif, chain A (#6), sequence alignment score = 3498.5 RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs: 8.497) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_1.cif, chain A (#7), sequence alignment score = 3452.9 RMSD between 413 pruned atom pairs is 0.685 angstroms; (across all 675 pairs: 21.616) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_2.cif, chain A (#8), sequence alignment score = 3432.5 RMSD between 452 pruned atom pairs is 0.784 angstroms; (across all 675 pairs: 21.495) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_3.cif, chain A (#9), sequence alignment score = 3462.5 RMSD between 455 pruned atom pairs is 0.601 angstroms; (across all 675 pairs: 22.545) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_4.cif, chain A (#10), sequence alignment score = 3448.1 RMSD between 460 pruned atom pairs is 0.796 angstroms; (across all 675 pairs: 22.634) > show #2 models > show #3 models > show #4 models > show #5 models > show #6 models > show #8 models > show #9 models > show #10 models > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2-10 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 fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score = 3442.7 RMSD between 431 pruned atom pairs is 0.644 angstroms; (across all 675 pairs: 20.990) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif, chain A (#3), sequence alignment score = 3505.1 RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs: 5.895) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif, chain A (#4), sequence alignment score = 3502.7 RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs: 4.976) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif, chain A (#5), sequence alignment score = 3506.3 RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs: 7.536) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif, chain A (#6), sequence alignment score = 3498.5 RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs: 8.497) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_1.cif, chain A (#7), sequence alignment score = 3452.9 RMSD between 413 pruned atom pairs is 0.685 angstroms; (across all 675 pairs: 21.616) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_2.cif, chain A (#8), sequence alignment score = 3432.5 RMSD between 452 pruned atom pairs is 0.784 angstroms; (across all 675 pairs: 21.495) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_3.cif, chain A (#9), sequence alignment score = 3462.5 RMSD between 455 pruned atom pairs is 0.601 angstroms; (across all 675 pairs: 22.545) Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_hy5_complex_model_4.cif, chain A (#10), sequence alignment score = 3448.1 RMSD between 460 pruned atom pairs is 0.796 angstroms; (across all 675 pairs: 22.634) > ui mousemode right "play coordinates" > lighting simple > lighting soft > lighting full > hide #3 models > hide #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > select /A:1-40 2840 atoms, 2880 bonds, 400 residues, 10 models selected > color (#1-2 & sel) yellow > select /B 6465 atoms, 6500 bonds, 840 residues, 5 models selected > color (#2 & sel) magenta > clear all Unknown command: clear all > select clear > select /a:1-40 2840 atoms, 2880 bonds, 400 residues, 10 models selected > ui tool show "Color Actions" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color sel goldenrod [Repeated 4 time(s)] > select /a:368-675 24290 atoms, 24840 bonds, 3080 residues, 10 models selected > color sel medium blue > color sel royal blue > select /a:41-367 26290 atoms, 26680 bonds, 3270 residues, 10 models selected > color sel indigo > color sel medium slate blue > ui tool show "Show Sequence Viewer" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select /a:10-11 140 atoms, 140 bonds, 20 residues, 10 models selected > color sel tomato > show sel & #1-2 surfaces > select all 59885 atoms, 60920 bonds, 7590 residues, 10 models selected > show sel & #!1-2 surfaces > transparency (#!1-2 & sel) 30 > transparency (#!1-2 & sel) 90 > transparency (#!1-2 & sel) 50 > select /A:1-40 2840 atoms, 2880 bonds, 400 residues, 10 models selected > color sel goldenrod > select /A:11-12 120 atoms, 120 bonds, 20 residues, 10 models selected > color sel tomato > select /A:368-675 24290 atoms, 24840 bonds, 3080 residues, 10 models selected > color sel royal blue > select /A:41-367 26290 atoms, 26680 bonds, 3270 residues, 10 models selected > color sel medium slate blue > hide #!1 models > select /B:1-100 3805 atoms, 3830 bonds, 500 residues, 5 models selected > select /B:80-100 905 atoms, 905 bonds, 105 residues, 5 models selected > ui tool show "Show Sequence Viewer" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #2/B #7/B #8/B #9/B #10/B Alignment identifier is 1 > select #2/B:43 #7/B:43 #8/B:43 #9/B:43 #10/B:43 35 atoms, 30 bonds, 5 residues, 5 models selected > select #2/B:43-44 #7/B:43-44 #8/B:43-44 #9/B:43-44 #10/B:43-44 70 atoms, 70 bonds, 10 residues, 5 models selected . [ID: 1] region 5 chains [43-44] RMSD: 0.358 > color sel tomato [Repeated 3 time(s)] > select /B 6465 atoms, 6500 bonds, 840 residues, 5 models selected > color sel deep pink > transparency (#!2 & sel) 70 > color sel orchid > transparency (#!2 & sel) 70 > transparency (#!2 & sel) 40 > hide sel & #!2 cartoons > select /A 53420 atoms, 54420 bonds, 6750 residues, 10 models selected > hide sel & #!2 cartoons > select /b:41-43 145 atoms, 140 bonds, 15 residues, 5 models selected > select /b:42-43 90 atoms, 85 bonds, 10 residues, 5 models selected > color sel tomato > set bgColor white > set bgColor #ffffff00 > show #!1 models > select add #7 6707 atoms, 6810 bonds, 851 residues, 6 models selected > select subtract #7 72 atoms, 68 bonds, 8 residues, 5 models selected > select add #8 6689 atoms, 6793 bonds, 849 residues, 5 models selected > select subtract #8 54 atoms, 51 bonds, 6 residues, 4 models selected > select add #9 6671 atoms, 6776 bonds, 847 residues, 4 models selected > select subtract #9 36 atoms, 34 bonds, 4 residues, 3 models selected > select add #10 6653 atoms, 6759 bonds, 845 residues, 3 models selected > select subtract #10 18 atoms, 17 bonds, 2 residues, 2 models selected > select add #2 6635 atoms, 6742 bonds, 843 residues, 2 models selected > select subtract #2 2 models selected > select all 59885 atoms, 60920 bonds, 7590 residues, 10 models selected > show sel & #!1-2 cartoons > hide #!2 models > select clear > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #2.2 models > show #2.2 models > hide #2.1 models > show #2.1 models > show #3 models > show #4 models > show #5 models > show #6 models > hide #!2 models > hide #2.1 models > hide #2.2 models > hide #!1 models > hide #1.1 models > show #!1 models > hide #6 models > show #6 models > hide #6 models > hide #5 models > show #5 models > show #6 models > show #!2 models > show #7 models > show #8 models > show #9 models > show #10 models > hide #10 models > hide #8 models > hide #9 models > hide #7 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > save /Users/lau/Documentos/Ongoing/COP1/full_data_session.cxs ——— End of log from Mon Sep 16 20:24:56 2024 ——— opened ChimeraX session > hide #!2 models > show #3-6#!1 surfaces > hide #!1,3-6 surfaces > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!1 surfaces > hide #!1 cartoons > hide #1.1 models > hide #3.1 models > show #3.1 models > show #!1,3 surfaces > hide #!1,3 surfaces > show #!1,3 surfaces > show #!4 models > hide #!3 models > show #!1,4 surfaces > show #!5 models > show #!6 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1,3-6 cartoons > show #!1,3-6 surfaces > transparency #1,3-6 50 > select /A1-40 Nothing selected > select /A:1-40 2840 atoms, 2880 bonds, 400 residues, 10 models selected > color sel goldenrod > select /A:11-12 120 atoms, 120 bonds, 20 residues, 10 models selected > color sel tomato > select /A:368-675 24290 atoms, 24840 bonds, 3080 residues, 10 models selected > color sel royal blue > select /A:41-367 26290 atoms, 26680 bonds, 3270 residues, 10 models selected > color sel indigo > color sel dark magenta > select all 59885 atoms, 60920 bonds, 7590 residues, 10 models selected > transparency (#!1,3-6 & sel) 40 > lighting soft > lighting simple > select clear > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/lau/Desktop/movie1.mp4 Movie saved to /Users/lau/Desktop/movie1.mp4 > save /Users/lau/Desktop/image1.png supersample 3 > hide #1.1 models > show #!3 models > show #1.1 models > hide #1.1 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/lau/Desktop/movie2.mp4 Movie saved to /Users/lau/Desktop/movie2.mp4 > save /Users/lau/Desktop/image2.png supersample 3 > hide #!3 models > show #!4 models > hide #!1 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/lau/Desktop/movie3.mp4 Movie saved to /Users/lau/Desktop/movie3.mp4 > save /Users/lau/Desktop/image3.png supersample 3 > hide #!4 models > show #!5 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/lau/Desktop/movie4.mp4 Movie saved to /Users/lau/Desktop/movie4.mp4 > save /Users/lau/Desktop/image4.png supersample 3 > show #!6 models > hide #!5 models > movie record > turn y 2 180 > wait 180 > movie encode /Users/lau/Desktop/movie5.mp4 Movie saved to /Users/lau/Desktop/movie5.mp4 > save /Users/lau/Desktop/image5.png supersample 3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > set bgColor black > set bgColor transparent > save /Users/lau/Documentos/Ongoing/COP1/ChimeraX/COP!_open&closed&hy5ed.cxs > includeMaps true ——— End of log from Tue Sep 17 20:22:45 2024 ——— opened ChimeraX session > hide #!6 models > show #!2 models > show #!2 surfaces > hide #!2 cartoons > transparency #2 60 > set bgColor white > show #!2 atoms > select /A:1-367 29130 atoms, 29570 bonds, 3670 residues, 10 models selected > hide sel & #!2 atoms > select /B:1-80 2955 atoms, 2975 bonds, 400 residues, 5 models selected > select /B:1-40 1460 atoms, 1470 bonds, 200 residues, 5 models selected > select /B:1-30 1065 atoms, 1075 bonds, 150 residues, 5 models selected > hide sel & #!2 atoms > select /B:55-168 4470 atoms, 4480 bonds, 570 residues, 5 models selected > hide sel & #!2 atoms > select /A:140:180 170 atoms, 150 bonds, 20 residues, 10 models selected > select /A:368-400 2630 atoms, 2680 bonds, 330 residues, 10 models selected > hide sel & #!2 atoms > select /A:400-500 8080 atoms, 8250 bonds, 1010 residues, 10 models selected > select /A:450-500 4130 atoms, 4200 bonds, 510 residues, 10 models selected > select /A:1-500 39730 atoms, 40400 bonds, 5000 residues, 10 models selected > select /A:1-4500 53420 atoms, 54420 bonds, 6750 residues, 10 models selected > select /A:1-450 35670 atoms, 36260 bonds, 4500 residues, 10 models selected > hide sel & #!2 atoms > select /A:500-675 13770 atoms, 14090 bonds, 1760 residues, 10 models selected > hide sel & #!2 atoms > select add #2.2 15063 atoms, 14090 bonds, 1928 residues, 16 models selected > hide #2.2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #2.1 models > show #2.2 models > select /A:365-675 24490 atoms, 25040 bonds, 3110 residues, 10 models selected > show sel & #!2 atoms > select /A:600-675 5830 atoms, 5950 bonds, 760 residues, 10 models selected > select /A:600-630 2550 atoms, 2610 bonds, 310 residues, 10 models selected > hide sel & #!2 atoms > select /A:630-640 830 atoms, 840 bonds, 110 residues, 10 models selected > hide sel & #!2 atoms > select /A:640-650 820 atoms, 830 bonds, 110 residues, 10 models selected > show #2.1 models > hide #2.1 models > select /A:530-600 5770 atoms, 5910 bonds, 710 residues, 10 models selected > hide sel & #!2 atoms > show sel & #!2 atoms > show #2.1 models > hide #2.1 models > hide #!2 models > hide #2.2 models > show #!1 models > show sel & #!1 surfaces > select clear > show #!3 models > show #!4 models > show #!5 models > show #!6 models > hide #!1 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!3 models > show #!4 models > show #!1 models > show #!3 models > hide #!3 models > hide #!4 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > hide #!3 models > show #!4 models > show #!3 models > show #!1 models > hide #!1 models > hide #!3 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > show #!2 models > show #!2,6 surfaces > hide #!2 models > show #!2 models > hide #!6 models > hide #!2 models > show #!1 models > ui tool show Contacts The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > contacts resSeparation 5 intraRes true ignoreHiddenModels true color #9d1700 > radius 0.105 1589 contacts > select add #11 1589 pseudobonds, 1 model selected > view clip false > show #!1 cartoons > hide #!1 surfaces > hbonds #!1 reveal true 8904 hydrogen bonds found > hide #11 models > show #11 models > ui tool show Clashes The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > clashes overlapCutoff 1.0 ignoreHiddenModels true color #0a500b reveal true No clashes > hide #!1 models > show #7 models > hide #7 models > show #!1 models > select add #12 10493 pseudobonds, 2 models selected > select clear > show #!1 atoms > hide #!1 cartoons > hide #!1 surfaces > show #!1 surfaces > hide #!1 surfaces > ui tool show "Show Sequence Viewer" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select /A:11-12 120 atoms, 120 bonds, 20 residues, 10 models selected > select /A:10-11 140 atoms, 140 bonds, 20 residues, 10 models selected > ui tool show "Color Actions" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color sel tomato > select /A:12 50 atoms, 40 bonds, 10 residues, 10 models selected > color sel goldenrod > select /A:10-11 140 atoms, 140 bonds, 20 residues, 10 models selected > hide #13 models > select subtract #13 140 atoms, 140 bonds, 20 residues, 16 models selected > select add #11 140 atoms, 140 bonds, 1589 pseudobonds, 20 residues, 17 models selected > select subtract #11 140 atoms, 140 bonds, 20 residues, 16 models selected > show #13 models > select subtract #13 140 atoms, 140 bonds, 20 residues, 16 models selected > select add #12 140 atoms, 140 bonds, 8904 pseudobonds, 20 residues, 17 models selected > hide #11 models > hide #13 models > select subtract #13 140 atoms, 140 bonds, 8904 pseudobonds, 20 residues, 17 models selected > hbonds sel & #!1 reveal true 0 hydrogen bonds found > select all 59885 atoms, 60920 bonds, 1611 pseudobonds, 7590 residues, 16 models selected > show #11 models > hide #12 models > select subtract #12 59885 atoms, 60920 bonds, 1611 pseudobonds, 7590 residues, 23 models selected > close #12 > show #13 models > hide #11 models > select subtract #11 59885 atoms, 60920 bonds, 22 pseudobonds, 7590 residues, 22 models selected > close #13 > show #11 models > select add #11 59885 atoms, 60920 bonds, 1611 pseudobonds, 7590 residues, 23 models selected > select /A:1-40 2840 atoms, 2880 bonds, 400 residues, 10 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #11 > ui tool show Contacts The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > contacts sel resSeparation 5 intraRes true ignoreHiddenModels true color > #9d1700 radius 0.105 25 contacts > show sel & #!1 surfaces > hide sel & #!1 surfaces > select /A 53420 atoms, 54420 bonds, 47 pseudobonds, 6750 residues, 16 models selected > show sel & #!1 surfaces > select /A:442 90 atoms, 80 bonds, 10 residues, 10 models selected > select /A:467 140 atoms, 150 bonds, 10 residues, 10 models selected > color (#!1 & sel) lime > hide sel & #!1 surfaces > select all 59885 atoms, 60920 bonds, 47 pseudobonds, 7590 residues, 16 models selected > select all 59885 atoms, 60920 bonds, 47 pseudobonds, 7590 residues, 16 models selected > hide sel & #!1 surfaces > hbonds sel & #!1 reveal true 8904 hydrogen bonds found > select add #12 59885 atoms, 60920 bonds, 8951 pseudobonds, 7590 residues, 24 models selected > select subtract #11 59885 atoms, 60920 bonds, 8926 pseudobonds, 7590 residues, 23 models selected > select subtract #10 53250 atoms, 54178 bonds, 8011 pseudobonds, 6747 residues, 22 models selected > select subtract #9 46615 atoms, 47436 bonds, 7036 pseudobonds, 5904 residues, 21 models selected > select subtract #8 39980 atoms, 40694 bonds, 6134 pseudobonds, 5061 residues, 20 models selected > select subtract #7 33345 atoms, 33952 bonds, 5247 pseudobonds, 4218 residues, 19 models selected > select subtract #6 28003 atoms, 28510 bonds, 4386 pseudobonds, 3543 residues, 17 models selected > select subtract #5 22661 atoms, 23068 bonds, 3425 pseudobonds, 2868 residues, 14 models selected > select subtract #4 17319 atoms, 17626 bonds, 2443 pseudobonds, 2193 residues, 11 models selected > select subtract #3 11977 atoms, 12184 bonds, 1481 pseudobonds, 1518 residues, 8 models selected > select subtract #2 5342 atoms, 5442 bonds, 559 pseudobonds, 675 residues, 5 models selected > select /A:593 90 atoms, 80 bonds, 10 residues, 10 models selected > show sel & #!1 cartoons > select all 59885 atoms, 60920 bonds, 8951 pseudobonds, 7590 residues, 17 models selected > hide sel & #!1 atoms > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > show sel & #!1 atoms > select /A:3-20 1330 atoms, 1360 bonds, 6 pseudobonds, 180 residues, 11 models selected > label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}" > select /A:467 140 atoms, 150 bonds, 10 residues, 10 models selected > select /A:467-470 350 atoms, 360 bonds, 11 pseudobonds, 40 residues, 11 models selected > select /A:460-470 970 atoms, 990 bonds, 16 pseudobonds, 110 residues, 15 models selected > select /A:460-480 1770 atoms, 1810 bonds, 151 pseudobonds, 210 residues, 15 models selected > select add #11 1770 atoms, 1810 bonds, 176 pseudobonds, 210 residues, 22 models selected > view clip false > ui tool show Contacts The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > contacts sel saveFile /Users/lau/Desktop/COP1_contacts resSeparation 4 color > #9d1700 radius 0.105 name contacts_2 reveal true 99163 contacts > hide #12 models > hide #11 models Cell requested for row 3 is out of bounds for table with 18 rows! Resizing table model. > show #11 models > hide #13 models > show #13 models > hide #13 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #7 models > hide #7 models > show #8 models > hide #8 models > show #9 models > hide #9 models > show #10 models > hide #10 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #12 models > hide #12 models > show #13 models > hide #13 models > show #13 models > select /A 53420 atoms, 54420 bonds, 106213 pseudobonds, 6750 residues, 18 models selected > select clear > show #!1 cartoons > hide #!1 atoms > hide #11 models > hide #13 models > show #11 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #13 models > show #!1 atoms > hide #!1 cartoons > ui tool show Contacts The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > contacts sel saveFile /Users/lau/Desktop/contactsCOP1_closed resSeparation 4 > interModel false color #e03200 radius 0.105 reveal true No atoms match given atom specifier > contacts sel resSeparation 5 interModel false select true makePseudobonds > false No atoms match given atom specifier > show #12 models > hide #12 models > show #12 models > style #!1 ball Changed 5342 atom styles > select /A:1-7 550 atoms, 540 bonds, 5 pseudobonds, 70 residues, 11 models selected > select /A:1-7 550 atoms, 540 bonds, 5 pseudobonds, 70 residues, 11 models selected > hide sel & #!1 atoms > select /A:15-200 14640 atoms, 14840 bonds, 1283 pseudobonds, 1860 residues, 13 models selected > hide sel & #!1 atoms > select /A:201-300 7890 atoms, 8020 bonds, 682 pseudobonds, 1000 residues, 11 models selected > hide sel & #!1 atoms > select /A:300-340 3380 atoms, 3410 bonds, 341 pseudobonds, 410 residues, 11 models selected > hide sel & #!1 atoms > show sel & #!1 cartoons > hide sel & #!1 cartoons > select /A:341-360 1650 atoms, 1670 bonds, 241 pseudobonds, 200 residues, 11 models selected > hide sel & #!1 atoms > select /A:340-350 870 atoms, 880 bonds, 199 pseudobonds, 110 residues, 11 models selected > hide sel & #!1 atoms > select /A:340-380 3340 atoms, 3400 bonds, 347 pseudobonds, 410 residues, 11 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > show sel & #!1 cartoons > hide sel & #!1 cartoons > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:400-420 1600 atoms, 1620 bonds, 159 pseudobonds, 210 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > show sel & #!1 cartoons > hide sel & #!1 atoms > hide sel & #!1 cartoons > select /A:600-675 5830 atoms, 5950 bonds, 1102 pseudobonds, 760 residues, 15 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:400-450 4020 atoms, 4110 bonds, 624 pseudobonds, 510 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:300-450 12150 atoms, 12370 bonds, 2053 pseudobonds, 1510 residues, 15 models selected > hide sel & #!1 cartoons > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:450-500 4130 atoms, 4200 bonds, 84864 pseudobonds, 510 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > select /A:450-470 1810 atoms, 1840 bonds, 39355 pseudobonds, 210 residues, 12 models selected > show sel & #!1 cartoons > select /A:450-464 1300 atoms, 1310 bonds, 17649 pseudobonds, 150 residues, 12 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:550-675 9810 atoms, 10010 bonds, 2098 pseudobonds, 1260 residues, 15 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 atoms > show sel & #!1 atoms > select /A:590-675 6610 atoms, 6740 bonds, 1304 pseudobonds, 860 residues, 15 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > hide #12 models > select add #12 6610 atoms, 6740 bonds, 8908 pseudobonds, 860 residues, 21 models selected > select subtract #12 6610 atoms, 6740 bonds, 4 pseudobonds, 860 residues, 20 models selected > select add #2 12584 atoms, 12808 bonds, 248 pseudobonds, 1617 residues, 22 models selected > select subtract #2 5949 atoms, 6066 bonds, 4 pseudobonds, 774 residues, 20 models selected > select add #3 10630 atoms, 10834 bonds, 227 pseudobonds, 1363 residues, 19 models selected > select subtract #3 5288 atoms, 5392 bonds, 3 pseudobonds, 688 residues, 16 models selected > select add #4 9969 atoms, 10160 bonds, 226 pseudobonds, 1277 residues, 16 models selected > select subtract #4 4627 atoms, 4718 bonds, 2 pseudobonds, 602 residues, 13 models selected > select add #5 9308 atoms, 9486 bonds, 223 pseudobonds, 1191 residues, 13 models selected > select subtract #5 3966 atoms, 4044 bonds, 1 pseudobond, 516 residues, 10 models selected > select add #6 8647 atoms, 8812 bonds, 228 pseudobonds, 1105 residues, 10 models selected > select subtract #6 3305 atoms, 3370 bonds, 430 residues, 7 models selected > select add #7 9279 atoms, 9438 bonds, 262 pseudobonds, 1187 residues, 7 models selected > select subtract #7 2644 atoms, 2696 bonds, 344 residues, 5 models selected > select add #8 8618 atoms, 8764 bonds, 248 pseudobonds, 1101 residues, 6 models selected > select subtract #8 1983 atoms, 2022 bonds, 258 residues, 4 models selected > select add #9 7957 atoms, 8090 bonds, 241 pseudobonds, 1015 residues, 5 models selected > select subtract #9 1322 atoms, 1348 bonds, 172 residues, 3 models selected > select add #10 7296 atoms, 7416 bonds, 262 pseudobonds, 929 residues, 4 models selected > select subtract #10 661 atoms, 674 bonds, 86 residues, 2 models selected > select /A:593 90 atoms, 80 bonds, 10 residues, 10 models selected > show sel & #!1 cartoons > show sel & #!1 atoms > show #12 models > hide #13 models > show #13 models > hide #11 models > show #11 models > hide #11 models > hide #13 models > hide #12 models > show #12 models > hide #12 models > show #11 models > show #13 models > select /A:590-600 850 atoms, 850 bonds, 9 pseudobonds, 110 residues, 11 models selected > show sel & #!1 atoms > select /A:465-500 2830 atoms, 2880 bonds, 61219 pseudobonds, 360 residues, 12 models selected > show sel & #!1 cartoons > select /A:465-490 2010 atoms, 2040 bonds, 59279 pseudobonds, 260 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > show sel & #!1 atoms > select /A:465-480 1310 atoms, 1340 bonds, 55637 pseudobonds, 160 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > select /A:465-475 950 atoms, 970 bonds, 37900 pseudobonds, 110 residues, 12 models selected > show sel & #!1 cartoons > select A:14-464 Expected an objects specifier or a keyword > select /A:14-464 35950 atoms, 36540 bonds, 22504 pseudobonds, 4510 residues, 17 models selected > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 atoms > show sel & #!1 atoms > select /A:14 90 atoms, 80 bonds, 10 residues, 10 models selected > select all 59885 atoms, 60920 bonds, 108111 pseudobonds, 7590 residues, 19 models selected > select /A:1-5 400 atoms, 390 bonds, 50 residues, 10 models selected > select /A:1-5 400 atoms, 390 bonds, 50 residues, 10 models selected > hide sel & #!1 atoms > select /A:15-464 35860 atoms, 36450 bonds, 22502 pseudobonds, 4500 residues, 17 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:600-675 5830 atoms, 5950 bonds, 1102 pseudobonds, 760 residues, 15 models selected > hide sel & #!1 atoms > show sel & #!1 cartoons > hide sel & #!1 cartoons > ui tool show "Show Sequence Viewer" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain #1/A #3/A #4/A #5/A #6/A #2/A #7/A #8/A #9/A #10/A Alignment identifier is 1 > select #1/A:491 #3/A:491 #4/A:491 #5/A:491 #6/A:491 #2/A:491 #7/A:491 > #8/A:491 #9/A:491 #10/A:491 140 atoms, 150 bonds, 10 residues, 10 models selected > select #1/A:491-507 #3/A:491-507 #4/A:491-507 #5/A:491-507 #6/A:491-507 > #2/A:491-507 #7/A:491-507 #8/A:491-507 #9/A:491-507 #10/A:491-507 1360 atoms, 1370 bonds, 52 pseudobonds, 170 residues, 11 models selected . [ID: 1] region 10 chains [491-507] RMSD: 0.512 > show sel & #!1 cartoons > hide sel & #!1 cartoons > show sel & #!1 cartoons > select /A:540-550 900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:540-550 900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected > select /A:540-550 900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected > select /A:540-550 900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected > select /A:469-490 1650 atoms, 1660 bonds, 42159 pseudobonds, 220 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:490-507 1430 atoms, 1440 bonds, 101 pseudobonds, 180 residues, 11 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:441 120 atoms, 120 bonds, 2 pseudobonds, 10 residues, 11 models selected > hide sel & #!1 cartoons > show sel & #!1 cartoons > hide sel & #!1 cartoons > select /A:468 60 atoms, 50 bonds, 1444 pseudobonds, 10 residues, 12 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:465 110 atoms, 100 bonds, 2596 pseudobonds, 10 residues, 11 models selected > hide sel & #!1 cartoons > show sel & #!1 cartoons > hide sel & #!1 atoms > hide sel & #!1 cartoons > select /A:466 50 atoms, 40 bonds, 1115 pseudobonds, 10 residues, 11 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:508 80 atoms, 70 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:509 60 atoms, 50 bonds, 10 residues, 10 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:510-525 1150 atoms, 1170 bonds, 178 pseudobonds, 160 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > show sel & #!1 cartoons > select /A:539-550 960 atoms, 990 bonds, 9 pseudobonds, 120 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:510-525 1150 atoms, 1170 bonds, 178 pseudobonds, 160 residues, 11 models selected > hide sel & #!1 cartoons > select up 1290 atoms, 1310 bonds, 178 pseudobonds, 180 residues, 17 models selected > select /A:470-490 1580 atoms, 1590 bonds, 38773 pseudobonds, 210 residues, 12 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > ui tool show Toolbar The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select /A:8-14 490 atoms, 500 bonds, 70 residues, 10 models selected > select sel : select sel : show sel & #!1 cartoons > hide sel & #!1 cartoons > select /A:8-14 490 atoms, 500 bonds, 70 residues, 10 models selected > select sel : select /A:527-531 460 atoms, 480 bonds, 43 pseudobonds, 50 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:532-536 510 atoms, 520 bonds, 73 pseudobonds, 50 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 atoms > hide sel & #!1 cartoons > select /A:532-536 510 atoms, 520 bonds, 73 pseudobonds, 50 residues, 11 models selected > select /A:532-538 670 atoms, 680 bonds, 92 pseudobonds, 70 residues, 11 models selected > show sel & #!1 surfaces > hide sel & #!1 surfaces > show sel & #!1 cartoons > select /A:532-539 730 atoms, 740 bonds, 128 pseudobonds, 80 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:578-590 1080 atoms, 1100 bonds, 9 pseudobonds, 130 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:569-575 620 atoms, 630 bonds, 47 pseudobonds, 70 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:577 70 atoms, 60 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > select /A:578 90 atoms, 80 bonds, 10 residues, 10 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:576 80 atoms, 70 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > select /A:560-567 550 atoms, 540 bonds, 9 pseudobonds, 80 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:559-553 Nothing selected > select /A:553-559 590 atoms, 600 bonds, 9 pseudobonds, 70 residues, 11 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:595-559 Nothing selected > select /A:595-599 370 atoms, 370 bonds, 1 pseudobond, 50 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:594-599 450 atoms, 450 bonds, 1 pseudobond, 60 residues, 11 models selected > hide sel & #!1 cartoons > hide sel & #!1 atoms > select /A:552 70 atoms, 60 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > select /A:592 90 atoms, 80 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > select /A:591 80 atoms, 70 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > select /A:593 90 atoms, 80 bonds, 10 residues, 10 models selected > hide sel & #!1 atoms > show sel & #!1 atoms > select /A 53420 atoms, 54420 bonds, 106213 pseudobonds, 6750 residues, 18 models selected > show sel & #!1 surfaces > transparency (#!1 & sel) 90 > show sel & #!1 cartoons > select /A:465 110 atoms, 100 bonds, 2596 pseudobonds, 10 residues, 11 models selected > color (#!1 & sel) blue > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 atoms > select /A:464 90 atoms, 80 bonds, 2349 pseudobonds, 10 residues, 11 models selected > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 atoms > show sel & #!1 atoms > hide sel & #!1 atoms > select /A:458 90 atoms, 80 bonds, 10 residues, 10 models selected > show sel & #!1 atoms > hide sel & #!1 atoms > select /A:459 120 atoms, 120 bonds, 10 residues, 10 models selected > show sel & #!1 atoms > hide sel & #!1 atoms > select /A:528 100 atoms, 100 bonds, 10 residues, 10 models selected > hide sel & #!1 cartoons > show sel & #!1 cartoons > select /A:441 120 atoms, 120 bonds, 2 pseudobonds, 10 residues, 11 models selected > ui tool show "Color Actions" > color sel royal blue > select /A:441 120 atoms, 120 bonds, 2 pseudobonds, 10 residues, 11 models selected > hide sel & #!1 cartoons > show sel & #!1 cartoons > select /A:492 60 atoms, 50 bonds, 10 residues, 10 models selected > select /A:392 60 atoms, 50 bonds, 2 pseudobonds, 10 residues, 11 models selected > show sel & #!1 cartoons > hide sel & #!1 cartoons > show sel & #!1 cartoons > select /A:370 60 atoms, 50 bonds, 2 pseudobonds, 10 residues, 11 models selected > select /A:467 140 atoms, 150 bonds, 5216 pseudobonds, 10 residues, 11 models selected > show sel & #!1 atoms > hide sel & #!1 atoms > show sel & #!1 atoms > ui tool show "Color Actions" > color sel royal blue > select /A:467,593 230 atoms, 230 bonds, 5216 pseudobonds, 20 residues, 11 models selected > color sel medium spring green > select /A:467,593,568 300 atoms, 290 bonds, 5221 pseudobonds, 30 residues, 12 models selected > color sel medium aquamarine > color sel medium spring green > select /A:467,593,568,551 350 atoms, 330 bonds, 5242 pseudobonds, 40 residues, 12 models selected > color sel medium spring green > select /A:467,593,568,551,526 400 atoms, 370 bonds, 5242 pseudobonds, 50 residues, 12 models selected > color sel medium spring green > label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}" > select /A 53420 atoms, 54420 bonds, 106213 pseudobonds, 6750 residues, 18 models selected > hide sel & #!1 surfaces > select clear > lighting simple > lighting shadows true > select A:3-8 Expected an objects specifier or a keyword > select /A:3-8 450 atoms, 450 bonds, 5 pseudobonds, 60 residues, 11 models selected > ~label (#!1 & sel) residues > ui tool show "Side View" ===== 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 INTEL-22.5.11 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: 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: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 25 days, 14 hours, 27 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2425: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: BNPC304 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 DELL P2425: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 1CRC304 Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort 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
Change History (2)
comment:1 by , 13 months ago
Component: | Unassigned → Graphics |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 13 months ago
Resolution: | → nonchimerax |
---|---|
Status: | assigned → closed |
Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics 655 |
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Crash in Apple's Intel graphics driver.