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Opened 7 months ago
Closed 7 months ago
#17233 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.7.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x000000028d89f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028c893000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028b887000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028a87b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028986f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000288863000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000287857000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028684b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028583f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000284833000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000283827000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e57b2140 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lxml.builder, psutil._psutil_osx, psutil._psutil_posix (total: 64)
{"app_name":"ChimeraX","timestamp":"2025-03-29 08:54:47.00 +0900","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.7.2 (22H313)","roots_installed":0,"name":"ChimeraX","incident_id":"89A8975D-2194-488B-B6C5-F772D0156F99"}
{
"uptime" : 410000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 7575,
"osVersion" : {
"train" : "macOS 13.7.2",
"build" : "22H313",
"releaseType" : "User"
},
"captureTime" : "2025-03-29 08:54:39.8521 +0900",
"incident" : "89A8975D-2194-488B-B6C5-F772D0156F99",
"pid" : 7891,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-24 12:47:47.0740 +0900",
"procStartAbsTime" : 391723085705,
"procExitAbsTime" : 10040794936904,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0BCC1ED9-576A-58B8-86B6-CB15F777D8CD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "172E29E3-EF5B-75BB-7E2E-8DE6A2739BD0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 5,
"sleepWakeUUID" : "10B7DB4C-3C75-4099-9254-646BC937E3BD",
"sip" : "enabled",
"vmRegionInfo" : "0x78cc9293dad8 is not in any region. Bytes after previous region: 27262616591065 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 6000f8000000-600100000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000f8cc9293dad8","rawCodes":[1,273557516180184],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000f8cc9293dad8 -> 0x000078cc9293dad8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":7891},
"vmregioninfo" : "0x78cc9293dad8 is not in any region. Bytes after previous region: 27262616591065 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 6000f8000000-600100000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":274237,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":0},{"value":101},{"value":101},{"value":11697034400},{"value":0},{"value":14480748015834496940},{"value":14480748015213272812},{"value":14757395258967641293},{"value":4294967286},{"value":4832328274},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8223553616},{"value":0},{"value":11},{"value":8145019200,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8145019424,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4384179760,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8102772736,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":8102772736,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6650199080},"cpsr":{"value":1073745920},"fp":{"value":4832328416},"sp":{"value":4832328384},"esr":{"value":1442840704,"description":" 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,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":277419,"frames":[{"imageOffset":18160,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":165},{"imageOffset":30068,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":166},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":277420,"frames":[{"imageOffset":18160,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":165},{"imageOffset":30068,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":166},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":277421,"frames":[{"imageOffset":18160,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":165},{"imageOffset":30068,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":166},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":277422,"frames":[{"imageOffset":18160,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":165},{"imageOffset":30068,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":166},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":277423,"frames":[{"imageOffset":18160,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":165},{"imageOffset":30068,"symbol":"_pthread_cond_wait","symbolLocation":1232,"imageIndex":166},{"imageOffset":1502040,"symbol":"blas_thread_server","symbolLocation":360,"imageIndex":19},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":298611,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3828,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":165},{"imageOffset":78368,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":165},{"imageOffset":39768,"symbol":"mach_msg_overwrite","symbolLocation":604,"imageIndex":165},{"imageOffset":4720,"symbol":"mach_msg","symbolLocation":24,"imageIndex":165},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":300836,"name":"NetworkConfigWatcher","frames":[{"imageOffset":3828,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":165},{"imageOffset":78368,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":165},{"imageOffset":39768,"symbol":"mach_msg_overwrite","symbolLocation":604,"imageIndex":165},{"imageOffset":4720,"symbol":"mach_msg","symbolLocation":24,"imageIndex":165},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70677152,"imageIndex":56},{"imageOffset":70343492,"imageIndex":56},{"imageOffset":70809656,"imageIndex":56},{"imageOffset":70544784,"imageIndex":56},{"imageOffset":70952276,"imageIndex":56},{"imageOffset":70952656,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":1522257,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":3828,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":165},{"imageOffset":78368,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":165},{"imageOffset":39768,"symbol":"mach_msg_overwrite","symbolLocation":604,"imageIndex":165},{"imageOffset":4720,"symbol":"mach_msg","symbolLocation":24,"imageIndex":165},{"imageOffset":71161832,"imageIndex":56},{"imageOffset":70677284,"imageIndex":56},{"imageOffset":70900888,"imageIndex":56},{"imageOffset":70904380,"imageIndex":56},{"imageOffset":70902644,"imageIndex":56},{"imageOffset":71057880,"imageIndex":56},{"imageOffset":28584,"symbol":"_pthread_start","symbolLocation":148,"imageIndex":166},{"imageOffset":7584,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":7527165,"frames":[{"imageOffset":7564,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":166}]},{"id":7527166,"frames":[{"imageOffset":7564,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":166}]},{"id":7528544,"frames":[{"imageOffset":7564,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":166}]},{"id":7528545,"frames":[{"imageOffset":7564,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":166}]},{"id":7528717,"frames":[{"imageOffset":7564,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":166}]}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6646005760,
"size" : 3586424832,
"uuid" : "61399007-0047-30d8-9bb0-14e526b3aedf"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=8.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 2560K 115 \nCG raster data 480K 10 \nColorSync 656K 30 \nCoreAnimation 6896K 357 \nCoreGraphics 48K 3 \nCoreImage 16K 1 \nCoreServices 624K 2 \nCoreUI image data 5040K 37 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 6.4G 2827 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 720.0M 6 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 128K 7 \nOpenGL GLSL 384K 4 \nSTACK GUARD 784K 49 \nStack 391.6M 50 \nStack Guard 56.0M 1 \nVM_ALLOCATE 391.9M 442 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__AUTH 1931K 400 \n__AUTH_CONST 29.5M 639 \n__CTF 824 1 \n__DATA 21.0M 800 \n__DATA_CONST 40.8M 806 \n__DATA_DIRTY 2040K 248 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 834.3M 166 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 893.2M 826 \ndyld private memory 320K 4 \nmapped file 625.0M 114 \nshared memory 3728K 27 \n=========== ======= ======= \nTOTAL 10.9G 8002 \nTOTAL, minus reserved VM space 9.7G 8002 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "c335cd39aa47a5f770481132c7622824e9f9b7de",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62c74108bcb0435c2153f963",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "657a4921d6ad146894c1b003"
},
"deploymentId" : 240000394
},
{
"rolloutId" : "6425c75e4327780c10cc4252",
"factorPackIds" : {
"SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE" : "642600a457e7664b1698eb32"
},
"deploymentId" : 240000004
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}
}
===== Log before crash start =====
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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX1RD-
> NCP/20230427073130/NCP_SSX1_class13_20230405/Show_NCP_SS1_class13_RR_20_DyadView.cxs
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 2/R
> sequence chain /S
Alignment identifier is 2/S
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX2RD-
> NCP/2023-0403-谷解析結果/20230403080221/NCP_SSX2_class2_20230403/NCP_SSX2_class2_RR_09_H3(purple)H4(green)H2A(yellow)H2B(red)_2.cxs
opened ChimeraX session
> close #1
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX2RD-
> NCP/2023-0403-谷解析結果/20230403080221/NCP_SSX2_class2_20230403/NCP_SSX2_class2_RR_09_Show.cxs
opened ChimeraX session
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX2RD-
> NCP/2023-0403-谷解析結果/20230403080221/NCP_SSX2_class3_20230403/NCP_SSX2_class2_RR_09_imposeH.pdb
Chain information for NCP_SSX2_class2_RR_09_imposeH.pdb #1
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
52 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX1RD-
> NCP/20230427073130/CompSSX1_SSX2/NCP_SSX2_class2_RR_09_trH.pdb
Chain information for NCP_SSX2_class2_RR_09_trH.pdb #1
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
52 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/StructuralAnalysis/others/NCP_SS1_class4and13_SSX2_class2-with-
> Hbonds.cxs
opened ChimeraX session
> hide #!1 models
> hide #!2 models
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/Align_allSSXRD/Align_allSSXRD_to_SSX2_24S.cxs
opened ChimeraX session
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX1RD-
> NCP/20230427073130/ShowSSX1NucClass4and13_roll90D_DyadView.cxs
opened ChimeraX session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX2RD-
> NCP/2023-0403-谷解析結果/20230403080221/NCP_SSX2_class2_20230403/NCP_SSX2_class2_RR_09.pdb
Chain information for NCP_SSX2_class2_RR_09.pdb #3
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
52 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #3 to #1
Computing secondary structure
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 NCP_SS1_class4_RR_19.pdb, chain X (#1) with
NCP_SSX2_class2_RR_09.pdb, chain X (#3), sequence alignment score = 721.8
RMSD between 129 pruned atom pairs is 0.539 angstroms; (across all 129 pairs:
0.539)
> matchmaker #3 to #1
Computing secondary structure
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 NCP_SS1_class4_RR_19.pdb, chain X (#1) with
NCP_SSX2_class2_RR_09.pdb, chain X (#3), sequence alignment score = 721.8
RMSD between 129 pruned atom pairs is 0.539 angstroms; (across all 129 pairs:
0.539)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2
11548 atoms, 12273 bonds, 1051 residues, 17 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.14992,-0.63009,-0.76191,294.31,0.57978,0.56818,-0.58397,48.887,0.80086,-0.52929,0.28014,62.024
> view matrix models
> #2,-0.14992,-0.63009,-0.76191,225.8,0.57978,0.56818,-0.58397,46.749,0.80086,-0.52929,0.28014,67.861
> select clear
> ui tool show Matchmaker
> matchmaker #!2 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 NCP_SS1_class4_RR_19.pdb, chain X (#1) with
NCP_SS1_class13_RR_20.pdb, chain X (#2), sequence alignment score = 721.8
RMSD between 129 pruned atom pairs is 0.388 angstroms; (across all 129 pairs:
0.388)
Mismatch between Cocoa '\x0' and Carbon 'r' for virtual key 15 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'R' for virtual key 15 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'r' for virtual key 15 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'r' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ae' for virtual key 15 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2030' for virtual key 15 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ae' for virtual key 15 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2030' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x12' for virtual key 15 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> reset
Unknown command: reset
> ui tool show Matchmaker
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX1RD-
> NCP/20230427073130/ShowSSX1NucClass4and13_roll90D_DyadView.cxs format
> session
opened ChimeraX session
> view
> view orient
> undo
> toolshed show
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'T' for virtual key 17 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> tile
2 models tiled
> tile 1
Expected a models specifier or a keyword
> ui tool show "File History"
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/Data/GST-SSX1RD-
> NCP/20230427073130/ShowSSX1NucClass4and13_roll90D_DyadView.cxs format
> session
opened ChimeraX session
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> set bgColor white
> set bgColor #ffffff00
> tile
2 models tiled
> tile 1
Expected a models specifier or a keyword
> tile #1-2 1
Expected a keyword
> tile #1,2 1
Expected a keyword
> tile #1,2 2
Expected a keyword
> tile #1,2 columns 1
2 models tiled
> =tile
Unknown command: =tile
> ~tile
> tile #1,2 columns 2 spacingFactors 0.7
Expected a keyword
> tile #1,2 columns 2 spacingFactor 0.7
2 models tiled
> tile #1,2 columns 2 spacingFactor 0.8
2 models tiled
> tile #1,2 columns 2 spacingFactor 0.9
2 models tiled
> 8
Unknown command: 8
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> tile #1,2 columns 2 spacingFactor 0.75
2 models tiled
> tile #1,2 columns 2 spacingFactor 0.8
2 models tiled
> lighting soft
> graphics silhouettes true
> roll x 1 90
> roll z 1 90
> ui tool show "Show Sequence Viewer"
> sequence chain #2/R
Alignment identifier is 2/R
> sequence chain #2/S
Alignment identifier is 2/S
> cd /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs
Current working directory is:
/Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NC-class1p3_and_-
> class4-show-DyadViews.cxs
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NC-class1p3_and_-
> class4-show-DyadViews.cxs includeMaps true
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NCP-
> class1p3/loc_scale_02_B45.mrc
Opened loc_scale_02_B45.mrc as #3, grid size 256,256,256, pixel 1.06, shown at
level 0.0432, step 1, values float32
> ui tool show "Volume Viewer"
> volume #3 color #b2b2b288
> ui tool show "Fit in Map"
> volume #3 color #b2b2b287
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NCP-
> class1p3/loc_scale_02_B45.mrc format mrc
Opened loc_scale_02_B45.mrc as #1, grid size 256,256,256, pixel 1.06, shown at
level 0.0432, step 1, values float32
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NCP-
> class1p3/NCP_SS1_class13_RR_20.pdb
Chain information for NCP_SS1_class13_RR_20.pdb #2
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
51 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> volume #1 color #b2b2b283
> volume #1 color #b2b2b282
> volume #1 color #73fdff
> volume #1 color #73fdff84
> volume #1 color #73fdff
> volume #1 color #73fdff81
> roll z 1 90 cartoon style width 3 thickness 1
Expected a keyword
> set bgColor white
> lightning soft
Unknown command: lightning soft
> lighting soft
> color #1/X dim gray
> hide atoms
> show cartoons
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #1/A-H,X,Y
Nothing selected
> select #2/A-H,X,Y
11292 atoms, 12013 bonds, 1019 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> hide #!1 models
> select #2/R,SY
98 atoms, 100 bonds, 12 residues, 1 model selected
> select #2/R,S
256 atoms, 260 bonds, 32 residues, 1 model selected
> show sel cartoons
> cartoon style width 3 thickness 1
> color sel white
> show sel atoms
> style sel stick
Changed 256 atom styles
> color sel byhetero
> style sel ball
Changed 256 atom styles
> color sel byhetero
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> style sel stick
Changed 256 atom styles
> size stickRadius 0.5
Changed 12273 bond radii
> color #2/X dim gray
> select clear
> color #2/Y dark gray
> color #1/A,E purple
> color #2/A,E purple
> color #2/B,F green
> color #2/C,G yellow
> color #2/D,H red
> ui tool show "Show Sequence Viewer"
> sequence chain /X
Alignment identifier is 2/X
> sequence chain /Y
Alignment identifier is 2/Y
> select #2/X 144
Expected a keyword
> select #2/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> volume #1 color #73fcd6
> color sel ice
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel Ice
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> volume #1 color #73fdff
> color sel bynucleotide ice
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel surfaces
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel ice surfaces
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel surfaces
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color (#!2 & sel) blue
> color (#!2 & sel) cornflower blue
> select #2/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select #2/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select #2/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select clear
> show #!1 models
> volume #1 color #73fdff80
> interfaces ~solvent
28 buried areas: Y X 6008, E F 2552, A B 2532, G H 2523, C D 2518, X E 704, Y
E 683, C E 663, G S 630, E A 601, G A 593, X C 570, X A 519, H F 506, Y C 505,
Y A 504, D B 497, X G 488, C F 461, G B 457, Y G 424, Y D 401, C R 362, Y F
350, D R 344, H S 341, X B 338, X H 336
> color zone #1 near #2 distance 6.36
> volume #1 color #73fdff30
> volume #1 color #73fdff20
> volume #1 color #73fdff2c
> volume #1 color #ff7e79
> volume #1 color #ff7e793b
> volume #1 color #fffb00
> volume #1 color #fffb0052
> volume #1 color #00fdff
> volume #1 color #00fdff2b
> volume #1 color #00fdff27
> volume #1 color #00fdff
> volume #1 color turquise
Invalid "color" argument: Invalid color name or specifier
> volume #1 color turquoise
> volume #1 color #00fdff25
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX2RD-NCPs/SSX2RD-NCP-
> class2/loc_scale_12_B60.mrc
Opened loc_scale_12_B60.mrc as #3, grid size 256,256,256, pixel 1.06, shown at
level 0.0484, step 1, values float32
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX2RD-NCPs/SSX2RD-NCP-
> class2/NCP_SSX2_class2_RR_09.pdb
Chain information for NCP_SSX2_class2_RR_09.pdb #4
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
52 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> volume #3 color #ffffb261
> volume #3 color #ffffb226
> hide #4 atoms
> show #4/A-H,X,Y surfaces
> show #4/R,S cartoons
> cartoon style width 3 thickness 1
> color #4/R,S white
> show #4/R,S atomswhite
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #4/R,S atoms
> style sel stick
Changed 0 atom styles
> size stickRadius 0.5
Changed 24550 bond radii
> color byhetero
> undo
> color #4/R,S byhetero
> select clear
> color #4/X dim gray
> color #4/Y dark gray
> color #4/A,E purple
> color #4/B,F green
> color #4/C,G yellow
> color #4/D,H red
> ui tool show "Show Sequence Viewer"
> sequence chain #4/X
Alignment identifier is 4/X
> sequence chain #4/Y
Alignment identifier is 4/Y
> select #4/X:16,144
39 atoms, 41 bonds, 2 residues, 1 model selected
> color (#!4 & sel) cornflower blue
> hide #!2 models
> hide #!1 models
> hide #!3 models
> select #4/Y:1,132
42 atoms, 46 bonds, 2 residues, 1 model selected
> color (#!4 & sel) cornflower blue
> select clear
> show #!3 models
> show #!2 models
> show #!1 models
> select #3,4
11543 atoms, 12277 bonds, 1043 residues, 3 models selected
> ui mousemode right "rotate selected models"
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!4 models
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!2 models
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX2RD-NCPs/SSX2RD-NCP-
> class3/loc_scale_07_B60.mrc
Opened loc_scale_07_B60.mrc as #5, grid size 256,256,256, pixel 1.06, shown at
level 0.0439, step 1, values float32
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX2RD-NCPs/SSX2RD-NCP-
> class3/NCP_SSX2_class3_RR_24.pdb
Chain information for NCP_SSX2_class3_RR_24.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
54 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!5 models
> hide #6 models
> select #3,4,5,6
22297 atoms, 23672 bonds, 2048 residues, 6 models selected
> view matrix models
> #3,0.94692,-0.20016,-0.25157,67.593,0.22049,0.97383,0.05511,-33.756,0.23395,-0.10765,0.96627,-12.808,#4,0.94692,-0.20016,-0.25157,67.593,0.22049,0.97383,0.05511,-33.756,0.23395,-0.10765,0.96627,-12.808,#5,0.94692,-0.20016,-0.25157,67.593,0.22049,0.97383,0.05511,-33.756,0.23395,-0.10765,0.96627,-12.808,#6,0.94692,-0.20016,-0.25157,67.593,0.22049,0.97383,0.05511,-33.756,0.23395,-0.10765,0.96627,-12.808
> view matrix models
> #3,0.48763,0.67722,-0.55099,50.688,-0.87231,0.35191,-0.33948,251.52,-0.036003,0.64617,0.76234,-51.35,#4,0.48763,0.67722,-0.55099,50.688,-0.87231,0.35191,-0.33948,251.52,-0.036003,0.64617,0.76234,-51.35,#5,0.48763,0.67722,-0.55099,50.688,-0.87231,0.35191,-0.33948,251.52,-0.036003,0.64617,0.76234,-51.35,#6,0.48763,0.67722,-0.55099,50.688,-0.87231,0.35191,-0.33948,251.52,-0.036003,0.64617,0.76234,-51.35
> view matrix models
> #3,0.36091,0.58633,-0.72523,103.28,-0.9304,0.17302,-0.32313,281.53,-0.063981,0.79138,0.60797,-46.849,#4,0.36091,0.58633,-0.72523,103.28,-0.9304,0.17302,-0.32313,281.53,-0.063981,0.79138,0.60797,-46.849,#5,0.36091,0.58633,-0.72523,103.28,-0.9304,0.17302,-0.32313,281.53,-0.063981,0.79138,0.60797,-46.849,#6,0.36091,0.58633,-0.72523,103.28,-0.9304,0.17302,-0.32313,281.53,-0.063981,0.79138,0.60797,-46.849
> view matrix models
> #3,0.25131,0.68408,-0.68474,99.603,-0.95838,0.076856,-0.27496,292.02,-0.13547,0.72534,0.67493,-36.999,#4,0.25131,0.68408,-0.68474,99.603,-0.95838,0.076856,-0.27496,292.02,-0.13547,0.72534,0.67493,-36.999,#5,0.25131,0.68408,-0.68474,99.603,-0.95838,0.076856,-0.27496,292.02,-0.13547,0.72534,0.67493,-36.999,#6,0.25131,0.68408,-0.68474,99.603,-0.95838,0.076856,-0.27496,292.02,-0.13547,0.72534,0.67493,-36.999
> hide #!2 models
> hide #!4 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide sel & #6 atoms
> show sel & #6 surfaces
> view matrix models
> #3,0.21479,0.10678,-0.97081,221.24,-0.97615,-0.0087673,-0.21694,298.12,-0.031676,0.99424,0.10235,-9.1031,#4,0.21479,0.10678,-0.97081,221.24,-0.97615,-0.0087673,-0.21694,298.12,-0.031676,0.99424,0.10235,-9.1031,#5,0.21479,0.10678,-0.97081,221.24,-0.97615,-0.0087673,-0.21694,298.12,-0.031676,0.99424,0.10235,-9.1031,#6,0.21479,0.10678,-0.97081,221.24,-0.97615,-0.0087673,-0.21694,298.12,-0.031676,0.99424,0.10235,-9.1031
> view matrix models
> #3,0.51112,0.26585,-0.81736,138.52,-0.853,0.27376,-0.44436,274.38,0.10562,0.92433,0.36669,-54.472,#4,0.51112,0.26585,-0.81736,138.52,-0.853,0.27376,-0.44436,274.38,0.10562,0.92433,0.36669,-54.472,#5,0.51112,0.26585,-0.81736,138.52,-0.853,0.27376,-0.44436,274.38,0.10562,0.92433,0.36669,-54.472,#6,0.51112,0.26585,-0.81736,138.52,-0.853,0.27376,-0.44436,274.38,0.10562,0.92433,0.36669,-54.472
> view matrix models
> #3,0.56902,0.25008,-0.78338,128.11,-0.81421,0.037817,-0.57934,319.24,-0.11526,0.96749,0.22514,-10.838,#4,0.56902,0.25008,-0.78338,128.11,-0.81421,0.037817,-0.57934,319.24,-0.11526,0.96749,0.22514,-10.838,#5,0.56902,0.25008,-0.78338,128.11,-0.81421,0.037817,-0.57934,319.24,-0.11526,0.96749,0.22514,-10.838,#6,0.56902,0.25008,-0.78338,128.11,-0.81421,0.037817,-0.57934,319.24,-0.11526,0.96749,0.22514,-10.838
> view matrix models
> #3,0.44116,0.23083,-0.86724,159.57,-0.89101,0.22805,-0.39255,278.65,0.10716,0.94589,0.30628,-49.328,#4,0.44116,0.23083,-0.86724,159.57,-0.89101,0.22805,-0.39255,278.65,0.10716,0.94589,0.30628,-49.328,#5,0.44116,0.23083,-0.86724,159.57,-0.89101,0.22805,-0.39255,278.65,0.10716,0.94589,0.30628,-49.328,#6,0.44116,0.23083,-0.86724,159.57,-0.89101,0.22805,-0.39255,278.65,0.10716,0.94589,0.30628,-49.328
> view matrix models
> #3,0.23714,0.49429,-0.83633,147.85,-0.96948,0.17551,-0.17117,266.3,0.062174,0.8514,0.52083,-59.916,#4,0.23714,0.49429,-0.83633,147.85,-0.96948,0.17551,-0.17117,266.3,0.062174,0.8514,0.52083,-59.916,#5,0.23714,0.49429,-0.83633,147.85,-0.96948,0.17551,-0.17117,266.3,0.062174,0.8514,0.52083,-59.916,#6,0.23714,0.49429,-0.83633,147.85,-0.96948,0.17551,-0.17117,266.3,0.062174,0.8514,0.52083,-59.916
> view matrix models
> #3,0.24679,0.60431,-0.75757,121.06,-0.9664,0.21142,-0.14617,257.66,0.071833,0.76819,0.63618,-65.796,#4,0.24679,0.60431,-0.75757,121.06,-0.9664,0.21142,-0.14617,257.66,0.071833,0.76819,0.63618,-65.796,#5,0.24679,0.60431,-0.75757,121.06,-0.9664,0.21142,-0.14617,257.66,0.071833,0.76819,0.63618,-65.796,#6,0.24679,0.60431,-0.75757,121.06,-0.9664,0.21142,-0.14617,257.66,0.071833,0.76819,0.63618,-65.796
> view matrix models
> #3,0.30263,0.6503,-0.6968,98.981,-0.95264,0.22937,-0.19969,260.68,0.029965,0.72423,0.68891,-61.39,#4,0.30263,0.6503,-0.6968,98.981,-0.95264,0.22937,-0.19969,260.68,0.029965,0.72423,0.68891,-61.39,#5,0.30263,0.6503,-0.6968,98.981,-0.95264,0.22937,-0.19969,260.68,0.029965,0.72423,0.68891,-61.39,#6,0.30263,0.6503,-0.6968,98.981,-0.95264,0.22937,-0.19969,260.68,0.029965,0.72423,0.68891,-61.39
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view matrix models
> #3,0.52894,0.56881,-0.62983,69.995,-0.81913,0.53625,-0.20363,201.78,0.22192,0.62362,0.74957,-82.45,#4,0.52894,0.56881,-0.62983,69.995,-0.81913,0.53625,-0.20363,201.78,0.22192,0.62362,0.74957,-82.45,#5,0.52894,0.56881,-0.62983,69.995,-0.81913,0.53625,-0.20363,201.78,0.22192,0.62362,0.74957,-82.45,#6,0.52894,0.56881,-0.62983,69.995,-0.81913,0.53625,-0.20363,201.78,0.22192,0.62362,0.74957,-82.45
> view matrix models
> #3,0.22059,0.43331,-0.87384,163.58,-0.97489,0.12607,-0.18358,275.46,0.030619,0.89239,0.45023,-51.651,#4,0.22059,0.43331,-0.87384,163.58,-0.97489,0.12607,-0.18358,275.46,0.030619,0.89239,0.45023,-51.651,#5,0.22059,0.43331,-0.87384,163.58,-0.97489,0.12607,-0.18358,275.46,0.030619,0.89239,0.45023,-51.651,#6,0.22059,0.43331,-0.87384,163.58,-0.97489,0.12607,-0.18358,275.46,0.030619,0.89239,0.45023,-51.651
> view matrix models
> #3,0.33912,0.28386,-0.89689,170.67,-0.93742,0.18204,-0.29683,278.3,0.079014,0.94143,0.32783,-48.127,#4,0.33912,0.28386,-0.89689,170.67,-0.93742,0.18204,-0.29683,278.3,0.079014,0.94143,0.32783,-48.127,#5,0.33912,0.28386,-0.89689,170.67,-0.93742,0.18204,-0.29683,278.3,0.079014,0.94143,0.32783,-48.127,#6,0.33912,0.28386,-0.89689,170.67,-0.93742,0.18204,-0.29683,278.3,0.079014,0.94143,0.32783,-48.127
> view matrix models
> #3,0.23191,0.42024,-0.87728,164.26,-0.97213,0.13199,-0.19376,275.69,0.034365,0.89776,0.43913,-51.359,#4,0.23191,0.42024,-0.87728,164.26,-0.97213,0.13199,-0.19376,275.69,0.034365,0.89776,0.43913,-51.359,#5,0.23191,0.42024,-0.87728,164.26,-0.97213,0.13199,-0.19376,275.69,0.034365,0.89776,0.43913,-51.359,#6,0.23191,0.42024,-0.87728,164.26,-0.97213,0.13199,-0.19376,275.69,0.034365,0.89776,0.43913,-51.359
> ui tool show Matchmaker
> matchmaker #!4 to #2
Computing secondary structure
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 NCP_SS1_class13_RR_20.pdb, chain X (#2) with
NCP_SSX2_class2_RR_09.pdb, chain X (#4), sequence alignment score = 721.8
RMSD between 129 pruned atom pairs is 0.546 angstroms; (across all 129 pairs:
0.546)
> hide #!6 models
> show #!4 models
> ui tool show "Volume Viewer"
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map loc_scale_12_B60.mrc in map loc_scale_02_B45.mrc using 167638 points
correlation = 0.4576, correlation about mean = 0.2144, overlap = 4396
steps = 160, shift = 1.82, angle = 11 degrees
Position of loc_scale_12_B60.mrc (#3) relative to loc_scale_02_B45.mrc (#1)
coordinates:
Matrix rotation and translation
0.31379993 0.55428332 -0.77090831 121.78727063
-0.94941738 0.19315502 -0.24758392 272.47504541
0.01167317 0.80960555 0.58685824 -57.21308752
Axis 0.52917721 -0.39172191 -0.75267883
Axis point 230.69570446 66.62046473 0.00000000
Rotation angle (degrees) 87.31146372
Shift along axis 0.77568189
> fitmap #4 inMap #1
Fit molecule NCP_SSX2_class2_RR_09.pdb (#4) to map loc_scale_02_B45.mrc (#1)
using 11543 atoms
average map value = 0.439, steps = 44
shifted from previous position = 0.0348
rotated from previous position = 0.0384 degrees
atoms outside contour = 124, contour level = 0.043192
Position of NCP_SSX2_class2_RR_09.pdb (#4) relative to loc_scale_02_B45.mrc
(#1) coordinates:
Matrix rotation and translation
0.25306056 0.71403646 -0.65277278 92.74502500
-0.96072150 0.10603261 -0.25645918 287.25168076
-0.11390600 0.69203254 0.71282284 -39.42165266
Axis 0.47455275 -0.26960775 -0.83792085
Axis point 212.82834165 92.48089320 0.00000000
Rotation angle (degrees) 87.93931378
Shift along axis -0.40064698
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!1 models
> show #!5 models
> color #5 #73fa79ff models
> color #5 #73fa7927 models
> hide #!4 models
> color #5 #73fa7926 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!4 models
> select clear
> tile columns 2
2 models tiled
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> tile columns 2
4 models tiled
> show #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NC-class1p3_and_-
> class4-show-DyadViews.cxs
opened ChimeraX session
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX1RD-NCPs/SSX1RD-NCP-
> class1p3/NCP_SS1_class13_RR_20.pdb format pdb
Chain information for NCP_SS1_class13_RR_20.pdb #1
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
51 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show cartoons
> hide atoms
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/NSMB2024/SSX1-NCP/8HR1/8hr1.pdb1
8hr1.pdb1 title:
Cryo-em structure of SSX1 bound to the unmodified nucleosome At A resolution
of 3.02 angstrom [more info...]
Chain information for 8hr1.pdb1 #2
---
Chain | Description
A E | No description available
B F | No description available
C G | No description available
D H | No description available
I | No description available
J | No description available
S | No description available
> show cartoons
> hide atoms
> ui tool show Matchmaker
> matchmaker #2 to #1
Computing secondary structure
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 NCP_SS1_class13_RR_20.pdb, chain X (#1) with 8hr1.pdb1, chain J
(#2), sequence alignment score = 707.8
RMSD between 128 pruned atom pairs is 0.610 angstroms; (across all 129 pairs:
0.643)
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #2/I
3031 atoms, 3404 bonds, 147 residues, 1 model selected
> color sel dark gray
> select #2/J
2996 atoms, 3356 bonds, 147 residues, 1 model selected
> color sel dim gray
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> color sel black
> select #2/I
3031 atoms, 3404 bonds, 147 residues, 1 model selected
> color sel black
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #1,2/A-H
11957 atoms, 12114 bonds, 1512 residues, 2 models selected
> hide sel cartoons
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #1/X,Y
5289 atoms, 5932 bonds, 258 residues, 1 model selected
> color sel blue
> select #1/X
2628 atoms, 2944 bonds, 129 residues, 1 model selected
> color sel blue
> select #1/Y
2661 atoms, 2988 bonds, 129 residues, 1 model selected
> color sel red
> select #2/I
3031 atoms, 3404 bonds, 147 residues, 1 model selected
> color sel orange
> select #2/J
2996 atoms, 3356 bonds, 147 residues, 1 model selected
> color sel light sea green
> select #2/I
3031 atoms, 3404 bonds, 147 residues, 1 model selected
> color sel blue
> select #1/X
2628 atoms, 2944 bonds, 129 residues, 1 model selected
> color sel orange red
> select #1/Y
2661 atoms, 2988 bonds, 129 residues, 1 model selected
> color sel red
> select #1/X
2628 atoms, 2944 bonds, 129 residues, 1 model selected
> color sel red
> select #2/I
3031 atoms, 3404 bonds, 147 residues, 1 model selected
> select #2/J
2996 atoms, 3356 bonds, 147 residues, 1 model selected
> color sel blue
> select clear
> select #1/S
158 atoms, 160 bonds, 20 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 158 atom styles
> color sel byhetero
> color sel magenta
> color sel byhetero
> size stickRadius 0.5
Changed 25198 bond radii
> cartoon style width 3 thickness 1
> select #2/S
129 atoms, 132 bonds, 14 residues, 1 model selected
> color sel cornflower blue
> show sel atoms
> style sel stick
Changed 129 atom styles
> color sel byhetero
> select #1/R
98 atoms, 100 bonds, 12 residues, 1 model selected
> color sel magenta
> show sel atoms
> style sel stick
Changed 98 atom styles
> color sel byhetero
> select clear
> cd /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp
Current working directory is:
/Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1.cxs includeMaps true
> select A-H
Expected an objects specifier or a keyword
> select #2-3/A-H
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> show sel cartoons
> select #1/A
784 atoms, 794 bonds, 95 residues, 1 model selected
> select #1/F
657 atoms, 664 bonds, 84 residues, 1 model selected
> select #2/G
815 atoms, 825 bonds, 106 residues, 1 model selected
> select #1/G
817 atoms, 827 bonds, 107 residues, 1 model selected
> hide #2 models
> select #2/A-H
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> show #1 cartoons
> select #2,3/A-H
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> select clear
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1.cxs
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowAll.cxs includeMaps true
> select #2,3/A-H
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> hide sel cartoons
> select #2/A-H,3/A-H
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> hide sel cartoons
> select #2/A-H,#3/A-H
Expected an objects specifier or a keyword
> select #2/A-H & #3/A-H
Nothing selected
> select (#2/A-H & #3/A-H)
Nothing selected
> select (#2/A-H && #3/A-H)
Expected an objects specifier or a keyword
> select (#2/A-H & #3/A-H)
Nothing selected
> select #1/A#2/A
1585 atoms, 1607 bonds, 192 residues, 2 models selected
> select #2/A-H#3/A-H
5954 atoms, 6033 bonds, 751 residues, 1 model selected
> hide sel cartoons
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> select #2/A#3/A
801 atoms, 813 bonds, 97 residues, 1 model selected
> hide sel cartoons
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #1/A-H#1/A-H
6003 atoms, 6081 bonds, 761 residues, 1 model selected
> hide sel cartoons
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowDNAandSSX.cxs
> select #1/R
98 atoms, 100 bonds, 12 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowDNAandSSX_Schain.cxs
> select ions
Nothing selected
> select solvent
3 atoms, 3 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowDNAandSSX_Schain.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain #1/X
Alignment identifier is 1/X
> sequence chain #1/Y
Alignment identifier is 1/Y
> sequence chain #2/J
Alignment identifier is 2/J
> sequence chain #2/S
Alignment identifier is 2/S
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowDNAandSSX_Schain format fasta alignment 1/X
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowDNAandSSX_Schain.cxs includeMaps true
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/SSX1RD-NCP-
> class1p3.fasta format fasta alignment 1/X
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/8HR1_chainJ.fasta
> format fasta alignment 1/Y
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/SSX1RD-NCP-
> class1p3_chainX.fasta format fasta alignment 1/X
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/SSX1RD-NCP-
> class1p3_chainY.fasta format fasta alignment 1/Y
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/8HR1_chainJ.fasta
> format fasta alignment 2/J
> ui tool show "Show Sequence Viewer"
> sequence chain #2/I
Alignment identifier is 2/I
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/8HR1_chainI.fasta
> format fasta alignment 2/I
Mismatch between Cocoa '\x0' and Carbon 'e' for virtual key 14 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'E' for virtual key 14 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'e' for virtual key 14 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'e' for virtual key 14 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'L' for virtual key 37 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ac' for virtual key 37 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d2' for virtual key 37 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ac' for virtual key 37 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d2' for virtual key 37 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '#' for virtual key 20 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a3' for virtual key 20 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2039' for virtual key 20 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a3' for virtual key 20 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2039' for virtual key 20 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '3' for virtual key 20 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2/I:56
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-73-56
2684 atoms, 3015 bonds, 130 residues, 1 model selected
> select #2/I:57
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/I:73
44 atoms, 48 bonds, 2 residues, 1 model selected
> select #2/I:57-73
347 atoms, 388 bonds, 17 residues, 1 model selected
> color sel medium blue
> color sel cornflower blue
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #1/X:17
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #1/X:18
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/X:19
84 atoms, 91 bonds, 4 residues, 1 model selected
> select add #1/X:144
104 atoms, 112 bonds, 5 residues, 1 model selected
> select #2/J:-57
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #2/J:-73
38 atoms, 40 bonds, 2 residues, 1 model selected
> select add #2/J:-72
58 atoms, 61 bonds, 3 residues, 1 model selected
> select add #2/J:-71
80 atoms, 85 bonds, 4 residues, 1 model selected
> select add #2/J:-58
102 atoms, 109 bonds, 5 residues, 1 model selected
> select add #2/J:-59
122 atoms, 130 bonds, 6 residues, 1 model selected
> select add #2/J:-61
144 atoms, 154 bonds, 7 residues, 1 model selected
> select add #2/J:-60
166 atoms, 178 bonds, 8 residues, 1 model selected
> select add #2/J:-62
185 atoms, 198 bonds, 9 residues, 1 model selected
> select add #2/J:-64
204 atoms, 218 bonds, 10 residues, 1 model selected
> select add #2/J:-63
223 atoms, 238 bonds, 11 residues, 1 model selected
> select add #2/J:-65
243 atoms, 259 bonds, 12 residues, 1 model selected
> select add #2/J:-66
264 atoms, 282 bonds, 13 residues, 1 model selected
> select add #2/J:-67
285 atoms, 305 bonds, 14 residues, 1 model selected
> select add #2/J:-68
307 atoms, 329 bonds, 15 residues, 1 model selected
> select add #2/J:-70
329 atoms, 353 bonds, 16 residues, 1 model selected
> select add #2/J:-69
350 atoms, 376 bonds, 17 residues, 1 model selected
> color sel cornflower blue
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:69
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/J:-64-69
2727 atoms, 3054 bonds, 134 residues, 1 model selected
> select #2/J:-64-69
2727 atoms, 3054 bonds, 134 residues, 1 model selected
> select #2/J:-64-69
2727 atoms, 3054 bonds, 134 residues, 1 model selected
> select #2/J:-64-69
2727 atoms, 3054 bonds, 134 residues, 1 model selected
> select #2/I:73
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/J:-64-69
2727 atoms, 3054 bonds, 134 residues, 1 model selected
> select clear
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #1/X:144
39 atoms, 41 bonds, 2 residues, 1 model selected
> select #1/X:97-100
88 atoms, 99 bonds, 4 residues, 1 model selected
> select #1/X:16-100
1734 atoms, 1943 bonds, 85 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/X
2628 atoms, 2944 bonds, 129 residues, 1 model selected
> select subtract #1/X:144
2608 atoms, 2922 bonds, 128 residues, 1 model selected
> select add #1/X:144
2628 atoms, 2943 bonds, 129 residues, 1 model selected
> select #2/J:-64-69
2727 atoms, 3054 bonds, 134 residues, 1 model selected
> ui dockable false "Sequence Viewer"
> select #2/J:70
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/J:-56-70
2584 atoms, 2894 bonds, 127 residues, 1 model selected
> select #2/J:69
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/J:-56-69
2565 atoms, 2873 bonds, 126 residues, 1 model selected
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/X:144
40 atoms, 42 bonds, 2 residues, 2 models selected
> select add #2/J:72
62 atoms, 66 bonds, 3 residues, 2 models selected
> select add #2/J:71
82 atoms, 87 bonds, 4 residues, 2 models selected
> select add #1/X:142
104 atoms, 111 bonds, 5 residues, 2 models selected
> select subtract #1/X:142
82 atoms, 87 bonds, 4 residues, 2 models selected
> select add #2/I:-73
103 atoms, 110 bonds, 5 residues, 2 models selected
> select add #1/Y:1
124 atoms, 133 bonds, 6 residues, 2 models selected
> select subtract #2/I:-73
103 atoms, 110 bonds, 5 residues, 2 models selected
> select clear
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:70-73
81 atoms, 89 bonds, 4 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/X:141-144
82 atoms, 91 bonds, 4 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/X:142-144
63 atoms, 70 bonds, 3 residues, 1 model selected
> color sel light sea green
> color sel blue
> color sel red
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:71
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #2/J:72
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #1/X:144
82 atoms, 87 bonds, 4 residues, 2 models selected
> select add #1/X:143
103 atoms, 110 bonds, 5 residues, 2 models selected
> select add #1/X:142
125 atoms, 134 bonds, 6 residues, 2 models selected
> select subtract #1/X:142
103 atoms, 110 bonds, 5 residues, 2 models selected
> select add #1/X:142
125 atoms, 134 bonds, 6 residues, 2 models selected
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:70-73
81 atoms, 89 bonds, 4 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/X:142-144
63 atoms, 70 bonds, 3 residues, 1 model selected
> color sel cornflower blue
> color sel red
> color sel orange red
> color sel orange
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:70-73
81 atoms, 89 bonds, 4 residues, 1 model selected
> select add #2/I:-73
102 atoms, 112 bonds, 5 residues, 1 model selected
> select #2/I:-70
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-70--69
44 atoms, 49 bonds, 2 residues, 1 model selected
> select #2/I:-69
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-69--64
126 atoms, 141 bonds, 6 residues, 1 model selected
> select #2/I:-64
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:-64-56
2496 atoms, 2803 bonds, 121 residues, 1 model selected
> select #2/I:56
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-69-56
2601 atoms, 2921 bonds, 126 residues, 1 model selected
> select #2/I:-70--69
44 atoms, 49 bonds, 2 residues, 1 model selected
> select #2/I:-70
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-73--70
83 atoms, 93 bonds, 4 residues, 1 model selected
> color sel cornflower blue
> select #1/Y:3-4
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #1/Y:1-4
82 atoms, 91 bonds, 4 residues, 1 model selected
> select #1/Y:3
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/Y:1-3
60 atoms, 66 bonds, 3 residues, 1 model selected
> color sel cornflower blue
> color sel orange red
> color sel orange
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:72
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #2/J:71
62 atoms, 66 bonds, 3 residues, 1 model selected
> color sel cornflower blue
> select #2/J:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:70-73
81 atoms, 89 bonds, 4 residues, 1 model selected
> color sel cornflower blue
> select #2/J:-73
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/J:-73--52
456 atoms, 512 bonds, 22 residues, 1 model selected
> select #2/J:-58--57
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #2/J:-73--57
350 atoms, 392 bonds, 17 residues, 1 model selected
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:73
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/I:57
44 atoms, 48 bonds, 2 residues, 1 model selected
> select #2/I:73
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:57-73
347 atoms, 388 bonds, 17 residues, 1 model selected
> select #2/I:-71--69,57-73
412 atoms, 461 bonds, 20 residues, 1 model selected
> select #2/I:-71--69,57-73
412 atoms, 461 bonds, 20 residues, 1 model selected
> select #2/I:-73--69,57-73
452 atoms, 506 bonds, 22 residues, 1 model selected
> select #2/I:-73--69,57-73
452 atoms, 506 bonds, 22 residues, 1 model selected
> select #2/I:-73
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:-73--70
83 atoms, 93 bonds, 4 residues, 1 model selected
> select #2/I:-69
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-69-61
2701 atoms, 3033 bonds, 131 residues, 1 model selected
> select #2/I:56
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:-69-56
2601 atoms, 2921 bonds, 126 residues, 1 model selected
> select #1/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/Y:84-129
945 atoms, 1059 bonds, 46 residues, 1 model selected
> select #1/Y:4-129
2601 atoms, 2921 bonds, 126 residues, 1 model selected
> select #1/A-H#2/A-H
11957 atoms, 12114 bonds, 1512 residues, 2 models selected
> show sel cartoons
> ui tool show "Side View"
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> hide sel cartoons
> select #1/S
158 atoms, 160 bonds, 20 residues, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> select #1/A-H#2/A-H
11957 atoms, 12114 bonds, 1512 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/SSX1comp/Comp_SSX1RD-NCP-
> class1p3_vs_8HR1_ShowDNAandSSX_Schain.cxs
> select #2/I
3031 atoms, 3404 bonds, 147 residues, 1 model selected
> select #1/Y#2/I
5692 atoms, 6392 bonds, 276 residues, 2 models selected
> select #1/Y
2661 atoms, 2988 bonds, 129 residues, 1 model selected
> color sel #0433ffff
> color sel #ff2600ff
> color sel red
> color sel #ff2600ff
> color sel #ff2600fe
> color sel #ff2600f4
> color sel #ff2600f2
> color sel #ff2600f1
> color sel #ff2600e8
> color sel #ff2600e4
> color sel #ff2600e2
[deleted to fit within ticket limits]
> matchmaker #3 to #1 alg Smith-Waterman ssFraction 0.2022 cutoffDistance none
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-62
SS fraction | 0.2022
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
No iteration
Matchmaker NCP_SS1_class13_RR_20.pdb (#1) with NCP_SS1_class4_RR_19.pdb (#3),
sequence alignment score = 750.553
RMSD between 129 atom pairs is 0.388 angstroms
> select #3/A-H
6044 atoms, 6124 bonds, 764 residues, 1 model selected
> hide sel cartoons
> select #3/A-H,R
6137 atoms, 6219 bonds, 775 residues, 1 model selected
> hide sel cartoons
> cartoon style width 3 thickness 1
> select #3/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #3/Y:130
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/X
Alignment identifier is 3/X
> sequence chain #3/Y
Alignment identifier is 3/Y
> select #3/Y:130-131
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #3/Y:130-144
309 atoms, 346 bonds, 15 residues, 1 model selected
> color sel #73fa79ff
> select #3/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #3/Y:1-129
2661 atoms, 2988 bonds, 129 residues, 1 model selected
> color sel #73fa79ff
> color sel #73fa79fe
> color sel #73fa79f0
> color sel #73fa79d7
> color sel #73fa79bf
> color sel #73fa7992
> color sel #73fa7979
> color sel #73fa795e
> color sel #73fa794d
> color sel #73fa7942
> color sel #73fa793e
> color sel #73fa793c
> color sel #73fa793b
> color sel #73fa793a
> color sel #73fa7939
> color sel #73fa7938
> color sel #73fa7936
> color sel #73fa7933
> color sel #73fa792c
> color sel #73fa792a
> color sel #73fa7927
> color sel #73fa7925
> color sel #73fa7923
> color sel #73fa7921
> color sel #73fa7920
> color sel #73fa791f
> color sel #73fa791e
> color sel #73fa791d
> color sel #73fa791c
> color sel #73fa791a
> color sel #73fa7919
> color sel #73fa7918
> color sel #73fa7916
> color sel #73fa7915
> color sel #73fa7914
> color sel #73fa7912
> color sel #73fa7911
> color sel #73fa7910
> color sel #73fa790f
> color sel #73fa790e
> color sel #73fa790d
> color sel #73fa790c
> select #3/X:18
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/X:17-18
43 atoms, 48 bonds, 2 residues, 1 model selected
> select #3/X:1-18
368 atoms, 412 bonds, 18 residues, 1 model selected
> color sel #73fa79ff
> select #3/X:19
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #3/X:19-144
2566 atoms, 2874 bonds, 126 residues, 1 model selected
> color sel #73fa79ff
> color sel #73fa79fe
> color sel #73fa79f4
> color sel #73fa79cc
> color sel #73fa79b1
> color sel #73fa7992
> color sel #73fa797e
> color sel #73fa796f
> color sel #73fa796c
> color sel #73fa7967
> color sel #73fa795f
> color sel #73fa795d
> color sel #73fa795b
> color sel #73fa7953
> color sel #73fa794e
> color sel #73fa794d
> color sel #73fa794c
> color sel #73fa794a
> color sel #73fa7948
> color sel #73fa7946
> color sel #73fa7944
> color sel #73fa793f
> color sel #73fa793d
> color sel #73fa793c
> color sel #73fa793b
> color sel #73fa7938
> color sel #73fa7935
> color sel #73fa7932
> color sel #73fa7931
> color sel #73fa792f
> color sel #73fa792e
> color sel #73fa792d
> color sel #73fa792c
> color sel #73fa792a
> color sel #73fa7927
> color sel #73fa7925
> color sel #73fa7923
> color sel #73fa7922
> color sel #73fa7921
> color sel #73fa7920
> color sel #73fa791f
> color sel #73fa791d
> color sel #73fa791a
> color sel #73fa7918
> color sel #73fa7915
> color sel #73fa7912
> color sel #73fa7911
> color sel #73fa7910
> color sel #73fa790f
> color sel #73fa790e
> color sel #73fa790d
> color sel #73fa790c
> select #2/J:18
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select clear
> select #2/J:20
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select #2/J:21
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select #3/X:19
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel #73fa79ff
> select #3/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel #73fa79ff
> select #2/I:131
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:132
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:132
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:131
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:130
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:130-137
165 atoms, 185 bonds, 8 residues, 1 model selected
> color sel #7a81ffff
> hide #1 models
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_RIBBON.cxs
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_RIBBON.cxs
> select #3/S1
Nothing selected
> select #3/S
103 atoms, 104 bonds, 13 residues, 1 model selected
> color sel #73fa79ff
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_RIBBON.cxs
> select #2/J:131
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/J:131-146
326 atoms, 364 bonds, 16 residues, 1 model selected
> select #2/J:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:12
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #2/J:14
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add #2/J:13
82 atoms, 88 bonds, 4 residues, 1 model selected
> select add #2/J:16
101 atoms, 108 bonds, 5 residues, 1 model selected
> select add #2/J:15
121 atoms, 129 bonds, 6 residues, 1 model selected
> select add #2/J:17
141 atoms, 150 bonds, 7 residues, 1 model selected
> select add #2/J:18
163 atoms, 174 bonds, 8 residues, 1 model selected
> select add #2/J:21
184 atoms, 197 bonds, 9 residues, 1 model selected
> select #2/I:137
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:130
40 atoms, 43 bonds, 2 residues, 1 model selected
> select add #2/I:131
61 atoms, 66 bonds, 3 residues, 1 model selected
> select add #2/I:132
83 atoms, 90 bonds, 4 residues, 1 model selected
> select add #2/I:133
104 atoms, 113 bonds, 5 residues, 1 model selected
> select add #2/I:134
124 atoms, 134 bonds, 6 residues, 1 model selected
> select add #2/I:135
145 atoms, 157 bonds, 7 residues, 1 model selected
> select add #2/I:136
165 atoms, 178 bonds, 8 residues, 1 model selected
> select #3/Y:143
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #3/Y:144
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3/Y:130
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #3/Y:129
65 atoms, 71 bonds, 3 residues, 1 model selected
> select #3/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #3/Y:144
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #3/Y:143
65 atoms, 71 bonds, 3 residues, 1 model selected
> select #3/X:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/X:18
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #3/X:19
63 atoms, 68 bonds, 3 residues, 1 model selected
> select #3/S
103 atoms, 104 bonds, 13 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 103 atom styles
> size sel stickRadius 0.5
Changed 104 bond radii
> color sel byhetero
> select solvent
6 atoms, 6 residues, 2 models selected
> hide sel & #3 atoms
> select #1/S
158 atoms, 160 bonds, 20 residues, 1 model selected
> select #2/S
180 atoms, 185 bonds, 23 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 180 atom styles
> color sel byhetero
> size sel stickRadius 0.5
Changed 185 bond radii
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_STICK.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX2RD-NCPs/SSX2RD-NCP-
> class2/NCP_SSX2_class2_RR_09.pdb
Chain information for NCP_SSX2_class2_RR_09.pdb #4
---
Chain | Description
A | No description available
B F | No description available
C | No description available
D | No description available
E | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
52 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #4
11543 atoms, 12277 bonds, 1043 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #4/A-H,R
6057 atoms, 6136 bonds, 766 residues, 1 model selected
> hide sel cartoons
> ui tool show Matchmaker
> matchmaker #4 to #1 alg Smith-Waterman ssFraction 0.2022 cutoffDistance none
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-62
SS fraction | 0.2022
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
No iteration
Matchmaker NCP_SS1_class13_RR_20.pdb (#1) with NCP_SSX2_class2_RR_09.pdb (#4),
sequence alignment score = 750.553
RMSD between 129 atom pairs is 0.546 angstroms
> matchmaker #4 to #1 alg Smith-Waterman ssFraction 0.2022 cutoffDistance none
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-62
SS fraction | 0.2022
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
No iteration
Matchmaker NCP_SS1_class13_RR_20.pdb (#1) with NCP_SSX2_class2_RR_09.pdb (#4),
sequence alignment score = 750.553
RMSD between 129 atom pairs is 0.546 angstroms
> cartoon style width 3 thickness 1
> hide #3 models
> select #4/Y:132
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #4/Y:131
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #4/Y:132
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4/Y:131
40 atoms, 43 bonds, 2 residues, 1 model selected
> color sel #fffc79ff
> ui tool show "Show Sequence Viewer"
> sequence chain #4/Y
Alignment identifier is 4/Y
> sequence chain #4/X
Alignment identifier is 4/X
> select #4/Y:130
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/Y:1-130
2683 atoms, 3013 bonds, 130 residues, 1 model selected
> color sel #fffc79ff
> color sel #fffc79fc
> color sel #fffc79e8
> color sel #fffc79a4
> color sel #fffc7984
> color sel #fffc7969
> color sel #fffc7942
> color sel #fffc7930
> color sel #fffc792c
> color sel #fffc792b
> color sel #fffc7928
> color sel #fffc7926
> color sel #fffc7924
> color sel #fffc7923
> color sel #fffc7922
> color sel #fffc7921
> color sel #fffc7920
> color sel #fffc791f
> color sel #fffc791e
> color sel #fffc791c
> color sel #fffc791b
> color sel #fffc791a
> color sel #fffc7919
> color sel #fffc7918
> color sel #fffc7917
> color sel #fffc7916
> color sel #fffc7915
> color sel #fffc7912
> color sel #fffc7911
> color sel #fffc790e
> select #4/X:18
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #4/X:143-144
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #4/X:18-144
2587 atoms, 2898 bonds, 127 residues, 1 model selected
> color sel #fffc79ff
> color sel #fffc79fe
> color sel #fffc79e4
> color sel #fffc7998
> color sel #fffc7988
> color sel #fffc7987
> color sel #fffc7985
> color sel #fffc797b
> color sel #fffc796b
> color sel #fffc7962
> color sel #fffc795d
> color sel #fffc7953
> color sel #fffc7949
> color sel #fffc7944
> color sel #fffc7943
> color sel #fffc793e
> color sel #fffc7937
> color sel #fffc7934
> color sel #fffc7933
> color sel #fffc7931
> color sel #fffc7930
> color sel #fffc792d
> color sel #fffc792a
> color sel #fffc7929
> color sel #fffc7928
> color sel #fffc7927
> color sel #fffc7925
> color sel #fffc7924
> color sel #fffc7923
> color sel #fffc7922
> color sel #fffc7921
> color sel #fffc7920
> color sel #fffc791f
> color sel #fffc791e
> color sel #fffc791c
> color sel #fffc791a
> color sel #fffc7917
> color sel #fffc7916
> color sel #fffc7914
> color sel #fffc7913
> color sel #fffc7912
> color sel #fffc7911
> color sel #fffc7912
> color sel #fffc7911
> color sel #fffc790e
> color sel #fffc790d
> color sel #fffc790c
> color sel #fffc790b
> color sel #fffc790c
> color sel #fffc790d
> select #4/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #4/X:16-17
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel #fffc79ff
> color sel #fffc79f6
> color sel #fffc79ec
> color sel #fffc79d3
> color sel #fffc79b3
> color sel #fffc79b2
> color sel #fffc79b0
> color sel #fffc79ab
> color sel #fffc79a6
> color sel #fffc79a4
> color sel #fffc79a1
> color sel #fffc799f
> color sel #fffc799c
> color sel #fffc7994
> color sel #fffc798c
> color sel #fffc798a
> color sel #fffc7989
> color sel #fffc7988
> color sel #fffc7983
> color sel #fffc7972
> color sel #fffc796b
> color sel #fffc796a
> color sel #fffc7969
> color sel #fffc7968
> color sel #fffc7966
> color sel #fffc795f
> color sel #fffc7959
> color sel #fffc7955
> color sel #fffc794d
> color sel #fffc7948
> color sel #fffc7932
> color sel #fffc7922
> color sel #fffc7921
> color sel #fffc7920
> color sel #fffc791f
> color sel #fffc791e
> color sel #fffc791d
> color sel #fffc791a
> color sel #fffc7919
> color sel #fffc7914
> color sel #fffc7913
> color sel #fffc7912
> color sel #fffc7910
> color sel #fffc790e
> color sel #fffc790d
> color sel #fffc790c
> color sel #fffc790b
> color sel #fffc790a
> color sel #fffc7909
> color sel #fffc7908
> color sel #fffc7909
> color sel #fffc790a
> color sel #fffc790b
> color sel #fffc790c
> color sel #fffc790d
> select #4/S
135 atoms, 139 bonds, 16 residues, 1 model selected
> color sel #fffc79ff
> show sel atoms
> style sel stick
Changed 135 atom styles
> size sel stickRadius 0.5
Changed 139 bond radii
> color sel byhetero
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class2_ShowDNAandSSX_Schain_STICK.cxs includeMaps true
> save /Users/kenjiman/Desktop/image2.png supersample 3
> select #2/S#4/S
315 atoms, 324 bonds, 39 residues, 2 models selected
> hide sel atoms
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class2_ShowDNAandSSX_Schain_RIBBON.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> hide #4 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> select #2/J:19
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select #4/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #4/X:17
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #4/X:18
62 atoms, 67 bonds, 3 residues, 1 model selected
> color sel #fffc79ff
> select add #4/X:19
84 atoms, 91 bonds, 4 residues, 1 model selected
> color sel #fffc79ff
> select add #4/X:20
106 atoms, 115 bonds, 5 residues, 1 model selected
> color sel #fffc79ff
> select #2/J:22
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select clear
> select #2/I:137
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:130
40 atoms, 43 bonds, 2 residues, 1 model selected
> select #2/J:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:22
39 atoms, 41 bonds, 2 residues, 1 model selected
> select #4/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #4/X:20
41 atoms, 44 bonds, 2 residues, 1 model selected
> select #4/Y:132
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #4/Y:131
40 atoms, 43 bonds, 2 residues, 1 model selected
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class2_ShowDNAandSSX_Schain_RIBBON.cxs
> select add #4/Y:130
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #4/Y:129
44 atoms, 48 bonds, 2 residues, 1 model selected
> color sel #fffc79ff
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class2_ShowDNAandSSX_Schain_RIBBON.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> select #2/S#4/S
315 atoms, 324 bonds, 39 residues, 2 models selected
> show sel atoms
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class2_ShowDNAandSSX_Schain_STICK.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/SSX2RD-NCPs/SSX2RD-NCP-
> class3/NCP_SSX2_class3_RR_24.pdb
Chain information for NCP_SSX2_class3_RR_24.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
R | No description available
S | No description available
X | No description available
Y | No description available
54 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #5
10754 atoms, 11395 bonds, 1005 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #4 models
> ui tool show Matchmaker
> matchmaker #5 to #1 alg Smith-Waterman ssFraction 0.2022 cutoffDistance none
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-62
SS fraction | 0.2022
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
No iteration
Matchmaker NCP_SS1_class13_RR_20.pdb (#1) with NCP_SSX2_class3_RR_24.pdb (#5),
sequence alignment score = 657.024
RMSD between 112 atom pairs is 0.720 angstroms
> select #5/A-H,R
6008 atoms, 6087 bonds, 762 residues, 1 model selected
> hide sel cartoons
> cartoon style width 3 thickness 1
> select #2/S
180 atoms, 185 bonds, 23 residues, 1 model selected
> hide sel atoms
> select clear
> select #5/X,Y
4592 atoms, 5150 bonds, 224 residues, 1 model selected
> color sel #ff7e79ff
> select #5/S
154 atoms, 158 bonds, 19 residues, 1 model selected
> color sel #ff7e79ff
> select clear
> select #5/X,Y
4592 atoms, 5150 bonds, 224 residues, 1 model selected
> color sel #ff7e79fc
> color sel #ff7e79e8
> color sel #ff7e79aa
> color sel #ff7e799d
> color sel #ff7e7991
> color sel #ff7e7984
> color sel #ff7e797a
> color sel #ff7e796c
> color sel #ff7e795a
> color sel #ff7e7949
> color sel #ff7e793c
> color sel #ff7e793b
> color sel #ff7e793a
> color sel #ff7e7938
> color sel #ff7e7937
> color sel #ff7e7936
> color sel #ff7e7934
> color sel #ff7e7933
> color sel #ff7e7932
> color sel #ff7e7931
> color sel #ff7e7930
> color sel #ff7e792f
> color sel #ff7e792a
> color sel #ff7e7928
> color sel #ff7e7927
> color sel #ff7e7925
> color sel #ff7e7924
> color sel #ff7e791f
> color sel #ff7e791b
> color sel #ff7e791a
> color sel #ff7e7917
> color sel #ff7e7916
> color sel #ff7e7915
> color sel #ff7e7914
> color sel #ff7e7913
> color sel #ff7e7912
> color sel #ff7e7911
> color sel #ff7e7910
> color sel #ff7e790f
> color sel #ff7e790e
> color sel #ff7e790f
> select #2/J:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/J:22
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #2/J:21
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add #2/J:20
81 atoms, 87 bonds, 4 residues, 1 model selected
> select add #2/J:19
102 atoms, 110 bonds, 5 residues, 1 model selected
> select add #2/J:18
124 atoms, 134 bonds, 6 residues, 1 model selected
> select add #2/J:17
144 atoms, 155 bonds, 7 residues, 1 model selected
> select add #2/J:16
163 atoms, 175 bonds, 8 residues, 1 model selected
> select add #2/J:14
184 atoms, 198 bonds, 9 residues, 1 model selected
> select add #2/J:15
204 atoms, 219 bonds, 10 residues, 1 model selected
> select add #2/J:13
224 atoms, 240 bonds, 11 residues, 1 model selected
> select add #2/J:12
245 atoms, 263 bonds, 12 residues, 1 model selected
> select add #2/J:11
265 atoms, 284 bonds, 13 residues, 1 model selected
> color sel #7a81ffff
> select #2/I:125
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #2/I:126
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #2/I:128
63 atoms, 68 bonds, 3 residues, 1 model selected
> select add #2/I:127
83 atoms, 89 bonds, 4 residues, 1 model selected
> select add #2/I:129
103 atoms, 110 bonds, 5 residues, 1 model selected
> select add #2/I:130
122 atoms, 130 bonds, 6 residues, 1 model selected
> select add #2/I:131
143 atoms, 153 bonds, 7 residues, 1 model selected
> select add #2/I:132
165 atoms, 177 bonds, 8 residues, 1 model selected
> select add #2/I:133
186 atoms, 200 bonds, 9 residues, 1 model selected
> select add #2/I:134
206 atoms, 221 bonds, 10 residues, 1 model selected
> select add #2/I:135
227 atoms, 244 bonds, 11 residues, 1 model selected
> select add #2/I:136
247 atoms, 265 bonds, 12 residues, 1 model selected
> select add #2/I:137
268 atoms, 288 bonds, 13 residues, 1 model selected
> color sel #7a81ffff
> ui tool show "Show Sequence Viewer"
> sequence chain #5/X
Alignment identifier is 5/X
> sequence chain #5/Y
Alignment identifier is 5/Y
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> select #2/I:124
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select clear
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> color sel #ff7e79fe
> color sel #ff7e79f7
> color sel #ff7e79d2
> color sel #ff7e79c0
> color sel #ff7e799f
> color sel #ff7e7989
> color sel #ff7e797a
> color sel #ff7e7978
> color sel #ff7e7976
> color sel #ff7e796e
> color sel #ff7e795e
> color sel #ff7e7956
> color sel #ff7e7953
> color sel #ff7e7952
> color sel #ff7e7951
> color sel #ff7e7950
> color sel #ff7e794d
> color sel #ff7e794b
> color sel #ff7e7949
> color sel #ff7e7945
> color sel #ff7e7943
> color sel #ff7e7942
> color sel #ff7e7941
> color sel #ff7e7940
> color sel #ff7e793f
> color sel #ff7e793e
> color sel #ff7e793d
> color sel #ff7e793c
> color sel #ff7e793b
> color sel #ff7e793a
> color sel #ff7e7938
> color sel #ff7e7937
> color sel #ff7e7935
> color sel #ff7e7933
> color sel #ff7e7932
> color sel #ff7e7930
> color sel #ff7e792e
> color sel #ff7e792d
> color sel #ff7e792c
> color sel #ff7e792b
> color sel #ff7e792a
> color sel #ff7e7929
> color sel #ff7e7928
> color sel #ff7e7926
> color sel #ff7e7925
> color sel #ff7e7924
> color sel #ff7e7923
> color sel #ff7e7922
> color sel #ff7e7921
> color sel #ff7e7920
> color sel #ff7e791f
> color sel #ff7e791e
> color sel #ff7e791d
> color sel #ff7e791c
> color sel #ff7e791a
> color sel #ff7e7919
> color sel #ff7e7917
> color sel #ff7e7914
> color sel #ff7e7911
> color sel #ff7e7910
> color sel #ff7e790f
> color sel #ff7e790d
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/X:22
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #5/X:22
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> select #5/X:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #5/X:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> color sel #ff7e79fd
> color sel #ff7e79ef
> color sel #ff7e79e4
> color sel #ff7e79de
> color sel #ff7e79d9
> color sel #ff7e79d5
> color sel #ff7e79d4
> color sel #ff7e79d3
> color sel #ff7e79cf
> color sel #ff7e79ca
> color sel #ff7e79c3
> color sel #ff7e79c0
> color sel #ff7e79b7
> color sel #ff7e79b4
> color sel #ff7e79a9
> color sel #ff7e798e
> color sel #ff7e797a
> color sel #ff7e796d
> color sel #ff7e7968
> color sel #ff7e7967
> color sel #ff7e7966
> color sel #ff7e7960
> color sel #ff7e7957
> color sel #ff7e7954
> color sel #ff7e794d
> color sel #ff7e793b
> color sel #ff7e7930
> color sel #ff7e792e
> color sel #ff7e792d
> color sel #ff7e792c
> color sel #ff7e792b
> color sel #ff7e7928
> color sel #ff7e7921
> color sel #ff7e7919
> color sel #ff7e7917
> color sel #ff7e7916
> color sel #ff7e7915
> color sel #ff7e7914
> color sel #ff7e7913
> color sel #ff7e7912
> color sel #ff7e7911
> color sel #ff7e7910
> color sel #ff7e790f
> color sel #ff7e790e
> color sel #ff7e790d
> color sel #ff7e790e
> color sel #ff7e7913
> color sel #ff7e791d
> color sel #ff7e7937
> color sel #ff7e794e
> color sel #ff7e796b
> color sel #ff7e7988
> color sel #ff7e799b
> color sel #ff7e79aa
> color sel #ff7e79c6
> color sel #ff7e79d9
> color sel #ff7e79ed
> color sel #ff7e79fc
> color sel #ff7e79ff
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> select clear
> select #2/J:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:145
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #2/J:144
60 atoms, 64 bonds, 3 residues, 1 model selected
> select add #2/J:142
79 atoms, 84 bonds, 4 residues, 1 model selected
> select add #2/J:143
99 atoms, 105 bonds, 5 residues, 1 model selected
> select add #2/J:141
119 atoms, 126 bonds, 6 residues, 1 model selected
> select add #2/J:140
139 atoms, 147 bonds, 7 residues, 1 model selected
> select add #2/J:139
160 atoms, 170 bonds, 8 residues, 1 model selected
> select add #2/J:137
182 atoms, 194 bonds, 9 residues, 1 model selected
> select add #2/J:136
204 atoms, 218 bonds, 10 residues, 1 model selected
> color sel #7a81ffff
> select #5/X:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> color sel #ff7e79fc
> color sel #ff7e79ed
> color sel #ff7e79d3
> color sel #ff7e79cd
> color sel #ff7e79c6
> color sel #ff7e79b6
> color sel #ff7e79af
> color sel #ff7e79a8
> color sel #ff7e799e
> color sel #ff7e7995
> color sel #ff7e798c
> color sel #ff7e7982
> color sel #ff7e796f
> color sel #ff7e796a
> color sel #ff7e7969
> color sel #ff7e7967
> color sel #ff7e7964
> color sel #ff7e795c
> color sel #ff7e7950
> color sel #ff7e7948
> color sel #ff7e793d
> color sel #ff7e7935
> color sel #ff7e7930
> color sel #ff7e792d
> color sel #ff7e792c
> color sel #ff7e792a
> color sel #ff7e7927
> color sel #ff7e7926
> color sel #ff7e7924
> color sel #ff7e7923
> color sel #ff7e7922
> color sel #ff7e7921
> color sel #ff7e791b
> color sel #ff7e7917
> color sel #ff7e7916
> color sel #ff7e7915
> color sel #ff7e7914
> color sel #ff7e7913
> color sel #ff7e7912
> color sel #ff7e7911
> color sel #ff7e7910
> color sel #ff7e790f
> color sel #ff7e790e
> color sel #ff7e790d
> color sel #ff7e790c
> select #2/I:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:5
42 atoms, 46 bonds, 2 residues, 1 model selected
> select add #2/I:9
62 atoms, 67 bonds, 3 residues, 1 model selected
> select add #2/I:11
81 atoms, 87 bonds, 4 residues, 1 model selected
> select add #2/I:12
100 atoms, 107 bonds, 5 residues, 1 model selected
> select #2/I:12
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:2-12
225 atoms, 252 bonds, 11 residues, 1 model selected
> color sel #7a81ffff
> select #2/J:59
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> undo
> select #5/X:56
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:137
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/J:136
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #2/J:139
65 atoms, 71 bonds, 3 residues, 1 model selected
> select add #2/J:141
85 atoms, 92 bonds, 4 residues, 1 model selected
> select #2/J:136
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/J:136-146
226 atoms, 252 bonds, 11 residues, 1 model selected
> color sel #7a81ffff
> select #5/X:58
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:12
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:12
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:2-12
225 atoms, 252 bonds, 11 residues, 1 model selected
> color sel #7a81ffff
> select #2/I:13
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:2-13
247 atoms, 277 bonds, 12 residues, 1 model selected
> color sel #7a81ffff
> select clear
> select #2/J:59
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #5/X:56
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:59
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> color sel #7a81fffe
> color sel #7a81fffb
> color sel #7a81fffa
> color sel #7a81fff9
> color sel #7a81fff8
> color sel #7a81fff7
> color sel #7a81ffff
> color sel #ff7e79ff
> color sel #ff7e79f4
> color sel #ff7e79c1
> color sel #ff7e79ae
> color sel #ff7e798e
> color sel #ff7e7972
> color sel #ff7e7964
> color sel #ff7e795d
> color sel #ff7e795c
> color sel #ff7e795b
> color sel #ff7e795a
> color sel #ff7e7957
> color sel #ff7e7949
> color sel #ff7e793e
> color sel #ff7e792c
> color sel #ff7e791c
> color sel #ff7e7912
> color sel #ff7e790f
> color sel #ff7e790e
> color sel #ff7e790d
> color sel #ff7e790e
> color sel #ff7e790f
> select clear
> select #5/X:133
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #ff7e79ff
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class3_ShowDNAandSSX_Schain_RIBBON.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> select clear
> save /Users/kenjiman/Desktop/image1.png supersample 3
> select #5/S#2/S
334 atoms, 343 bonds, 42 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 334 atom styles
> size sel stickRadius 0.5
Changed 343 bond radii
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class3_ShowDNAandSSX_Schain_STICK.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/SequenceComp/SSX2RD-
> NCP-class3_chainX.fasta format fasta alignment 5/X
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/SequenceComp/SSX2RD-
> NCP-class3_chainY.fasta format fasta alignment 5/Y
> ui tool show "Show Sequence Viewer"
> sequence chain #4/X
Alignment identifier is 4/X
> sequence chain #4/Y
Alignment identifier is 4/Y
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/SequenceComp/SSX2RD-
> NCP-class2_chainX.fasta format fasta alignment 4/X
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/SequenceComp/SSX2RD-
> NCP-class2_chainY.fasta format fasta alignment 4/Y
> hide #5 models
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/Y
Alignment identifier is 1/Y
> sequence chain #1/X
Alignment identifier is 1/X
> select #1/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/Y:1-2
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #1/Y:1-2
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #1/Y:1-4
82 atoms, 91 bonds, 4 residues, 1 model selected
> select #2/I:13-14
44 atoms, 49 bonds, 2 residues, 1 model selected
> select #2/I:4-14
228 atoms, 256 bonds, 11 residues, 1 model selected
> select #2/I:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:2-10
187 atoms, 210 bonds, 9 residues, 1 model selected
> select #1/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/Y:1-9
186 atoms, 208 bonds, 9 residues, 1 model selected
> select #2/I:2-3
41 atoms, 45 bonds, 2 residues, 1 model selected
> select #2/I:2-15
289 atoms, 324 bonds, 14 residues, 1 model selected
> undo
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX2comp/CXS/Comp_8HQY_vs_SSX2RD-
> NCP-class3_ShowDNAandSSX_Schain_STICK.cxs
opened ChimeraX session
> hide #5 models
> show #1 models
> select #2/I:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/J:67
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #1/X:65
65 atoms, 71 bonds, 3 residues, 2 models selected
> select subtract #2/J:67
43 atoms, 47 bonds, 2 residues, 2 models selected
> select add #2/J:67
65 atoms, 71 bonds, 3 residues, 2 models selected
> select #2/J:64
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/X:65
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1/X:66
41 atoms, 44 bonds, 2 residues, 2 models selected
> select subtract #1/X:66
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:3
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #1/X:64
60 atoms, 64 bonds, 3 residues, 2 models selected
> select add #1/Y:3
79 atoms, 84 bonds, 4 residues, 2 models selected
> select add #2/I:6
101 atoms, 108 bonds, 5 residues, 2 models selected
> select add #2/I:5
122 atoms, 131 bonds, 6 residues, 2 models selected
> select add #1/X:62
141 atoms, 151 bonds, 7 residues, 2 models selected
> select add #1/Y:7
163 atoms, 175 bonds, 8 residues, 2 models selected
> select add #1/Y:8
183 atoms, 196 bonds, 9 residues, 2 models selected
> select #2/I:2-5
84 atoms, 94 bonds, 4 residues, 1 model selected
> select #2/I:2-13
247 atoms, 277 bonds, 12 residues, 1 model selected
> color sel #7a81ffff
> color sel #7a81fffd
> color sel #7a81fff9
> color sel #7a81fff8
> color sel #7a81fff6
> color sel #7a81fff0
> color sel #7a81ffef
> color sel #7a81ffec
> color sel #7a81ffe9
> color sel #7a81ffe6
> color sel #7a81ffe2
> color sel #7a81ffdf
> color sel #7a81ffdd
> color sel #7a81ffdb
> color sel #7a81ffd4
> color sel #7a81ffd0
> color sel #7a81ffcd
> color sel #7a81ffcb
> color sel #7a81ffc8
> color sel #7a81ffc4
> color sel #7a81ffb7
> color sel #7a81ffab
> color sel #7a81ff9b
> color sel #7a81ff90
> color sel #7a81ff81
> color sel #7a81ff74
> color sel #7a81ff69
> color sel #7a81ff66
> color sel #7a81ff63
> color sel #7a81ff61
> color sel #7a81ff5b
> color sel #7a81ff54
> color sel #7a81ff4f
> color sel #7a81ff48
> color sel #7a81ff44
> color sel #7a81ff3e
> color sel #7a81ff3b
> color sel #7a81ff39
> color sel #7a81ff38
> color sel #7a81ff37
> color sel #7a81ff38
> color sel #7a81ff3a
> color sel #7a81ff3b
> color sel #7a81ff39
> color sel #7a81ff37
> color sel #7a81ff35
> color sel #7a81ff32
> color sel #7a81ff31
> color sel #7a81ff30
> color sel #7a81ff2d
> color sel #7a81ff2c
> color sel #7a81ff2b
> color sel #7a81ff2a
> color sel #7a81ff29
> color sel #7a81ff28
> color sel #7a81ff27
> color sel #7a81ff26
> color sel #7a81ff21
> color sel #7a81ff20
> color sel #7a81ff1f
> color sel #7a81ff1e
> color sel #7a81ff1d
> color sel #7a81ff1b
> color sel #7a81ff1a
> color sel #7a81ff18
> color sel #7a81ff17
> color sel #7a81ff16
> color sel #7a81ff15
> color sel #7a81ff14
> color sel #7a81ff13
> color sel #7a81ff12
> color sel #7a81ff11
> color sel #7a81ff10
> color sel #7a81ff0f
> color sel #7a81ff0e
> color sel #7a81ff0d
> color sel #7a81ff0c
> color sel #7a81ff0b
> color sel #7a81ff0a
> color sel #7a81ff0b
> color sel #7a81ff0c
> color sel #7a81ff0d
> color sel #7a81ff0e
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/Y:12-19
162 atoms, 180 bonds, 8 residues, 1 model selected
> select #2/J:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:141-146
119 atoms, 131 bonds, 6 residues, 1 model selected
> select #2/J:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:139-146
160 atoms, 177 bonds, 8 residues, 1 model selected
> select #2/J:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/J:136-146
226 atoms, 252 bonds, 11 residues, 1 model selected
> color sel #7a81ffff
> color sel #7a81fff7
> color sel #7a81ffed
> color sel #7a81ffdc
> color sel #7a81ffc4
> color sel #7a81ffb3
> color sel #7a81ffb0
> color sel #7a81ffae
> color sel #7a81ffac
> color sel #7a81ffa7
> color sel #7a81ffa1
> color sel #7a81ff99
> color sel #7a81ff93
> color sel #7a81ff90
> color sel #7a81ff8f
> color sel #7a81ff87
> color sel #7a81ff85
> color sel #7a81ff80
> color sel #7a81ff7f
> color sel #7a81ff7d
> color sel #7a81ff7c
> color sel #7a81ff77
> color sel #7a81ff75
> color sel #7a81ff74
> color sel #7a81ff72
> color sel #7a81ff68
> color sel #7a81ff60
> color sel #7a81ff51
> color sel #7a81ff4b
> color sel #7a81ff49
> color sel #7a81ff48
> color sel #7a81ff46
> color sel #7a81ff45
> color sel #7a81ff44
> color sel #7a81ff41
> color sel #7a81ff40
> color sel #7a81ff3f
> color sel #7a81ff3e
> color sel #7a81ff3d
> color sel #7a81ff3c
> color sel #7a81ff3b
> color sel #7a81ff39
> color sel #7a81ff38
> color sel #7a81ff37
> color sel #7a81ff36
> color sel #7a81ff35
> color sel #7a81ff34
> color sel #7a81ff33
> color sel #7a81ff29
> color sel #7a81ff24
> color sel #7a81ff21
> color sel #7a81ff20
> color sel #7a81ff1f
> color sel #7a81ff1b
> color sel #7a81ff17
> color sel #7a81ff14
> color sel #7a81ff13
> color sel #7a81ff12
> color sel #7a81ff11
> color sel #7a81ff10
> color sel #7a81ff0f
> color sel #7a81ff0e
> select #2/J:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:12
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #2/J:13
61 atoms, 65 bonds, 3 residues, 1 model selected
> select add #2/J:14
82 atoms, 88 bonds, 4 residues, 1 model selected
> select add #2/J:15
102 atoms, 109 bonds, 5 residues, 1 model selected
> select add #2/J:16
121 atoms, 129 bonds, 6 residues, 1 model selected
> select add #2/J:17
141 atoms, 150 bonds, 7 residues, 1 model selected
> select add #2/J:18
163 atoms, 174 bonds, 8 residues, 1 model selected
> select add #2/J:19
184 atoms, 197 bonds, 9 residues, 1 model selected
> select add #2/J:20
203 atoms, 217 bonds, 10 residues, 1 model selected
> select add #1/X:20
225 atoms, 241 bonds, 11 residues, 2 models selected
> select add #2/J:21
246 atoms, 264 bonds, 12 residues, 2 models selected
> select subtract #1/X:20
224 atoms, 240 bonds, 11 residues, 1 model selected
> select add #2/J:22
243 atoms, 260 bonds, 12 residues, 1 model selected
> select add #2/J:23
265 atoms, 284 bonds, 13 residues, 1 model selected
> color sel #7a81ffff
> color sel #7a81fffe
> color sel #7a81fffc
> color sel #7a81fff1
> color sel #7a81ffe6
> color sel #7a81ffd8
> color sel #7a81ffc6
> color sel #7a81ffb4
> color sel #7a81ffaf
> color sel #7a81ffad
> color sel #7a81ffac
> color sel #7a81ffab
> color sel #7a81ffa9
> color sel #7a81ffa8
> color sel #7a81ffa5
> color sel #7a81ffa4
> color sel #7a81ff99
> color sel #7a81ff8e
> color sel #7a81ff88
> color sel #7a81ff81
> color sel #7a81ff74
> color sel #7a81ff64
> color sel #7a81ff55
> color sel #7a81ff4d
> color sel #7a81ff4a
> color sel #7a81ff48
> color sel #7a81ff47
> color sel #7a81ff40
> color sel #7a81ff3d
> color sel #7a81ff3c
> color sel #7a81ff39
> color sel #7a81ff36
> color sel #7a81ff2e
> color sel #7a81ff27
> color sel #7a81ff26
> color sel #7a81ff25
> color sel #7a81ff24
> color sel #7a81ff23
> color sel #7a81ff22
> color sel #7a81ff21
> color sel #7a81ff20
> color sel #7a81ff1f
> color sel #7a81ff1e
> color sel #7a81ff1d
> color sel #7a81ff1c
> color sel #7a81ff1b
> color sel #7a81ff1a
> color sel #7a81ff19
> color sel #7a81ff18
> color sel #7a81ff17
> color sel #7a81ff14
> color sel #7a81ff13
> color sel #7a81ff12
> color sel #7a81ff11
> color sel #7a81ff10
> color sel #7a81ff0f
> color sel #7a81ff0e
> color sel #7a81ff0d
> color sel #7a81ff0c
> color sel #7a81ff0b
> color sel #7a81ff0c
> color sel #7a81ff0d
> color sel #7a81ff0e
> color sel #7a81ff0f
> color sel #7a81ff10
> color sel #7a81ff11
> color sel #7a81ff12
> color sel #7a81ff11
> color sel #7a81ff10
> color sel #7a81ff0f
> color sel #7a81ff0e
> color sel #7a81ff0d
> color sel #7a81ff0c
> color sel #7a81ff0d
> select #1/X:18
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel #ff9300ff
> select #2/J:18
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/J:17
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #2/J:16
61 atoms, 65 bonds, 3 residues, 1 model selected
> select add #2/J:14
82 atoms, 88 bonds, 4 residues, 1 model selected
> select add #2/J:13
102 atoms, 109 bonds, 5 residues, 1 model selected
> select add #2/J:15
122 atoms, 130 bonds, 6 residues, 1 model selected
> select add #2/J:12
143 atoms, 153 bonds, 7 residues, 1 model selected
> select add #2/J:11
163 atoms, 174 bonds, 8 residues, 1 model selected
> color sel #7a81ffff
> select #2/I:124
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/I:124-125
40 atoms, 44 bonds, 2 residues, 1 model selected
> select #2/I:124-137
289 atoms, 324 bonds, 14 residues, 1 model selected
> color sel #7a81fffe
> color sel #7a81fff0
> color sel #7a81ffad
> color sel #7a81ff90
> color sel #7a81ff60
> color sel #7a81ff4a
> color sel #7a81ff31
> color sel #7a81ff27
> color sel #7a81ff26
> color sel #7a81ff25
> color sel #7a81ff24
> color sel #7a81ff23
> color sel #7a81ff22
> color sel #7a81ff1d
> color sel #7a81ff1c
> color sel #7a81ff1b
> color sel #7a81ff1a
> color sel #7a81ff18
> color sel #7a81ff17
> color sel #7a81ff16
> color sel #7a81ff15
> color sel #7a81ff12
> color sel #7a81ff10
> color sel #7a81ff0e
> color sel #7a81ff0f
> color sel #7a81ff10
> color sel #7a81ff11
> color sel #7a81ff12
> color sel #7a81ff11
> color sel #7a81ff10
> color sel #7a81ff0e
> color sel #7a81ff0d
> select #2/I:131
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:132
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #2/I:133
64 atoms, 70 bonds, 3 residues, 1 model selected
> select add #2/I:134
84 atoms, 91 bonds, 4 residues, 1 model selected
> select add #2/I:135
105 atoms, 114 bonds, 5 residues, 1 model selected
> select add #2/I:136
125 atoms, 135 bonds, 6 residues, 1 model selected
> select add #2/I:137
146 atoms, 158 bonds, 7 residues, 1 model selected
> color sel #7a81ffff
> select clear
> select #1/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel #ff9300ff
> select clear
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #ff9300ff
> select #1/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #ff9300ff
> select #2/I:2
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select #2/J:146
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select clear
> select #1/S
158 atoms, 160 bonds, 20 residues, 1 model selected
> select #2/S
180 atoms, 185 bonds, 23 residues, 1 model selected
> hide sel atoms
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class1p3_ShowDNAandSSX_Schain_RIBBON.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> select #1/S#2/S
338 atoms, 345 bonds, 43 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 338 atom styles
> size sel stickRadius 0.5
Changed 345 bond radii
> select solvent
6 atoms, 6 residues, 2 models selected
> hide sel & #1 atoms
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class1p3_ShowDNAandSSX_Schain_STICK.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> hide #2 models
> show #2 models
> hide #1 models
> show #3 models
> select #2/J:21
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/J:20
40 atoms, 43 bonds, 2 residues, 1 model selected
> color sel #7a81ffff
> select add #2/J:22
59 atoms, 63 bonds, 3 residues, 1 model selected
> color sel #7a81ffff
> select #3/X:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel #73fa79ff
> select #2/I:130
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel #7a81ffff
> select #3/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel #73fa79ff
> select #3/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel #73fa79ff
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_STICK.cxs
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_STICK.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> select #3/S#2/S
283 atoms, 289 bonds, 36 residues, 2 models selected
> hide sel atoms
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_RIBBON.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> ui tool show "Show Sequence Viewer"
> sequence chain #3/X
Alignment identifier is 3/X
> sequence chain #3/Y
Alignment identifier is 3/Y
> select #2/I:137
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:130
40 atoms, 43 bonds, 2 residues, 1 model selected
> select #2/J:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:22
39 atoms, 41 bonds, 2 residues, 1 model selected
> select #3/X:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #3/X:1
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #3/Y:144
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3/Y:129
43 atoms, 47 bonds, 2 residues, 1 model selected
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class4_ShowDNAandSSX_Schain_RIBBON.cxs
> hide #3 models
> show #1 models
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class1p3_ShowDNAandSSX_Schain_RIBBON.cxs
opened ChimeraX session
> select #2/J:11
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #2/J:18
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #2/I:137
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:131
42 atoms, 46 bonds, 2 residues, 1 model selected
> select #2/J:98
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:130
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:136
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/I:137
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #2/I:131
42 atoms, 46 bonds, 2 residues, 1 model selected
> select #2/I:130
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/I:130-137
165 atoms, 185 bonds, 8 residues, 1 model selected
> color sel #7a81ffff
> select clear
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class1p3_ShowDNAandSSX_Schain_RIBBON.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> select #1/S#2/S
338 atoms, 345 bonds, 43 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 338 atom styles
> size sel stickRadius 0.5
Changed 345 bond radii
> select solvent
6 atoms, 6 residues, 2 models selected
> hide sel & #1 atoms
> save /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HQYvsOurs/SSX1comp/CXS/Comp_8HQY_vs_SSX1RD-
> NCP-class1p3_ShowDNAandSSX_Schain_STICK.cxs
> save /Users/kenjiman/Desktop/image1.png supersample 3
> close session
> open /Users/kenjiman/Dropbox/筑波大001/筑波大学/TARA/WORK1/WRITINGPAPER-02/SSX-
> Nuc/NatComm/原稿/Figures/Materials/CompOur2NSMB2024/8HR1vsOurs/SSX1comp/CXS/Comp_8HR1_vs_SSX1RD-
> NCP-class1p3_ShowDNAandSSX_Schain_RIBBON.cxs
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> select #1/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/X:17
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/X:16-20
106 atoms, 119 bonds, 5 residues, 1 model selected
> select #2/I:56
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/I:57
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #2/I:58
63 atoms, 68 bonds, 3 residues, 1 model selected
> select #1/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #2/I:56
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #2/I:59
43 atoms, 47 bonds, 2 residues, 1 model selected
> select #2/I:56
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/Y:128
41 atoms, 44 bonds, 2 residues, 2 models selected
> select #1/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/Y:128
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #1/Y:127
61 atoms, 65 bonds, 3 residues, 1 model selected
> select #1/Y:129
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/Y:125-129
99 atoms, 109 bonds, 5 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #2 models
> show #3 models
> hide #1 models
> hide #3 models
> show #4 models
> select #4/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/X
Alignment identifier is 1/X
> sequence chain #1/Y
Alignment identifier is 1/Y
> sequence chain #5/X
Alignment identifier is 5/X
> sequence chain #5/Y
Alignment identifier is 5/Y
> sequence chain #3/X
Alignment identifier is 3/X
> sequence chain #3/Y
Alignment identifier is 3/Y
> sequence chain #4/X
Alignment identifier is 4/X
> sequence chain #4/Y
Alignment identifier is 4/Y
> select #4/X:20
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/X:16-20
106 atoms, 119 bonds, 5 residues, 1 model selected
> hide #4 models
> show #5 models
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/X:22
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #5/X:23
41 atoms, 44 bonds, 2 residues, 1 model selected
> hide #5 models
> show #3 models
> select #3/Y:144
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #3/Y:143
43 atoms, 47 bonds, 2 residues, 1 model selected
> select #3/X:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/X:2
39 atoms, 41 bonds, 2 residues, 1 model selected
> hide #3 models
> show #1 models
> select #1/X:16
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #1/X:17
41 atoms, 44 bonds, 2 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/X:64
39 atoms, 41 bonds, 2 residues, 1 model selected
> select add #1/X:143
60 atoms, 64 bonds, 3 residues, 1 model selected
> select subtract #1/X:144
40 atoms, 43 bonds, 2 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/X:64
39 atoms, 41 bonds, 2 residues, 1 model selected
> select add #1/X:63
60 atoms, 64 bonds, 3 residues, 1 model selected
> select subtract #1/X:64
41 atoms, 44 bonds, 2 residues, 1 model selected
> select subtract #1/X:63
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/Y:82
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #1/X:142
62 atoms, 66 bonds, 3 residues, 1 model selected
> select subtract #1/Y:82
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #1/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/X:142-144
63 atoms, 70 bonds, 3 residues, 1 model selected
> select #1/X:66
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1/X:63
42 atoms, 46 bonds, 2 residues, 1 model selected
> select subtract #1/X:63
21 atoms, 23 bonds, 1 residue, 1 model selected
> select add #1/Y:3
40 atoms, 43 bonds, 2 residues, 1 model selected
> select #1/Y:1
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/Y:1-7
145 atoms, 162 bonds, 7 residues, 1 model selected
> hide #1 models
> show #3 models
> select #3/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/X:143
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #3/X:142
63 atoms, 68 bonds, 3 residues, 1 model selected
> select #3/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/X:140-144
102 atoms, 113 bonds, 5 residues, 1 model selected
> hide #3 models
> show #4 models
> select #4/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/X:65
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #4/X:65
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/X:65
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/X:65
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #4/X:144
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/X:142
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #4/X:143
63 atoms, 68 bonds, 3 residues, 1 model selected
> select #4/X:140-141
39 atoms, 42 bonds, 2 residues, 1 model selected
> select #4/X:140-144
102 atoms, 113 bonds, 5 residues, 1 model selected
> hide #4 models
> show #5 models
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/Y:13
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #5/Y:12
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/X:133
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #5/X:132
61 atoms, 65 bonds, 3 residues, 1 model selected
> select #5/X:129-130
43 atoms, 48 bonds, 2 residues, 1 model selected
> select #5/X:129-133
105 atoms, 118 bonds, 5 residues, 1 model selected
> select #5/Y:123
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #5/Y:122
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #5/Y:120
62 atoms, 67 bonds, 3 residues, 1 model selected
> select #5/X:22
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #5/X:23
41 atoms, 44 bonds, 2 residues, 1 model selected
> select add #5/X:24
60 atoms, 64 bonds, 3 residues, 1 model selected
> select #5/X:22
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #5/X:22-28
141 atoms, 157 bonds, 7 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15Z0004LJ/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.61.3
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.7.2 (22H313)
Kernel Version: Darwin 22.6.0
Time since boot: 5日 3時間 9分
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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