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Opened 5 months ago
Last modified 5 months ago
#17875 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-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: Bus error
Thread 0x000000032cf2f000 (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 0x000000032bf23000 (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 0x000000032af17000 (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 0x0000000329f0b000 (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 0x0000000328eff000 (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 0x0000000327ef3000 (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 0x0000000326ee7000 (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 0x0000000325edb000 (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 0x0000000324ecf000 (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 0x0000000323ec3000 (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 0x0000000322eb7000 (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 0x0000000321eab000 (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 0x0000000320e9f000 (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 0x00000001f1988c80 (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.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 62)
{"app_name":"ChimeraX","timestamp":"2025-06-02 16:50:46.00 -0400","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 15.4.1 (24E263)","roots_installed":0,"name":"ChimeraX","incident_id":"93FB58BA-8F08-4B1B-9AE5-01BA0CEBCF7C"}
{
"uptime" : 1300000,
"procRole" : "Background",
"version" : 2,
"userID" : 1816534185,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 8284,
"osVersion" : {
"train" : "macOS 15.4.1",
"build" : "24E263",
"releaseType" : "User"
},
"captureTime" : "2025-06-02 16:50:31.9036 -0400",
"codeSigningMonitor" : 1,
"incident" : "93FB58BA-8F08-4B1B-9AE5-01BA0CEBCF7C",
"pid" : 67717,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-23 16:33:40.9522 -0400",
"procStartAbsTime" : 26945999562820,
"procExitAbsTime" : 31528077298802,
"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":"90D244DC-5580-5E3D-8A91-5444033BFF8C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA6EEC6E-A890-96AC-901B-4A3BA4995AFD",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "2E24EE53-B8F6-4AC8-A5D8-025B88607688",
"wakeTime" : 2581,
"sleepWakeUUID" : "356AF2DE-BB80-49B4-A1A6-81CD47823F92",
"sip" : "enabled",
"vmRegionInfo" : "0x727272727272 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000101, 0x7272727272727272","rawCodes":[257,8246779703540740722],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"EXC_ARM_DA_ALIGN at 0x7272727272727272 -> 0x0000727272727272 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":67717},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x727272727272 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6098895000},{"value":99},{"value":95},{"value":1153027057737772128},{"value":1027},{"value":12770250494907104679},{"value":12770250500518523175},{"value":14757395258967641293},{"value":4294967286},{"value":6098894930},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8365509312},{"value":0},{"value":10},{"value":259},{"value":8348274016,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4390471216,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8306102272,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSDebugMenuResponderChainProvider._menuItem"},{"value":8306102272,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSDebugMenuResponderChainProvider._menuItem"},{"value":4},{"value":16}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6487234700},"cpsr":{"value":1073745920},"fp":{"value":6098895072},"sp":{"value":6098895040},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6486999944,"matchesCrashFrame":1},"far":{"value":0}},"id":113011534,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":37768,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":162},{"imageOffset":26764,"symbol":"pthread_kill","symbolLocation":296,"imageIndex":163},{"imageOffset":265476,"symbol":"raise","symbolLocation":32,"imageIndex":164},{"imageOffset":2417160,"symbol":"faulthandler_fatal_error","symbolLocation":392,"imageIndex":1},{"imageOffset":13860,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":165},{"imageOffset":349380,"imageIndex":69},{"imageOffset":349160,"imageIndex":69},{"imageOffset":381412,"symbol":"_NSViewHierarchyDidChangeBackingProperties","symbolLocation":244,"imageIndex":166},{"imageOffset":12002200,"symbol":"-[NSWindow 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"base" : 13131350016,
"size" : 16384,
"uuid" : "f07c07fb-2e38-3764-9cff-1bd00023b5ae",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/coulombic\/_esp.cpython-311-darwin.so",
"name" : "_esp.cpython-311-darwin.so"
},
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"arch" : "arm64e",
"base" : 6486962176,
"size" : 242444,
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
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"arch" : "arm64e",
"base" : 6487207936,
"size" : 51784,
"uuid" : "8d27ec9a-d919-31a4-8df8-31a2fd2e593c",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6485729280,
"size" : 529520,
"uuid" : "20ebe22e-66e2-3556-b70b-54a04e8363a8",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6487457792,
"size" : 31568,
"uuid" : "27ed40c8-6b18-3266-93a7-387fb33ca186",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6551203840,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21564928,
"uuid" : "1d6df541-4a74-3a0e-8a8f-15aee6f93da9",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.50.27"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6585176064,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5394304,
"uuid" : "ad34bb7b-8573-3892-8ca9-78cbb7477ce0",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
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"arch" : "arm64e",
"base" : 6485426176,
"size" : 288544,
"uuid" : "3329eb0a-e722-3db0-a627-e27297282a0f",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6487687168,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5500928,
"uuid" : "39e0f63a-3ab8-39e9-97f8-333cde9a7ba4",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3423"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6680014848,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3174368,
"uuid" : "6cc82a38-f1b5-3f2b-876b-9b3d7b278490",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6483410944,
"size" : 633476,
"uuid" : "aca43a8d-6369-3a2c-af92-3d4c458523d6",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6507651072,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14676544,
"uuid" : "5ab66e9b-19c0-3fe8-9793-d5156d1c7050",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
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}
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"sharedCache" : {
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},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=8.3G written=81.0M(1%) resident=4706K(0%) swapped_out=76.4M(1%) unallocated=8.2G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 864K 47 \nColorSync 624K 33 \nCoreAnimation 1232K 70 \nCoreGraphics 368K 23 \nCoreServices 624K 2 \nCoreUI image data 5552K 46 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 7.2G 187 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 50 \nStack 400.2M 50 \nVM_ALLOCATE 571.2M 416 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__AUTH 5486K 695 \n__AUTH_CONST 77.2M 942 \n__CTF 824 1 \n__DATA 34.2M 1091 \n__DATA_CONST 37.1M 1110 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 652.0M 163 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1129 \n__TEXT (graphics) 32K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 4000K 34 \nmapped file 549.9M 78 \npage table in kernel 4706K 1 \nshared memory 3152K 23 \n=========== ======= ======= \nTOTAL 11.1G 6573 \nTOTAL, minus reserved VM space 10.9G 6573 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
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{
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},
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"experiments" : [
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}
System Profile:
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Boot Volume File System Type: apfs
Memory Module: LPDDR5, Hynix
USB Device: USB31Bus
USB Device: USB31Bus
USB Device: USB31Bus
Display: spdisplays_display, 1920 x 1080 (1080p FHD - Full High Definition), Main, MirrorOff, Online
Model: MacBookPro18,3, BootROM 11881.101.1, proc 10:8:2 processors, 32 GB, SMC
Graphics: Apple M1 Pro, Apple M1 Pro, Built-In
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4387), wl0: Feb 22 2025 01:26:18 version 20.130.16.0.8.7.195 FWID 01-81c38859
IO80211_driverkit-1475.34 "IO80211_driverkit-1475.34" Mar 9 2025 20:59:13
AirPort:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== 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/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd461x2/fold_igaa_rcsd461x2_model_0.cif
Chain information for fold_igaa_rcsd461x2_model_0.cif #1
---
Chain | Description
A | .
B C | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/IgaA/AF3/fold_igaa_rcsd461x2_rcsf/fold_igaa_rcsd461x2_rcsf_model_0.cif
Chain information for fold_igaa_rcsd461x2_rcsf_model_0.cif #2
---
Chain | Description
A | .
B C | .
D | .
Computing secondary structure
> hide #2 models
> hide #1 models
> show #2 models
> color #2 bychain
> select #2/A:470-550
603 atoms, 606 bonds, 81 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1 & sel
No 'to' model specified
> matchmaker #1 to #2 & sel
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 fold_igaa_rcsd461x2_rcsf_model_0.cif, chain A (#2) with
fold_igaa_rcsd461x2_model_0.cif, chain A (#1), sequence alignment score =
409.3
RMSD between 81 pruned atom pairs is 0.324 angstroms; (across all 81 pairs:
0.324)
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> select #2/A:540
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:540
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel & #2 atoms
> show #1 models
> hide #2 models
> select /A:540
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel & #1 atoms
> show #2 models
> hide #1 models
> select /B:538,225,153,191,220
64 atoms, 56 bonds, 8 residues, 2 models selected
> show sel & #2 atoms
> show #1 models
> hide #2 models
> show sel & #1 atoms
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> select #1/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #1/B
3699 atoms, 3768 bonds, 461 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel plum
> select #1/C
3699 atoms, 3768 bonds, 461 residues, 1 model selected
> color sel cadet blue
> select clear
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> set bgColor white
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #1 models
> select #2/A:540
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:191
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:225
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/B:191
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #2/A:540@CA
25 atoms, 21 bonds, 4 residues, 1 model selected
> select add #2/B:153
33 atoms, 28 bonds, 5 residues, 1 model selected
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsD461x2_RcsF.cxs"
> select #2/C
3699 atoms, 3768 bonds, 461 residues, 1 model selected
> ui tool show "Color Actions"
> set bgColor honeydew
> set bgColor white
> color sel azure target acs
> color sel honeydew target acs
> color sel light green target acs
> color sel pale green target acs
> color sel light green target acs
> color sel dark gray target acs
> color sel pale green target acs
> color sel light cyan target acs
> color sel light green target acs
> select #2/B
3699 atoms, 3768 bonds, 461 residues, 1 model selected
> color sel peach puff target acs
> color sel navajo white target acs
> color sel moccasin target acs
> color sel bisque target acs
> color sel misty rose target acs
> color sel peach puff target acs
> color sel light goldenrod yellow target acs
> color sel old lace target acs
> color sel light pink target acs
> color sel misty rose target acs
> color sel bisque target acs
> color sel moccasin target acs
> color sel bisque target acs
> color sel thistle target acs
> color sel peach puff target acs
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> color sel thistle target acs
> select #2/D
984 atoms, 1001 bonds, 134 residues, 1 model selected
> color sel gray target acs
> select clear
> select #2/A:540
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel medium purple target acs
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select clear
> select add #2/B:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:225
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/B:220
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #2/B:191
32 atoms, 28 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange target acs
> color sel dark orange target acs
> color sel orange target acs
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select clear
> show #1 models
> hide #!2 models
> select #1/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> color sel light blue target acs
> select #1/A:540@CA
1 atom, 1 residue, 1 model selected
> select clear
> select #1/A:540
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel cornflower blue target acs
> select #1/B
3699 atoms, 3768 bonds, 461 residues, 1 model selected
> color sel light pink target acs
> select clear
> select add #1/B:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/B:225
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #1/B:220@CA
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #1/B:191
25 atoms, 21 bonds, 4 residues, 1 model selected
> color sel violet target acs
> select clear
> select #1/B:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel violet target acs
> select clear
> select add #1/B:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> select add #1/B:225
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #1/A:540
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #1/B:220
35 atoms, 31 bonds, 4 residues, 1 model selected
> select add #1/B:191
43 atoms, 38 bonds, 5 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select clear
> show #!2 models
Drag select of 56 atoms, 229 residues, 46 bonds
> ~label sel residues
> select #2/D:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #1 models
> show #1 models
> hide #1 models
> select #2?A
Expected an objects specifier or a keyword
> select #2/A
5603 atoms, 5737 bonds, 711 residues, 1 model selected
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/IgaA/AF3/IgaA_RcsD461x2_RcsF.cxs"
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE-
> NsrR/model/RpoE-NsrR.0.46.pdb
Chain information for RpoE-NsrR.0.46.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> color bychain
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_0.cif
Chain information for fold_nsrr_rpoe_model_0.cif #2
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_1.cif
Chain information for fold_nsrr_rpoe_model_1.cif #3
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_2.cif
Chain information for fold_nsrr_rpoe_model_2.cif #4
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_3.cif
Chain information for fold_nsrr_rpoe_model_3.cif #5
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrr_rpoe/fold_nsrr_rpoe_model_4.cif
Chain information for fold_nsrr_rpoe_model_4.cif #6
---
Chain | Description
A | .
B | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna/fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif
Chain information for
fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif #7
---
Chain | Description
A B | .
C | .
D | .
E | .
F | .
G | .
H | .
I | .
> select add #7
31862 atoms, 32543 bonds, 3921 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Computing secondary structure
> select #2/A
1092 atoms, 1107 bonds, 141 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2-7 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 RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_0.cif,
chain B (#2), sequence alignment score = 907.7
RMSD between 89 pruned atom pairs is 0.447 angstroms; (across all 191 pairs:
20.111)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_1.cif,
chain B (#3), sequence alignment score = 889.1
RMSD between 90 pruned atom pairs is 0.465 angstroms; (across all 191 pairs:
19.665)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_2.cif,
chain B (#4), sequence alignment score = 916.7
RMSD between 89 pruned atom pairs is 0.433 angstroms; (across all 191 pairs:
19.763)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_3.cif,
chain B (#5), sequence alignment score = 889.1
RMSD between 87 pruned atom pairs is 0.475 angstroms; (across all 191 pairs:
20.684)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with fold_nsrr_rpoe_model_4.cif,
chain B (#6), sequence alignment score = 917.3
RMSD between 89 pruned atom pairs is 0.433 angstroms; (across all 191 pairs:
20.441)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with
fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E (#7),
sequence alignment score = 899.1
RMSD between 70 pruned atom pairs is 0.646 angstroms; (across all 190 pairs:
39.997)
> hide #3 models
> show #3 models
> hide #1 models
> hide #7 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #3 models
> hide #3 models
> ui tool show Matchmaker
> select #2/A
1092 atoms, 1107 bonds, 141 residues, 1 model selected
> matchmaker #3-7 to #2 & sel
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 fold_nsrr_rpoe_model_0.cif, chain A (#2) with
fold_nsrr_rpoe_model_1.cif, chain A (#3), sequence alignment score = 691.7
RMSD between 125 pruned atom pairs is 0.432 angstroms; (across all 141 pairs:
5.993)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with
fold_nsrr_rpoe_model_2.cif, chain A (#4), sequence alignment score = 700.7
RMSD between 125 pruned atom pairs is 0.414 angstroms; (across all 141 pairs:
5.947)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with
fold_nsrr_rpoe_model_3.cif, chain A (#5), sequence alignment score = 685.7
RMSD between 123 pruned atom pairs is 0.503 angstroms; (across all 141 pairs:
5.951)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with
fold_nsrr_rpoe_model_4.cif, chain A (#6), sequence alignment score = 685.7
RMSD between 124 pruned atom pairs is 0.469 angstroms; (across all 141 pairs:
6.006)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain A (#2) with
fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain G (#7),
sequence alignment score = 685.7
RMSD between 110 pruned atom pairs is 0.636 angstroms; (across all 141 pairs:
6.185)
> matchmaker #1 to #2 & sel
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 fold_nsrr_rpoe_model_0.cif, chain A (#2) with RpoE-NsrR.0.46.pdb,
chain B (#1), sequence alignment score = 688.7
RMSD between 125 pruned atom pairs is 0.641 angstroms; (across all 141 pairs:
6.103)
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #7 models
> hide #2 models
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> color sel cornflower blue
> select clear
> show #2 models
> show #3 models
> hide #3 models
> hide #2 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #1 models
> hide #7 models
> show #7 models
> hide #1 models
> hide #7 models
> show #3 models
> show #4 models
> show #5 models
> hide #3 models
> hide #4 models
> hide #5 models
Enter a PDB ID in the entry field
> open 6jbq fromDatabase pdb format mmcif
6jbq title:
CryoEM structure of Escherichia coli sigmaE transcription initiation complex
containing 5nt of RNA [more info...]
Chain information for 6jbq #8
---
Chain | Description | UniProt
A B | DNA-directed RNA polymerase subunit alpha | RPOA_ECOLI 1-329
C | DNA-directed RNA polymerase subunit beta | RPOB_ECOLI 1-1342
D | DNA-directed RNA polymerase subunit beta' | RPOC_ECOLI 1-1407
E | DNA-directed RNA polymerase subunit omega | RPOZ_ECOLI 1-91
F | ECF RNA polymerase sigma-E factor | RPOE_ECOLI 1-191
G | DNA (48-MER) |
H | DNA (48-MER) |
I | RNA (5'-R(*CP*UP*CP*GP*A)-3') |
Non-standard residues in 6jbq #8
---
MG — magnesium ion
ZN — zinc ion
> open 1or7 fromDatabase pdb format mmcif
Summary of feedback from opening 1or7 fetched from pdb
---
warning | Atom CE has no neighbors to form bonds with according to residue template for MET /B:144
1or7 title:
Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of
its Anti-sigma RseA [more info...]
Chain information for 1or7 #9
---
Chain | Description | UniProt
A B | RNA polymerase sigma-E factor | RPOE_ECOLI 1-191
C F | Sigma-E factor negative regulatory protein | RSEA_ECOLI 1-90
1or7 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!8-9 atoms
> show #!8-9 cartoons
Drag select of 475 residues, 2 pseudobonds
> color sel bychain
> show #7 models
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> show #2 models
> hide #7 models
> select up
31862 atoms, 32543 bonds, 3921 residues, 1 model selected
> select #2/A
1092 atoms, 1107 bonds, 141 residues, 1 model selected
> show #7 models
> hide #2 models
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> matchmaker #!8-9 to #7 & sel
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 fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with 6jbq, chain F (#8), sequence alignment score = 876.9
RMSD between 156 pruned atom pairs is 1.135 angstroms; (across all 185 pairs:
1.567)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with 1or7, chain A (#9), sequence alignment score = 870.6
RMSD between 59 pruned atom pairs is 0.408 angstroms; (across all 178 pairs:
36.626)
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #7 models
> show #7 models
> show #!8 models
> hide #7 models
> show #7 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> hide #7 models
> show #!8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #!8 models
> show #!8 models
> hide #7 models
> show #7 models
> hide #!8 models
> show #!9 models
> hide #7 models
> select #9/B/F
1947 atoms, 1863 bonds, 1 pseudobond, 339 residues, 2 models selected
> delete atoms (#!9 & sel)
> delete bonds (#!9 & sel)
> ui tool show Matchmaker
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> show #7 models
> matchmaker #!9 to #7 & sel
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 fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with 1or7, chain A (#9), sequence alignment score = 870.6
RMSD between 59 pruned atom pairs is 0.408 angstroms; (across all 178 pairs:
36.626)
> hide #!9 models
> show #!9 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #2 models
> show #7 models
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> matchmaker #1-6 to #7 & sel
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 fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence alignment score = 899.1
RMSD between 70 pruned atom pairs is 0.646 angstroms; (across all 190 pairs:
39.997)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with fold_nsrr_rpoe_model_0.cif, chain B (#2), sequence alignment score =
898.5
RMSD between 53 pruned atom pairs is 0.429 angstroms; (across all 190 pairs:
50.910)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with fold_nsrr_rpoe_model_1.cif, chain B (#3), sequence alignment score =
873.3
RMSD between 64 pruned atom pairs is 0.339 angstroms; (across all 190 pairs:
50.319)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with fold_nsrr_rpoe_model_2.cif, chain B (#4), sequence alignment score =
900.9
RMSD between 71 pruned atom pairs is 0.332 angstroms; (across all 190 pairs:
50.885)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with fold_nsrr_rpoe_model_3.cif, chain B (#5), sequence alignment score =
879.9
RMSD between 6 pruned atom pairs is 1.532 angstroms; (across all 190 pairs:
34.202)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with fold_nsrr_rpoe_model_4.cif, chain B (#6), sequence alignment score =
901.5
RMSD between 6 pruned atom pairs is 1.537 angstroms; (across all 190 pairs:
33.265)
> hide #7 models
> show #7 models
> hide #!9 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #7 models
> show #7 models
> hide #2 models
> show #2 models
> hide #7 models
> select add #2
4138 atoms, 4201 bonds, 522 residues, 2 models selected
> color sel & #2 bychain
> select #2/B
1527 atoms, 1551 bonds, 191 residues, 1 model selected
> rainbow sel
> show #!8 models
> hide #!8 models
> show #!9 models
> show #6 models
> hide #6 models
> show #7 models
> hide #2 models
> hide #!9 models
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> rainbow sel
> select clear
> show #2 models
> hide #2 models
> show #2 models
> hide #7 models
> show #7 models
> hide #2 models
> show #!9 models
> hide #7 models
> select #9/A
1473 atoms, 1463 bonds, 1 pseudobond, 214 residues, 2 models selected
> rainbow sel
> select clear
> show #7 models
> hide #7 models
> show #2 models
> hide #!9 models
> show #7 models
> select #7/E
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> matchmaker #!8-9 to #7 & sel
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 fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with 6jbq, chain F (#8), sequence alignment score = 876.9
RMSD between 156 pruned atom pairs is 1.135 angstroms; (across all 185 pairs:
1.567)
Matchmaker fold_rpoax2_rpob_rpoc_rpoe_rpoz_nsrr_48merdna_model_0.cif, chain E
(#7) with 1or7, chain A (#9), sequence alignment score = 870.6
RMSD between 59 pruned atom pairs is 0.408 angstroms; (across all 178 pairs:
36.626)
> show #!9 models
> hide #7 models
> hide #2 models
> show #7 models
> hide #!9 models
> show #!9 models
> hide #7 models
> show #7 models
> hide #!9 models
> show #!9 models
> hide #7 models
> show #7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select clear
> show #!9 models
> show #2 models
> hide #7 models
> select #9/A:120-187
546 atoms, 551 bonds, 68 residues, 1 model selected
> matchmaker #1-6 to #9 & sel
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 1or7, chain A (#9) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence
alignment score = 318.7
RMSD between 64 pruned atom pairs is 0.531 angstroms; (across all 68 pairs:
1.615)
Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_0.cif, chain B (#2),
sequence alignment score = 319.6
RMSD between 63 pruned atom pairs is 0.468 angstroms; (across all 68 pairs:
2.300)
Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_1.cif, chain B (#3),
sequence alignment score = 324.4
RMSD between 64 pruned atom pairs is 0.429 angstroms; (across all 68 pairs:
2.533)
Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_2.cif, chain B (#4),
sequence alignment score = 318.7
RMSD between 64 pruned atom pairs is 0.349 angstroms; (across all 68 pairs:
2.870)
Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_3.cif, chain B (#5),
sequence alignment score = 324.4
RMSD between 64 pruned atom pairs is 0.502 angstroms; (across all 68 pairs:
2.315)
Matchmaker 1or7, chain A (#9) with fold_nsrr_rpoe_model_4.cif, chain B (#6),
sequence alignment score = 322.3
RMSD between 64 pruned atom pairs is 0.390 angstroms; (across all 68 pairs:
1.306)
> hide #2 models
> select #9/C
563 atoms, 540 bonds, 97 residues, 1 model selected
> color sel gray
> select clear
> show #2 models
> hide #!9 models
> show #!9 models
> hide #2 models
> select #9/A:120-187
546 atoms, 551 bonds, 68 residues, 1 model selected
> show #2 models
> hide #!9 models
> show #3 models
> hide #2 models
> select #2/B#/B#4/B#5/B
Expected an objects specifier or a keyword
> select #2/B#3/B#4/B#5/B
6108 atoms, 6204 bonds, 764 residues, 4 models selected
> select #2/B#3/B#4/B#5/B#6/B
7635 atoms, 7755 bonds, 955 residues, 5 models selected
> show #2 models
> show #4 models
> show #5 models
> show #6 models
> rainbow sel
Drag select of 5 residues
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #!9 models
> hide #2 models
> show #7 models
> hide #!9 models
> show #!8 models
> hide #7 models
> show #7 models
> hide #7 models
> select #2/B#3/B#4/B#5/B#6/B#8/F
9118 atoms, 9262 bonds, 1141 residues, 6 models selected
> rainbow sel & #!8
Drag select of 7 residues
> select #2/B#3/B#4/B#5/B#6/B#8/F
9118 atoms, 9262 bonds, 1141 residues, 6 models selected
> show sel & #!8 surfaces
> select #8/F
1483 atoms, 1507 bonds, 186 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> show #!9 models
> hide #!8 models
> select #9/A
1473 atoms, 1463 bonds, 1 pseudobond, 214 residues, 2 models selected
> show sel surfaces
> show #7 models
> show #!8 models
> hide #7 models
> hide #!8 models
> show #2 models
> hide #!9 models
> show #3 models
> show #4 models
> show #5 models
> show #6 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #!9 models
> hide sel surfaces
> hide #2 models
> show #2 models
> hide #!9 models
> show #!9 models
> show #3 models
> show #4 models
> show #5 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #2 models
> ui tool show ESMFold
> esmfold predict #1/A directory /Users/taic/Downloads/ChimeraX/ESMFold
ESMFold Service Broken
## ESMFold Prediction Service Broken
October 26, 2023
The ChimeraX ESMFold prediction service is down because Meta's prediction
server has an SSL certificate problem. Meta is working on fixing it as
described in this bug report
https://github.com/facebookresearch/esm/discussions/627
and there is a ChimeraX ticket ChimeraX ticket debugging this problem.
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10056
We do not have an estimate for when (if ever) the Meta sever will be working
again.
> show #!8 models
> hide #!8 models
> show #!8 models
> show #7 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #2 models
> hide #7 models
> show #!8 models
> hide #2#!8 surfaces
> hide #2 models
> show #!9 models
> open 1or7 fromDatabase pdb format mmcif
Summary of feedback from opening 1or7 fetched from pdb
---
warning | Atom CE has no neighbors to form bonds with according to residue template for MET /B:144
1or7 title:
Crystal Structure of Escherichia coli sigmaE with the Cytoplasmic Domain of
its Anti-sigma RseA [more info...]
Chain information for 1or7 #10
---
Chain | Description | UniProt
A B | RNA polymerase sigma-E factor | RPOE_ECOLI 1-191
C F | Sigma-E factor negative regulatory protein | RSEA_ECOLI 1-90
1or7 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Drag select of 450 residues, 2 pseudobonds
> color sel bychain
> select clear
> select #10/B/F
1947 atoms, 1863 bonds, 1 pseudobond, 339 residues, 2 models selected
> delete atoms (#!10 & sel)
> delete bonds (#!10 & sel)
> select #10/A
1473 atoms, 1463 bonds, 1 pseudobond, 214 residues, 2 models selected
> rainbow sel
> hide #!9 models
> select #8/F:1-110
841 atoms, 858 bonds, 106 residues, 1 model selected
> matchmaker #!10 to #8 & sel
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 6jbq, chain F (#8) with 1or7, chain A (#10), sequence alignment
score = 487.6
RMSD between 84 pruned atom pairs is 0.815 angstroms; (across all 106 pairs:
5.890)
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #10/C
563 atoms, 540 bonds, 97 residues, 1 model selected
> color sel gray
> select clear
> show #!8 models
> show #2 models
> select #8/F:1-110
841 atoms, 858 bonds, 106 residues, 1 model selected
> matchmaker #1-6 to #8 & sel
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 6jbq, chain F (#8) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence
alignment score = 505.6
RMSD between 83 pruned atom pairs is 0.778 angstroms; (across all 106 pairs:
10.486)
Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_0.cif, chain B (#2),
sequence alignment score = 506.8
RMSD between 83 pruned atom pairs is 0.756 angstroms; (across all 106 pairs:
18.674)
Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_1.cif, chain B (#3),
sequence alignment score = 506.2
RMSD between 83 pruned atom pairs is 0.769 angstroms; (across all 106 pairs:
15.065)
Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_2.cif, chain B (#4),
sequence alignment score = 506.2
RMSD between 83 pruned atom pairs is 0.734 angstroms; (across all 106 pairs:
18.352)
Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_3.cif, chain B (#5),
sequence alignment score = 503.2
RMSD between 83 pruned atom pairs is 0.754 angstroms; (across all 106 pairs:
18.529)
Matchmaker 6jbq, chain F (#8) with fold_nsrr_rpoe_model_4.cif, chain B (#6),
sequence alignment score = 506.2
RMSD between 83 pruned atom pairs is 0.768 angstroms; (across all 106 pairs:
18.847)
> hide #!9 models
> hide #!10 models
> hide #2 models
> show sel surfaces
> hide sel surfaces
> show #!10 models
> hide #!8 models
> show #!8 models
> show #2 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #2 models
> show #2 models
> hide #!10 models
> show #!10 models
> hide #2 models
> show #2 models
> hide #!10 models
> show #3 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!8 models
> hide #2 models
> show #2 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #2 models
> show #2 models
> show #6 models
> hide #5 models
> hide #2 models
> show #!10 models
> hide #6 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!10 models
> show #!10 models
> hide #2 models
> hide #!10 models
> show #2 models
> show #3 models
> hide #2 models
> show #2 models
> show #4 models
> hide #3 models
> hide #2 models
> hide #4 models
> show #5 models
> show #6 models
> hide #5 models
> show #2 models
> hide #6 models
> show #6 models
> hide #2 models
> show #!8 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> show #2 models
> hide #!8 models
> hide #7 models
> show #7 models
> ui tool show "Side View"
> hide #2 models
> show #3 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #6 models
> hide #5 models
> hide #7 models
> show #7 models
> hide #6 models
> show #!10 models
> hide #!10 models
> show #6 models
> hide #7 models
> select add #10
2877 atoms, 2861 bonds, 1 pseudobond, 417 residues, 5 models selected
> select subtract #10
841 atoms, 858 bonds, 106 residues, 2 models selected
> show #!10 models
> hide #6 models
> show #6 models
> hide #!10 models
> show #5 models
> hide #6 models
> show #4 models
> hide #5 models
> hide #4 models
> show #5 models
> show #!10 models
> hide #5 models
> show #1 models
> hide #!10 models
> show #2 models
> hide #1 models
> hide #2 models
> show #2 models
> show #1 models
> hide #2 models
> select #8/F:1-110
841 atoms, 858 bonds, 106 residues, 1 model selected
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> select #1/A:8
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A
3065 atoms, 3089 bonds, 191 residues, 1 model selected
> rainbow sel
> show #2 models
> hide #2 models
> show #!9 models
> hide #!9 models
> show #!10 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE-
> NsrR/model/RpoE-NsrR.0.46.pdb
Chain information for RpoE-NsrR.0.46.pdb #11
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE-
> NsrR/model/RpoE-NsrR.0.44.pdb
Chain information for RpoE-NsrR.0.44.pdb #12
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE-
> NsrR/model/RpoE-NsrR.0.437.pdb
Chain information for RpoE-NsrR.0.437.pdb #13
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> matchmaker #11-13 to #8 & sel
No 'to' model specified
> select #1/A
3065 atoms, 3089 bonds, 191 residues, 1 model selected
> matchmaker #11-13 to #1 & sel
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 RpoE-NsrR.0.46.pdb, chain A (#1) with RpoE-NsrR.0.46.pdb, chain A
(#11), sequence alignment score = 980.9
RMSD between 191 pruned atom pairs is 0.000 angstroms; (across all 191 pairs:
0.000)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with RpoE-NsrR.0.44.pdb, chain A
(#12), sequence alignment score = 980.9
RMSD between 191 pruned atom pairs is 0.688 angstroms; (across all 191 pairs:
0.688)
Matchmaker RpoE-NsrR.0.46.pdb, chain A (#1) with RpoE-NsrR.0.437.pdb, chain A
(#13), sequence alignment score = 973.7
RMSD between 191 pruned atom pairs is 0.660 angstroms; (across all 191 pairs:
0.660)
> hide #!10 models
> select add #11
8348 atoms, 8411 bonds, 523 residues, 2 models selected
> select add #12
13631 atoms, 13733 bonds, 855 residues, 3 models selected
> select add #13
18914 atoms, 19055 bonds, 1187 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> select add #1
2218 atoms, 2233 bonds, 141 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE-
> NsrR/model/RpoE-NsrR.0.46.pdb
Chain information for RpoE-NsrR.0.46.pdb #1
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_0.pdb
Chain information for ranked_0.pdb #11
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_1.pdb
Chain information for ranked_1.pdb #12
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_2.pdb
Chain information for ranked_2.pdb #13
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_3.pdb
Chain information for ranked_3.pdb #14
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_4.pdb
Chain information for ranked_4.pdb #15
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_5.pdb
Chain information for ranked_5.pdb #16
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_6.pdb
Chain information for ranked_6.pdb #17
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_7.pdb
Chain information for ranked_7.pdb #18
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_8.pdb
Chain information for ranked_8.pdb #19
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_9.pdb
Chain information for ranked_9.pdb #20
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_10.pdb
Chain information for ranked_10.pdb #21
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_11.pdb
Chain information for ranked_11.pdb #22
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_12.pdb
Chain information for ranked_12.pdb #23
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_13.pdb
Chain information for ranked_13.pdb #24
---
Chain | Description
A | No description available
B | No description available
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF2/RpoE_NsrR/ranked_14.pdb
Chain information for ranked_14.pdb #25
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> select #8/F:1-110
841 atoms, 858 bonds, 106 residues, 1 model selected
> matchmaker #1,11-25 to #8 & sel
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 6jbq, chain F (#8) with RpoE-NsrR.0.46.pdb, chain A (#1), sequence
alignment score = 505.6
RMSD between 83 pruned atom pairs is 0.778 angstroms; (across all 106 pairs:
10.486)
Matchmaker 6jbq, chain F (#8) with ranked_0.pdb, chain A (#11), sequence
alignment score = 505.6
RMSD between 83 pruned atom pairs is 0.778 angstroms; (across all 106 pairs:
10.486)
Matchmaker 6jbq, chain F (#8) with ranked_1.pdb, chain A (#12), sequence
alignment score = 505.6
RMSD between 83 pruned atom pairs is 0.779 angstroms; (across all 106 pairs:
10.474)
Matchmaker 6jbq, chain F (#8) with ranked_2.pdb, chain A (#13), sequence
alignment score = 505.6
RMSD between 83 pruned atom pairs is 0.794 angstroms; (across all 106 pairs:
10.448)
Matchmaker 6jbq, chain F (#8) with ranked_3.pdb, chain A (#14), sequence
alignment score = 496.6
RMSD between 85 pruned atom pairs is 0.903 angstroms; (across all 106 pairs:
8.808)
Matchmaker 6jbq, chain F (#8) with ranked_4.pdb, chain A (#15), sequence
alignment score = 505.6
RMSD between 85 pruned atom pairs is 0.852 angstroms; (across all 106 pairs:
8.184)
Matchmaker 6jbq, chain F (#8) with ranked_5.pdb, chain A (#16), sequence
alignment score = 505.6
RMSD between 85 pruned atom pairs is 0.852 angstroms; (across all 106 pairs:
8.155)
Matchmaker 6jbq, chain F (#8) with ranked_6.pdb, chain A (#17), sequence
alignment score = 513.4
RMSD between 84 pruned atom pairs is 0.909 angstroms; (across all 106 pairs:
10.037)
Matchmaker 6jbq, chain F (#8) with ranked_7.pdb, chain A (#18), sequence
alignment score = 516.4
RMSD between 86 pruned atom pairs is 0.856 angstroms; (across all 106 pairs:
9.728)
Matchmaker 6jbq, chain F (#8) with ranked_8.pdb, chain A (#19), sequence
alignment score = 517
RMSD between 85 pruned atom pairs is 0.813 angstroms; (across all 106 pairs:
8.015)
Matchmaker 6jbq, chain F (#8) with ranked_9.pdb, chain A (#20), sequence
alignment score = 506.8
RMSD between 86 pruned atom pairs is 0.790 angstroms; (across all 106 pairs:
9.591)
Matchmaker 6jbq, chain F (#8) with ranked_10.pdb, chain A (#21), sequence
alignment score = 497.8
RMSD between 82 pruned atom pairs is 0.931 angstroms; (across all 106 pairs:
10.773)
Matchmaker 6jbq, chain F (#8) with ranked_11.pdb, chain A (#22), sequence
alignment score = 517.6
RMSD between 83 pruned atom pairs is 1.032 angstroms; (across all 106 pairs:
9.232)
Matchmaker 6jbq, chain F (#8) with ranked_12.pdb, chain A (#23), sequence
alignment score = 497.8
RMSD between 80 pruned atom pairs is 0.799 angstroms; (across all 106 pairs:
14.376)
Matchmaker 6jbq, chain F (#8) with ranked_13.pdb, chain A (#24), sequence
alignment score = 509.8
RMSD between 76 pruned atom pairs is 0.805 angstroms; (across all 106 pairs:
16.260)
Matchmaker 6jbq, chain F (#8) with ranked_14.pdb, chain A (#25), sequence
alignment score = 496.6
RMSD between 88 pruned atom pairs is 0.801 angstroms; (across all 106 pairs:
11.350)
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> hide #22 models
> hide #23 models
> hide #24 models
> hide #25 models
> show #!8 models
> show #!10 models
> hide #!8 models
> hide #!10 models
> select #11-#25/A
Expected an objects specifier or a keyword
> select #11/A-#25/A
Expected an objects specifier or a keyword
> select #11/A#25/A
6130 atoms, 6178 bonds, 382 residues, 2 models selected
> rainbow sel & #11
> select add #11
8348 atoms, 8411 bonds, 523 residues, 2 models selected
> hide #1 models
> show #1 models
> hide #1 models
> show #12 models
> show #13 models
> show #14 models
> hide #14 models
> hide #12 models
> hide #13 models
> show #14 models
> select #14/A#25/A
6130 atoms, 6178 bonds, 382 residues, 2 models selected
> select #14/A
3065 atoms, 3089 bonds, 191 residues, 1 model selected
> rainbow sel
> hide #11 models
> show #11 models
> hide #11 models
> show #15 models
> hide #15 models
> hide #14 models
> show #15 models
> hide #15 models
> show #11 models
> show #15 models
> show #16 models
> hide #15 models
> show #15 models
> hide #16 models
> show #17 models
> hide #15 models
> hide #11 models
> show #11 models
> show #15 models
> show #18 models
> hide #11 models
> hide #15 models
> show #19 models
> hide #18 models
> hide #17 models
> show #20 models
> hide #19 models
> show #21 models
> hide #20 models
> show #22 models
> hide #21 models
> show #23 models
> hide #22 models
> show #11 models
> hide #11 models
> show #24 models
> show #25 models
> hide #23 models
> hide #24 models
> select add #11
8348 atoms, 8411 bonds, 523 residues, 2 models selected
> select add #12
13631 atoms, 13733 bonds, 855 residues, 3 models selected
> select add #13
18914 atoms, 19055 bonds, 1187 residues, 4 models selected
> select add #14
21132 atoms, 21288 bonds, 1328 residues, 4 models selected
> select add #15
26415 atoms, 26610 bonds, 1660 residues, 5 models selected
> select add #16
31698 atoms, 31932 bonds, 1992 residues, 6 models selected
> select add #17
36981 atoms, 37254 bonds, 2324 residues, 7 models selected
> select add #18
42264 atoms, 42576 bonds, 2656 residues, 8 models selected
> select add #19
47547 atoms, 47898 bonds, 2988 residues, 9 models selected
> select add #20
52830 atoms, 53220 bonds, 3320 residues, 10 models selected
> select add #21
58113 atoms, 58542 bonds, 3652 residues, 11 models selected
> select add #22
63396 atoms, 63864 bonds, 3984 residues, 12 models selected
> select add #23
68679 atoms, 69186 bonds, 4316 residues, 13 models selected
> select add #24
73962 atoms, 74508 bonds, 4648 residues, 14 models selected
> select add #25
79245 atoms, 79830 bonds, 4980 residues, 15 models selected
> delete atoms (#25 & sel)
> delete bonds (#25 & sel)
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show #18 models
> show #19 models
> show #20 models
> show #21 models
> show #22 models
> show #23 models
> show #24 models
> hide #11 models
> hide #12 models
> show #12 models
> hide #14 models
> show #14 models
> hide #14 models
> show #14 models
> hide #14 models
> hide #18 models
> show #18 models
> hide #17 models
> hide #21 models
> delete atoms (#12-13,15-16,18-20,22-24 & sel)
> delete bonds (#12-13,15-16,18-20,22-24 & sel)
> show #11 models
> show #14 models
> show #!10 models
> hide #11 models
> hide #!10 models
> show #17 models
> show #!10 models
> hide #14 models
> hide #!10 models
> show #21 models
> hide #17 models
> show #17 models
> show #14 models
> delete atoms (#14,17,21 & sel)
> delete bonds (#14,17,21 & sel)
> show #1 models
> show #!10 models
> hide #!10 models
> select #1/A
3065 atoms, 3089 bonds, 191 residues, 1 model selected
> rainbow sel
> show #2 models
> hide #1 models
> show #!10 models
> hide #2 models
> show #1 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #2 models
> hide #1 models
> show #!10 models
> hide #2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!10 models
> show #!10 models
> show #2 models
> hide #1 models
> hide #!10 models
> show #7 models
> hide #2 models
> select ::name="CYS"
598 atoms, 505 bonds, 93 residues, 11 models selected
> select clear
> select add #7/G:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #7/G:96
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #7/G:102
18 atoms, 15 bonds, 3 residues, 1 model selected
> color sel yellow
> show sel atoms
> style sel ball
Changed 18 atom styles
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_0.cif
Chain information for fold_nsrrx2_rpoe_model_0.cif #12
---
Chain | Description
A B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_1.cif
Chain information for fold_nsrrx2_rpoe_model_1.cif #13
---
Chain | Description
A B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_2.cif
Chain information for fold_nsrrx2_rpoe_model_2.cif #14
---
Chain | Description
A B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_3.cif
Chain information for fold_nsrrx2_rpoe_model_3.cif #15
---
Chain | Description
A B | .
C | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_model_4.cif
Chain information for fold_nsrrx2_rpoe_model_4.cif #16
---
Chain | Description
A B | .
C | .
Computing secondary structure
> show #2 models
> hide #7 models
> select #2/B:1-120
950 atoms, 968 bonds, 120 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #12-16 to #2 & sel
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 fold_nsrr_rpoe_model_0.cif, chain B (#2) with
fold_nsrrx2_rpoe_model_0.cif, chain C (#12), sequence alignment score = 549.2
RMSD between 85 pruned atom pairs is 0.293 angstroms; (across all 119 pairs:
10.408)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with
fold_nsrrx2_rpoe_model_1.cif, chain C (#13), sequence alignment score = 546.2
RMSD between 85 pruned atom pairs is 0.267 angstroms; (across all 119 pairs:
6.508)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with
fold_nsrrx2_rpoe_model_2.cif, chain C (#14), sequence alignment score = 570.4
RMSD between 83 pruned atom pairs is 0.357 angstroms; (across all 119 pairs:
18.762)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with
fold_nsrrx2_rpoe_model_3.cif, chain C (#15), sequence alignment score = 566.8
RMSD between 91 pruned atom pairs is 0.478 angstroms; (across all 119 pairs:
10.674)
Matchmaker fold_nsrr_rpoe_model_0.cif, chain B (#2) with
fold_nsrrx2_rpoe_model_4.cif, chain C (#16), sequence alignment score = 569.8
RMSD between 80 pruned atom pairs is 0.319 angstroms; (across all 119 pairs:
18.622)
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #2 models
> show #2 models
> hide #2 models
> color #12 bychain
> hide #12 models
> show #12 models
> show #2 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #2 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> color #12-16 bychain
> hide #13 models
> hide #14 models
> show #13 models
> hide #15 models
> hide #16 models
> show #2 models
> hide #13 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> hide #2 models
> show #13 models
> hide #12 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #13 models
> show #12 models
> hide #2 models
> show #2 models
> hide #2 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #!10 models
Drag select of 1 residues
> hide #!10 models
> show #15 models
> hide #14 models
> show #2 models
> hide #2 models
> show #16 models
> hide #15 models
> show #2 models
> hide #2 models
> show #!10 models
> hide #16 models
> show #2 models
> hide #!10 models
> show #12 models
> hide #2 models
> show #!10 models
> hide #12 models
> show #2 models
> hide #2 models
> show #11 models
> hide #!10 models
> hide #11 models
> show #11 models
> show #2 models
> hide #11 models
> show #!10 models
> hide #!10 models
> show #12 models
> hide #2 models
> show #13 models
> hide #12 models
> show #!10 models
> hide #13 models
> select ((#10/A & ::polymer_type>0 ) & ((#10/C & ::polymer_type>0 ) :0 ) & ((#10/A & ::polymer_type>0 ) : interfaces select #10/A & ::polymer_type>0 contacting #10/C &
> ::polymer_type>0 areaCutoff 0 bothSides true
98 contacting residues
> select (#10/A & ::polymer_type>0 ) & ((#10/C & ::polymer_type>0 ) : show sel atoms
> show #2 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #2 models
> show #2 models
> hide #!10 models
> show #3 models
> show #4 models
> hide #3 models
> hide #2 models
> show #5 models
> hide #4 models
> show #12 models
> hide #5 models
> select #12/C
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> rainbow sel
> show #13 models
> hide #12 models
> select #13/C
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> rainbow sel
> show #!10 models
> hide #13 models
> show #13 models
> hide #!10 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #16 models
> hide #15 models
> select #16/C
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> rainbow sel
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #16 models
> show #16 models
> hide #!10 models
> show #!10 models
> hide #16 models
> show #16 models
> hide #!10 models
> show #!10 models
> hide #16 models
> show #16 models
> hide #!10 models
> select clear
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_summary_confidences_0.json
Failed opening file /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_summary_confidences_0.json:
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2_rpoe/fold_nsrrx2_rpoe_summary_confidences_0.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> show #!10 models
> hide #16 models
> show #16 models
> hide #!10 models
> select #16/C
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show #12 models
> hide #!16 models
> select #12/C
1519 atoms, 1543 bonds, 190 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show #!10 models
> hide #!12 models
> show #!10 surfaces
> hide #!10 surfaces
> show #11 models
> hide #11 models
> hide #!10 models
> show #!12 models
> show sel surfaces
> select clear
> hide #!12 surfaces
> show #!12 surfaces
> show #13 models
> hide #!12 models
> show #13 surfaces
> hide #!13 surfaces
> show #!13 surfaces
> hide #!13 surfaces
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #!12 models
> hide #!12 surfaces
> select #12/A
1092 atoms, 1107 bonds, 141 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #14-15#!13,16 to #12 & sel
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 fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_rpoe_model_2.cif, chain A (#14), sequence alignment score = 707.3
RMSD between 136 pruned atom pairs is 0.403 angstroms; (across all 141 pairs:
0.756)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_rpoe_model_3.cif, chain A (#15), sequence alignment score = 714.5
RMSD between 137 pruned atom pairs is 0.403 angstroms; (across all 141 pairs:
0.863)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_rpoe_model_1.cif, chain A (#13), sequence alignment score = 714.5
RMSD between 136 pruned atom pairs is 0.420 angstroms; (across all 141 pairs:
0.746)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_rpoe_model_4.cif, chain A (#16), sequence alignment score = 707.3
RMSD between 135 pruned atom pairs is 0.443 angstroms; (across all 141 pairs:
0.785)
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> show #15 models
> hide #14 models
> show #!16 models
> hide #15 models
> show #!12 models
> show #14 models
> show #!13 models
> show #15 models
> hide #!13 models
> hide #14 models
> hide #15 models
> hide #!16 models
> show #!13 models
> hide #!12 models
> show #!12 models
> show #14 models
> hide #!13 models
> hide #!12 models
> show #15 models
> hide #14 models
> show #!16 models
> hide #15 models
> hide #!16 models
> show #2 models
> show #!12 models
> hide #2 models
> select clear
> show #!10 models
> hide #!12 models
> hide #!10 models
> show #!8 models
> show #!12 models
> hide #!8 models
> show #!13 models
> hide #!13 models
> select ::name="CYS"
808 atoms, 680 bonds, 128 residues, 16 models selected
> show #!8 models
> hide #!12 models
> select clear
> select #6/F
Nothing selected
> show #!8 surfaces
> hide #!8 surfaces
> select #8/F
1483 atoms, 1507 bonds, 186 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!8 surfaces
> select (#8/F & ::polymer_type>0 ) & ((#8/G#8/H & ::polymer_type>0 ) : show sel atoms
> style (#!8 & sel) ball
Changed 376 atom styles
> show sel surfaces
> hide sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6jbq_F SES surface #8.4: minimum, -14.34, mean -1.22,
maximum 10.80
To also show corresponding color key, enter the above coulombic command and
add key true
> select #8/F
1483 atoms, 1507 bonds, 186 residues, 1 model selected
> coulombic sel
Coulombic values for 6jbq_F SES surface #8.4: minimum, -14.34, mean -1.22,
maximum 10.80
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!12 models
> hide #!8 models
> coulombic #!12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2:
minimum, -15.92, mean -0.58, maximum 9.52
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3:
minimum, -23.57, mean -0.56, maximum 12.88
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1:
minimum, -22.04, mean -1.05, maximum 12.16
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!12
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2:
minimum, -15.92, mean -0.58, maximum 9.52
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3:
minimum, -23.57, mean -0.56, maximum 12.88
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1:
minimum, -22.04, mean -1.05, maximum 12.16
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!12 surfaces
> coulombic #!12
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2:
minimum, -15.92, mean -0.58, maximum 9.52
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3:
minimum, -23.57, mean -0.56, maximum 12.88
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1:
minimum, -22.04, mean -1.05, maximum 12.16
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!10 models
> hide #!12 models
> coulombic #!10
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1or7_A SES surface #10.2: minimum, -20.54, mean -1.07,
maximum 9.07
Coulombic values for 1or7_C SES surface #10.3: minimum, -18.13, mean -4.40,
maximum 6.24
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!10 surfaces
> show #!8 models
> hide #!10 models
> hide sel surfaces
> show #!10 models
> hide #!8 models
> show #2 models
> hide #!10 models
> show #!12 models
> hide #2 models
> hide #!12 surfaces
> coulombic #!12
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2:
minimum, -15.92, mean -0.58, maximum 9.52
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3:
minimum, -23.57, mean -0.56, maximum 12.88
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1:
minimum, -22.04, mean -1.05, maximum 12.16
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!12
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2:
minimum, -15.92, mean -0.58, maximum 9.52
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3:
minimum, -23.57, mean -0.56, maximum 12.88
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1:
minimum, -22.04, mean -1.05, maximum 12.16
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!12 surfaces
> coulombic #!12
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_A SES surface #12.2:
minimum, -15.92, mean -0.58, maximum 9.52
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_B SES surface #12.3:
minimum, -23.57, mean -0.56, maximum 12.88
Coulombic values for fold_nsrrx2_rpoe_model_0.cif_C SES surface #12.1:
minimum, -22.04, mean -1.05, maximum 12.16
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!12 surfaces
> show #!13 models
> hide #!12 models
> coulombic #!13
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_nsrrx2_rpoe_model_1.cif_A SES surface #13.1:
minimum, -16.22, mean -0.58, maximum 10.51
Coulombic values for fold_nsrrx2_rpoe_model_1.cif_B SES surface #13.2:
minimum, -17.04, mean -0.57, maximum 9.45
Coulombic values for fold_nsrrx2_rpoe_model_1.cif_C SES surface #13.3:
minimum, -14.19, mean -1.40, maximum 9.93
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!13 surfaces
> show #14 models
> hide #!13 models
> show #!8 models
> hide #14 models
> show #!10 models
> hide #!8 models
> show #!12 models
> hide #!10 models
> show #!13 models
> show #14 models
> show #15 models
> show #!16 models
> hide #!13 models
> hide #14 models
> hide #15 models
> hide #!16 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_0.cif
Chain information for fold_nsrrx2_model_0.cif #17
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_1.cif
Chain information for fold_nsrrx2_model_1.cif #18
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_2.cif
Chain information for fold_nsrrx2_model_2.cif #19
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_3.cif
Chain information for fold_nsrrx2_model_3.cif #20
---
Chain | Description
A B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/KarlT/AF3/fold_nsrrx2/fold_nsrrx2_model_4.cif
Chain information for fold_nsrrx2_model_4.cif #21
---
Chain | Description
A B | .
Computing secondary structure
> hide #!12 models
> show #!12 models
> select #12/A
1092 atoms, 1107 bonds, 141 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #17-21 to #12 & sel
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 fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_model_0.cif, chain A (#17), sequence alignment score = 695.9
RMSD between 121 pruned atom pairs is 0.386 angstroms; (across all 141 pairs:
2.113)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_model_1.cif, chain A (#18), sequence alignment score = 678.5
RMSD between 123 pruned atom pairs is 0.411 angstroms; (across all 141 pairs:
1.724)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_model_2.cif, chain A (#19), sequence alignment score = 692.9
RMSD between 122 pruned atom pairs is 0.358 angstroms; (across all 141 pairs:
2.052)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_model_3.cif, chain B (#20), sequence alignment score = 692.9
RMSD between 123 pruned atom pairs is 0.360 angstroms; (across all 141 pairs:
1.914)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrrx2_model_4.cif, chain A (#21), sequence alignment score = 695.3
RMSD between 122 pruned atom pairs is 0.343 angstroms; (across all 141 pairs:
1.961)
> hide #17 models
> hide #18 models
> show #17 models
> hide #!12 models
> hide #19 models
> hide #20 models
> hide #21 models
> color #17 bychain
> show #!13 models
> show #!12 models
> hide #!13 models
> select clear
> hide #17 models
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> select #14/C#15/C#16/C
4557 atoms, 4629 bonds, 570 residues, 3 models selected
> show #15 models
> show #!16 models
> rainbow sel
> select clear
> show #!10 models
> hide #14 models
> hide #!16 models
> hide #15 models
> show #15 models
> hide #!10 models
> hide #15 models
> select add #18
2184 atoms, 2214 bonds, 282 residues, 1 model selected
> select add #19
4368 atoms, 4428 bonds, 564 residues, 2 models selected
> select add #20
6552 atoms, 6642 bonds, 846 residues, 3 models selected
> select add #21
8736 atoms, 8856 bonds, 1128 residues, 4 models selected
> show #18 models
> show #19 models
> show #20 models
> hide #20 models
> show #20 models
> show #21 models
> delete atoms sel
> delete bonds sel
> show #!12 models
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> show #15 models
> hide #14 models
> show #!16 models
> hide #15 models
> show #!8 models
> hide #!8 models
> show #!12 models
> hide #!16 models
> show #2 models
> hide #2 models
> select #12/A
1092 atoms, 1107 bonds, 141 residues, 1 model selected
> matchmaker #2-6 to #12 & sel
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 fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrr_rpoe_model_0.cif, chain A (#2), sequence alignment score = 685.7
RMSD between 124 pruned atom pairs is 0.497 angstroms; (across all 141 pairs:
6.290)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrr_rpoe_model_1.cif, chain A (#3), sequence alignment score = 710.9
RMSD between 134 pruned atom pairs is 0.560 angstroms; (across all 141 pairs:
1.076)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrr_rpoe_model_2.cif, chain A (#4), sequence alignment score = 700.1
RMSD between 134 pruned atom pairs is 0.596 angstroms; (across all 141 pairs:
1.018)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrr_rpoe_model_3.cif, chain A (#5), sequence alignment score = 718.1
RMSD between 129 pruned atom pairs is 0.523 angstroms; (across all 141 pairs:
1.401)
Matchmaker fold_nsrrx2_rpoe_model_0.cif, chain A (#12) with
fold_nsrr_rpoe_model_4.cif, chain A (#6), sequence alignment score = 718.1
RMSD between 134 pruned atom pairs is 0.617 angstroms; (across all 141 pairs:
1.130)
> show #2 models
> hide #!12 models
> show #3 models
> hide #2 models
> show #2 models
> hide #3 models
> show #!8 models
> hide #!8 models
> show #11 models
> hide #2 models
> show #!12 models
> hide #11 models
> select clear
> show #2 models
> hide #!12 models
> show #!12 models
> hide #2 models
> show #2 models
> hide #!12 models
> show #!12 models
> hide #2 models
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> show #15 models
> hide #14 models
> show #!16 models
> hide #15 models
> show #17 models
> hide #!16 models
> show #!12 models
> show #!13 models
> show #14 models
> show #15 models
> show #!16 models
> show #2 models
> hide #!13 models
> hide #14 models
> hide #15 models
> hide #!16 models
> hide #17 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #17 models
> hide #17 models
> show #!12 models
> hide #2 models
> show #2 models
> hide #!12 models
> show #!12 models
> hide #2 models
> show #2 models
> show #!13 models
> hide #!12 models
> hide #2 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #11 models
> hide #11 models
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> show #!12 models
> hide #14 models
> show #14 models
> hide #!12 models
> show #!13 models
> hide #14 models
> show #17 models
> hide #!13 models
> show #!13 models
> hide #17 models
> show #2 models
> hide #!13 models
> show #!13 models
> hide #2 models
> show #2 models
> hide #!13 models
> show #!12 models
> hide #2 models
> show #!13 models
> hide #!12 models
> select #13/C:124-190
547 atoms, 552 bonds, 67 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!8 to #13 & sel
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 fold_nsrrx2_rpoe_model_1.cif, chain C (#13) with 6jbq, chain F
(#8), sequence alignment score = 313.7
RMSD between 66 pruned atom pairs is 0.882 angstroms; (across all 66 pairs:
0.882)
> show #!8 models
> hide #!13 models
> show #!12 models
> show #!13 models
> hide #!12 models
> hide #!8 models
> show #!8 models
> hide #!13 models
> select #8/D
10334 atoms, 10485 bonds, 14 pseudobonds, 1338 residues, 3 models selected
> color (#!8 & sel) light gray
> select clear
> select #8/D
10334 atoms, 10485 bonds, 14 pseudobonds, 1338 residues, 3 models selected
> ui tool show "Color Actions"
> color sel gainsboro target acs
> color sel cornsilk target acs
> color sel antique white target acs
> color sel beige target acs
> color sel antique white target acs
> color sel pale goldenrod target acs
> color sel antique white target acs
> select clear
> select #8/C
10320 atoms, 10485 bonds, 1 pseudobond, 1312 residues, 2 models selected
> color sel light cyan target acs
> color sel lavender target acs
> color sel pale goldenrod target acs
> color sel lavender target acs
> color sel azure target acs
> color sel honeydew target acs
> select clear
> select #8/C
10320 atoms, 10485 bonds, 1 pseudobond, 1312 residues, 2 models selected
> color sel light cyan target acs
> select clear
> select #8/F
1483 atoms, 1507 bonds, 186 residues, 1 model selected
> hide sel atoms
> select #8/B:204
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #14 models
> hide #!13 models
> show #15 models
> hide #14 models
> show #!16 models
> hide #15 models
> show #!12 models
> hide #!16 models
> show #!8 models
> hide #!12 models
> show #!13 models
> hide #!8 models
> show #!12 models
> hide #!13 models
> show #14 models
> hide #!12 models
> show #!13 models
> show #15 models
> hide #!13 models
> show #!13 models
> hide #14 models
> hide #15 models
> show #14 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #14 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!8 models
> hide #!13 models
> show #!12 models
> hide #!8 models
> show #!13 models
> hide #!12 models
> show #15 models
> hide #!13 models
> show #!16 models
> hide #15 models
> hide #!16 models
> show #!13 models
> show #14 models
> hide #14 models
> show #!8 models
> hide #!13 models
> show #!12 models
> hide #!8 models
> show #!8 models
> hide #!12 models
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #7 models
> hide #!12 models
> show #!12 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!13 models
> show #7 models
> hide #7 models
> hide #!12 models
> show #7 models
> show #!8 models
> hide #7 models
> show #!12 models
> hide #!13 models
> hide #!8 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!12 models
> hide #!13 models
> show #14 models
> hide #!12 models
> show #15 models
> hide #14 models
> show #!16 models
> hide #15 models
> show #!13 models
> hide #!16 models
> show #!8 models
> hide #!13 models
> show #!12 models
> hide #!8 models
> show #14 models
> hide #!12 models
> show #!16 models
> hide #14 models
> show #17 models
> hide #!16 models
> show #!16 models
> hide #17 models
> show #!12 models
> hide #!16 models
> show #!13 models
> hide #!12 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #!8 models
> hide #!13 models
> show #!10 models
> hide #!8 models
> select #10
2036 atoms, 2003 bonds, 1 pseudobond, 311 residues, 3 models selected
> hide sel atoms
> select clear
Drag select of 11 residues
> select #10/A:120
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> show #!13 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!13 models
> show #!13 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!8 models
> hide #!13 models
> show #14 models
> hide #!12 models
> hide #14 models
> show #!13 models
> show #!16 models
> hide #!13 models
> hide #!16 models
> show #!13 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> show #!16 models
> hide #14 models
> show #17 models
> hide #!16 models
> show #!12 models
> hide #17 models
> select #12/C:120-160
332 atoms, 334 bonds, 41 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!8 to #12 & sel
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 fold_nsrrx2_rpoe_model_0.cif, chain C (#12) with 6jbq, chain F
(#8), sequence alignment score = 194.6
RMSD between 41 pruned atom pairs is 0.873 angstroms; (across all 41 pairs:
0.873)
> show #!8 models
> hide #!12 models
> show #!13 models
> show #!12 models
> hide #!8 models
> select clear
> hide #!13 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!12 models
> show #!12 models
> hide #!8 models
> show #!8 models
> hide #!12 models
> show #!12 models
> hide #!8 models
> show #!8 models
> hide #!12 models
> show #!12 models
> hide #!8 models
> show #!13 models
> hide #!12 models
> show #14 models
> hide #!13 models
> show #!12 models
> hide #14 models
> show #17 models
> hide #!12 models
> show #!12 models
> hide #17 models
> show #!13 models
> hide #!12 models
> show #!12 models
> show #14 models
> hide #!13 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #14 models
> show #!8 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!8 models
> show #17 models
> hide #!12 models
> show #!12 models
> hide #17 models
> show #!8 models
> hide #!12 models
> show #!12 models
> hide #!8 models
> show #!8 models
> hide #!12 models
> show #!13 models
> hide #!8 models
> show #14 models
> hide #!13 models
> show #17 models
> hide #14 models
> show #!12 models
> hide #17 models
> show #17 models
> show #!8 models
> hide #17 models
> hide #!12 models
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!12 models
> show #!8 models
> hide #!12 models
> select #8/I
102 atoms, 113 bonds, 5 residues, 1 model selected
> color sel dark sea green target acs
> color sel medium purple target acs
> color sel olive target acs
> select #8/C:499
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!12 models
> hide #!8 models
> show #17 models
> hide #!12 models
> show #2 models
> hide #17 models
> show #17 models
> hide #2 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/NsrR_RpoE.cxs"
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/Fig6C.NsrRx2.png" width 600 height
> 487 supersample 4 transparentBackground true
> show #!12 models
> hide #17 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/Fig6D.NsrRx2_RpoE.png" width 600
> height 487 supersample 4 transparentBackground true
> show #!8 models
> hide #!12 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1B.1OR7zoomin.png" width 600
> height 487 supersample 4 transparentBackground true
> show #!10 models
> hide #!8 models
> select #10/C
563 atoms, 540 bonds, 97 residues, 1 model selected
> color (#!10 & sel) light gray
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1C.RpoE_RseA.1OR7.png" width 600
> height 487 supersample 4 transparentBackground true
> show #!13 models
> hide #!10 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1A.NsrR_RpoE.AF3.png" width 600
> height 487 supersample 4 transparentBackground true
> show #14 models
> hide #!13 models
> show #!13 models
> hide #14 models
> show #14 models
> hide #!13 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1F.NsrRx2_RpoE-2.png" width 600
> height 487 supersample 4 transparentBackground true
> show #15 models
> hide #14 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1F.NsrRx2_RpoE-3.png" width 600
> height 487 supersample 4 transparentBackground true
> show #!16 models
> hide #15 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1G.NsrRx2_RpoE-4.png" width 600
> height 487 supersample 4 transparentBackground true
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/NsrR_RpoE.cxs"
> show #2 models
> hide #!16 models
> show #!12 models
> hide #2 models
> show #2 models
> hide #!12 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/FigS1A.NsrR_RpoE.png" width 600
> height 487 supersample 4 transparentBackground true
> ui tool show "Color Actions"
> show #17 models
> hide #2 models
> show #!8 models
> hide #17 models
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/KarlT/AF3/NsrRx2_RpoE.cxs"
> close session
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_0.cif
Chain information for fold_nucleosome_tf_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_1.cif
Chain information for fold_nucleosome_tf_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_2.cif
Chain information for fold_nucleosome_tf_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_3.cif
Chain information for fold_nucleosome_tf_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> open /Users/taic/Downloads/fold_nucleosome_tf/fold_nucleosome_tf_model_4.cif
Chain information for fold_nucleosome_tf_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
> show cartoons
Computing secondary structure
> hide atoms
> open 8VG1 fromDatabase pdb format mmcif
Summary of feedback from opening 8VG1 fetched from pdb
---
note | Fetching compressed mmCIF 8vg1 from http://files.rcsb.org/download/8vg1.cif
8vg1 title:
Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome [more
info...]
Chain information for 8vg1 #6
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_HUMAN 0-135
B F | Histone H4 | H4_HUMAN 0-102
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125
I | DNA (171-MER) |
J | DNA (171-MER) |
O | Hepatocyte nuclear factor 3-alpha | FOXA1_HUMAN 1-472
T | Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4 | MALE_ECOLI -378--13, GATA4_HUMAN 1-442
Non-standard residues in 8vg1 #6
---
ZN — zinc ion
> ui tool show Matchmaker
> matchmaker #1-5 to #6
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 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F
(#1), sequence alignment score = 3127.7
RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs:
8.007)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F
(#2), sequence alignment score = 3139.7
RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs:
7.604)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F
(#3), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs:
7.070)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F
(#4), sequence alignment score = 3127.7
RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs:
6.895)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F
(#5), sequence alignment score = 3115.7
RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs:
6.506)
> show cartoons
> hide atoms
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #1 models
> hide #!6 models
> color #1 bychain
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #2 models
> hide #1 models
> show #3 models
> hide #2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> show #1 models
> show #!6 models
> hide #5 models
> hide #1 models
> color #!6 bychain
> show #1 models
> hide #!6 models
> color #1 bychain
> show #!6 models
> hide #1 models
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #!6 models
> select /E
18309 atoms, 18831 bonds, 2487 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #2-5#!6 to #1 & sel
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 fold_nucleosome_tf_model_0.cif, chain E (#1) with
fold_nucleosome_tf_model_1.cif, chain E (#2), sequence alignment score =
2368.2
RMSD between 6 pruned atom pairs is 1.361 angstroms; (across all 478 pairs:
29.439)
Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with
fold_nucleosome_tf_model_2.cif, chain E (#3), sequence alignment score = 2247
RMSD between 91 pruned atom pairs is 0.595 angstroms; (across all 478 pairs:
24.901)
Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with
fold_nucleosome_tf_model_3.cif, chain E (#4), sequence alignment score =
2331.6
RMSD between 11 pruned atom pairs is 1.309 angstroms; (across all 478 pairs:
27.521)
Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with
fold_nucleosome_tf_model_4.cif, chain E (#5), sequence alignment score = 2385
RMSD between 9 pruned atom pairs is 1.233 angstroms; (across all 478 pairs:
25.503)
Matchmaker fold_nucleosome_tf_model_0.cif, chain E (#1) with 8vg1, chain O
(#6), sequence alignment score = 1924.2
RMSD between 82 pruned atom pairs is 0.853 angstroms; (across all 102 pairs:
2.172)
> show #2 models
> hide #1 models
> show #1 models
> show #3 models
> hide #1 models
> show #1 models
> hide #2 models
> show #4 models
> hide #3 models
> show #5 models
> hide #4 models
> hide #1 models
> show #1 models
> hide #5 models
> color sel & #1 bychain
> show #2 models
> hide #1 models
> color sel & #2 bychain
> select clear
> show #3 models
> hide #2 models
> color #3 bychain
> show #2 models
> hide #3 models
> select clear
> color #2 bychain
> show #4 models
> hide #2 models
> select clear
> color #4 bychain
> show #5 models
> hide #4 models
> color #5 bychain
> show #!6 models
> hide #5 models
> select clear
> color #!6 bychain
> show #1 models
> hide #!6 models
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> show #2 models
> hide #1 models
> show #!6 models
> hide #2 models
> show #1 models
> hide #!6 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #!6 models
> hide #1 models
> select /B
4662 atoms, 4709 bonds, 598 residues, 6 models selected
> color sel medium purple target acs
> select clear
> show #1 models
> hide #!6 models
> select /B
4662 atoms, 4709 bonds, 598 residues, 6 models selected
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> select clear
> color #1 bychain
> select clear
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> select /A
6204 atoms, 6286 bonds, 777 residues, 6 models selected
> color sel medium slate blue target acs
> select /B
4662 atoms, 4709 bonds, 598 residues, 6 models selected
> color sel cornflower blue target acs
> select /C
5820 atoms, 5890 bonds, 759 residues, 6 models selected
> color sel olive target acs
> color sel dark khaki target acs
> select /D
5630 atoms, 5716 bonds, 725 residues, 6 models selected
> color sel goldenrod target acs
> select /E
18309 atoms, 18831 bonds, 2487 residues, 6 models selected
> color sel coral target acs
> select /F
31577 atoms, 32394 bonds, 4258 residues, 6 models selected
> color sel plum target acs
> select clear
> select /G
19955 atoms, 22262 bonds, 1046 residues, 6 models selected
> color sel light gray target acs
> color sel gray target acs
> select /H
19830 atoms, 22186 bonds, 1025 residues, 6 models selected
> color sel tan target acs
> color sel light blue target acs
> select clear
> show #2 models
> hide #1 models
> select /C
5820 atoms, 5890 bonds, 759 residues, 6 models selected
> color sel olive drab target acs
> color sel dark sea green target acs
> select clear
> select /C
5820 atoms, 5890 bonds, 759 residues, 6 models selected
> color sel light green target acs
> select clear
> show #!6 models
> hide #2 models
> select /B
4662 atoms, 4709 bonds, 598 residues, 6 models selected
> select #6/B
662 atoms, 669 bonds, 83 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue target acs
> select #6/C
840 atoms, 850 bonds, 109 residues, 1 model selected
> color sel cornflower blue target acs
> select #6/A
799 atoms, 811 bonds, 97 residues, 1 model selected
> color sel light green target acs
> select #6/D
745 atoms, 756 bonds, 95 residues, 1 model selected
> color sel goldenrod target acs
> select #6/K
Nothing selected
> color coral target acs
> select #6/B
662 atoms, 669 bonds, 83 residues, 1 model selected
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select clear
> color bychain
> ui tool show Matchmaker
> matchmaker #1-5 to #6
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 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F
(#1), sequence alignment score = 3127.7
RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs:
8.007)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F
(#2), sequence alignment score = 3139.7
RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs:
7.604)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F
(#3), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs:
7.070)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F
(#4), sequence alignment score = 3127.7
RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs:
6.895)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F
(#5), sequence alignment score = 3115.7
RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs:
6.506)
> matchmaker #1-5 to #6
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 8vg1, chain T (#6) with fold_nucleosome_tf_model_0.cif, chain F
(#1), sequence alignment score = 3127.7
RMSD between 43 pruned atom pairs is 0.620 angstroms; (across all 53 pairs:
8.007)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_1.cif, chain F
(#2), sequence alignment score = 3139.7
RMSD between 43 pruned atom pairs is 0.499 angstroms; (across all 53 pairs:
7.604)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_2.cif, chain F
(#3), sequence alignment score = 3142.7
RMSD between 45 pruned atom pairs is 0.524 angstroms; (across all 53 pairs:
7.070)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_3.cif, chain F
(#4), sequence alignment score = 3127.7
RMSD between 44 pruned atom pairs is 0.550 angstroms; (across all 53 pairs:
6.895)
Matchmaker 8vg1, chain T (#6) with fold_nucleosome_tf_model_4.cif, chain F
(#5), sequence alignment score = 3115.7
RMSD between 44 pruned atom pairs is 0.584 angstroms; (across all 53 pairs:
6.506)
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15H00105LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 42 days, 7 hours, 5 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
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
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