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Opened 102 minutes ago
#20177 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x000000030805b000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030704f000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000306043000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 948 in wait
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000305037000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017f62b000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017e61f000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017d613000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017c607000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Thread 0x000000017b5fb000 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 982 in run
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x000000020bdbac40 (most recent call first):
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2831 in update_buffer_data
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1917 in update_buffers
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1929 in activate_bindings
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 791 in draw_self
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 784 in draw
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1572 in _draw_multiple
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559 in draw_opaque
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259 in _draw_scene
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py", line 2270 in moved_marker_cb
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/histogram.py", line 423 in move_marker_cb
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py", line 2188 in _drag
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume_viewer.py", line 2191 in mouseReleaseEvent
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, PIL._imagingmath, chimerax.mask._mask (total: 46)
{"app_name":"ChimeraX","timestamp":"2026-04-16 09:36:19.00 -0500","app_version":"1.11.1","slice_uuid":"c20e09a8-923e-3fb3-856b-3e765bcb267b","build_version":"1.11.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.2 (25C56)","roots_installed":0,"name":"ChimeraX","incident_id":"F215D06A-F7D2-46D6-854F-0E570F95CBAE"}
{
"uptime" : 2000000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac16,10",
"coalitionID" : 231455,
"osVersion" : {
"train" : "macOS 26.2",
"build" : "25C56",
"releaseType" : "User"
},
"captureTime" : "2026-04-16 09:36:03.8743 -0500",
"codeSigningMonitor" : 2,
"incident" : "F215D06A-F7D2-46D6-854F-0E570F95CBAE",
"pid" : 65245,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-04-15 15:36:15.7383 -0500",
"procStartAbsTime" : 47605065868169,
"procExitAbsTime" : 49159961849216,
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/*\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.11.1","CFBundleVersion":"1.11.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EBF66F08-FACE-5BB6-9843-DABDAF6540C8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "24374280-A249-7F68-3EA4-7564B13B1176",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn","siriAssetIsNotReady"]},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "DA963938-2411-4DC3-8A8B-0B8618AFB34A",
"sip" : "enabled",
"vmRegionInfo" : "0x313894000 is in 0x313894000-0x3172d8000; bytes after start: 0 bytes before end: 61095935
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
Stack 30b090000-30b894000 [ 8208K] rw-\/rwx SM=PRV thread 47
GAP OF 0x8000000 BYTES
---> mapped file 313894000-3172d8000 [ 58.3M] r--\/rwx SM=COW Object_id=1ac65460
mapped file 3172d8000-31a7a8000 [ 52.8M] r--\/rwx SM=COW Object_id=f910a7c2",
"exception" : {"codes":"0x0000000000000002, 0x0000000313894000","rawCodes":[2,13212663808],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000313894000"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":65245},
"vmregioninfo" : "0x313894000 is in 0x313894000-0x3172d8000; bytes after start: 0 bytes before end: 61095935
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
Stack 30b090000-30b894000 [ 8208K] rw-\/rwx SM=PRV thread 47
GAP OF 0x8000000 BYTES
---> mapped file 313894000-3172d8000 [ 58.3M] r--\/rwx SM=COW Object_id=1ac65460
mapped file 3172d8000-31a7a8000 [ 52.8M] r--\/rwx SM=COW Object_id=f910a7c2",
"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":6160299400},{"value":99},{"value":116},{"value":0},{"value":0},{"value":12681218416816932949},{"value":12681218408106714133},{"value":14757395258967641293},{"value":4294967286},{"value":6160299330},{"value":0},{"value":52},{"value":4294967280},{"value":328},{"value":8811678096},{"value":0},{"value":10},{"value":259},{"value":8788880672 ,"symbolLocation":224,"symbol": "_main_thread"},{"value":0},{"value":1},{"value":4330047032 ,"symbolLocation":0,"symbol": "faulthandler_handlers"},{"value":48526566064},{"value":520987082752},{"value":48684691264},{"value":6160301528}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6961076360},"cpsr":{"value":1073741824},"fp":{"value":6160299472},"sp":{"value":6160299440},"esr":{"value":1442840704,"description":"(Syscall)"},"pc":{"value":6960838064,"matchesCrashFrame":1},"far":{"value":0}},"id":22733119,"triggered":true,"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[
{"imageOffset":38320,"symbol": "__pthread_kill" ,"symbolLocation":8,"imageIndex":127},
{"imageOffset":26760,"symbol": "pthread_kill" ,"symbolLocation":296,"imageIndex":128},
{"imageOffset":269616,"symbol": "raise" ,"symbolLocation":32,"imageIndex":129},
{"imageOffset":2447420,"symbol": "faulthandler_fatal_error" ,"symbolLocation":392,"imageIndex":1},
{"imageOffset":14148,"symbol": "_sigtramp" ,"symbolLocation":56,"imageIndex":130},
{"imageOffset":178160,"symbol": "gldBufferSubData" ,"symbolLocation":300,"imageIndex":73},
{"imageOffset":256472,"symbol": "glBufferSubData_Exec" ,"symbolLocation":548,"imageIndex":131},
{"imageOffset":16464,"symbol": "ffi_call_SYSV" ,"symbolLocation":80,"imageIndex":132},
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Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 272K 11
ColorSync 128K 8
CoreAnimation 2016K 116
CoreGraphics 32K 2
CoreServices 224K 1
CoreUI image data 2784K 36
Foundation 32K 2
Kernel Alloc Once 80K 3
MALLOC 39.9G 773
MALLOC guard page 3360K 4
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 56.8M 52
Stack 416.2M 52
VM_ALLOCATE 11.7G 288
VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated)
__AUTH 5935K 652
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__DATA_DIRTY 8778K 901
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__TEXT (graphics) 112K 1
__TPRO_CONST 128K 2
dyld private memory 304K 4
mapped file 648.1M 73
page table in kernel 29.0M 1
shared memory 3152K 25
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TOTAL 55.3G 7689
TOTAL, minus reserved VM space 55.1G 7689
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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/guodongxie/Downloads/cryosparc_P3_J683_007_volume_map (1).mrc"
Opened cryosparc_P3_J683_007_volume_map (1).mrc as #1, grid size 256,256,256,
pixel 1.07, shown at level 0.00835, step 1, values float32
> surface dust #1 size 10.7
> ui mousemode right "mark plane"
> ui mousemode right "mark point"
> marker #2 position 98.24,170,175.6 color yellow radius 1
> marker change #2 radius 20
> marker change #2 radius 5
> ui mousemode right "mark point"
> marker #2 position 89.37,159.3,165.6 color yellow radius 5
> marker #2 position 113.4,172.3,187.2 color yellow radius 5
> marker #2 position 124.4,156.3,187.6 color yellow radius 5
> marker #2 position 133.8,152.4,182.5 color yellow radius 5
> marker #2 position 137.7,151.1,180.7 color yellow radius 5
> ui mousemode right "mark point"
> marker #2 position 137.2,152.4,183.4 color yellow radius 5
> marker #2 position 137.1,151.1,180.5 color yellow radius 5
> marker #2 position 134,149.5,176.2 color yellow radius 5
> marker #2 position 136.7,147.7,173 color yellow radius 5
> marker #2 position 134.1,145.1,165.9 color yellow radius 5
> marker #2 position 129.6,155.9,173.1 color yellow radius 5
> marker #2 position 119.5,145.2,149.1 color yellow radius 5
> marker #2 position 140.1,165,115.5 color yellow radius 5
> marker #2 position 133.9,169.5,124.3 color yellow radius 5
> marker #2 position 133.8,169.7,124.4 color yellow radius 5
> marker #2 position 127.4,173.6,134 color yellow radius 5
> marker #2 position 97.63,157.4,137.3 color yellow radius 5
> marker #2 position 93.53,158.9,148.6 color yellow radius 5
> marker #2 position 89.92,160.8,157.5 color yellow radius 5
> ui mousemode right "link markers"
> marker link #2:20,2 color #659cef radius 0.5
> marker link #2:2,19 color #659cef radius 0.5
> marker link #2:19,18 color #659cef radius 0.5
> marker link #2:18,17 color #659cef radius 0.5
> marker link #2:17,16 color #659cef radius 0.5
> marker link #2:16,14 color #659cef radius 0.5
> hide #!1 models
> marker link #2:14,13 color #659cef radius 0.5
> marker link #2:13,11 color #659cef radius 0.5
> marker link #2:11,10 color #659cef radius 0.5
> marker link #2:10,12 color #659cef radius 0.5
> marker link #2:12,9 color #659cef radius 0.5
> marker link #2:9,8 color #659cef radius 0.5
> marker link #2:8,7 color #659cef radius 0.5
> marker link #2:7,4 color #659cef radius 0.5
> marker link #2:4,12 color #659cef radius 0.5
> marker link #2:12,3 color #659cef radius 0.5
> marker link #2:3,1 color #659cef radius 0.5
> marker link #2:1,2 color #659cef radius 0.5
> marker link #2:20,19 color #659cef radius 0.5
> open /Users/guodongxie/Downloads/emd_54480.map
Opened emd_54480.map as #3, grid size 1024,1024,320, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> select add #2
20 atoms, 19 bonds, 20 residues, 1 model selected
> close #2
> ui tool show "Side View"
> view
> ui tool show "Marker Placement"
> close #4
> close #2
> ui mousemode right "mark point"
> marker #2 position 6883,5326,2436 color yellow radius 5
> marker change #2 radius 50
> marker #2 position 7017,5121,2601 color yellow radius 50
> marker #2 position 7030,4874,2711 color yellow radius 50
> marker #2 position 6998,4598,2795 color yellow radius 50
> marker #2 position 6890,4342,2861 color yellow radius 50
> marker #2 position 6739,4159,2907 color yellow radius 50
> marker #2 position 6513,3990,2938 color yellow radius 50
> marker #2 position 6268,3930,2948 color yellow radius 50
> marker #2 position 6042,3912,2943 color yellow radius 50
> marker #2 position 5794,3938,2951 color yellow radius 50
> marker #2 position 5609,3983,2937 color yellow radius 50
> marker #2 position 5420,4079,2915 color yellow radius 50
> marker #2 position 5273,4183,2895 color yellow radius 50
> marker #2 position 5161,4311,2874 color yellow radius 50
> marker #2 position 5034,4478,2849 color yellow radius 50
> marker #2 position 4980,4659,2824 color yellow radius 50
> marker #2 position 4967,4884,2796 color yellow radius 50
> marker #2 position 5003,5118,2769 color yellow radius 50
> marker #2 position 5095,5285,2753 color yellow radius 50
> marker #2 position 5180,5456,2738 color yellow radius 50
> marker #2 position 5341,5561,2731 color yellow radius 50
> marker #2 position 5493,5684,2725 color yellow radius 50
> marker #2 position 5739,5769,2728 color yellow radius 50
> marker #2 position 6003,5804,2738 color yellow radius 50
> marker #2 position 6213,5769,2754 color yellow radius 50
> marker #2 position 6437,5682,2776 color yellow radius 50
> marker #2 position 6624,5586,2800 color yellow radius 50
> marker #2 position 6903,4382,2964 color yellow radius 50
> marker link #2:27,28 color #659cef radius 0.5
> marker #2 position 6893,4376,2971 color yellow radius 50
> marker link #2:28,29 color #659cef radius 0.5
> marker #2 position 6969,4571,2955 color yellow radius 50
> marker link #2:29,30 color #659cef radius 0.5
> undo
Undo failed, probably because structures have been modified.
> select add #2
30 atoms, 3 bonds, 30 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
30 atoms, 3 bonds, 30 residues, 1 model selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> view
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select add #3
30 atoms, 3 bonds, 30 residues, 3 models selected
> select subtract #2
2 models selected
> select add #3
2 models selected
> select add #3
2 models selected
> select add #3
2 models selected
> select add #3
2 models selected
> hide #!3 models
> show #!3 models
> hide #2 models
> marker #4 position 5091,5161,2675 color yellow radius 50
> marker #4 position 5195,5319,2921 color yellow radius 50
> marker link #4:1,2 color #659cef radius 0.5
> marker #4 position 5365,5497,3037 color yellow radius 50
> marker link #4:2,3 color #659cef radius 0.5
> marker #4 position 5536,5604,3087 color yellow radius 50
> marker link #4:3,4 color #659cef radius 0.5
> marker #4 position 5804,5694,2942 color yellow radius 50
> marker link #4:4,5 color #659cef radius 0.5
> marker #4 position 6102,5689,2958 color yellow radius 50
> marker link #4:5,6 color #659cef radius 0.5
> marker #4 position 6288,5614,2966 color yellow radius 50
> marker link #4:6,7 color #659cef radius 0.5
> marker #4 position 6484,5561,2978 color yellow radius 50
> marker link #4:7,8 color #659cef radius 0.5
> marker #4 position 6651,5442,2986 color yellow radius 50
> marker link #4:8,9 color #659cef radius 0.5
> marker #4 position 6808,5284,2993 color yellow radius 50
> marker link #4:9,10 color #659cef radius 0.5
> marker #4 position 6908,5119,2996 color yellow radius 50
> marker link #4:10,11 color #659cef radius 0.5
> marker #4 position 6989,4954,2999 color yellow radius 50
> marker link #4:11,12 color #659cef radius 0.5
> marker #4 position 6998,4748,2995 color yellow radius 50
> marker link #4:12,13 color #659cef radius 0.5
> marker #4 position 6971,4549,2988 color yellow radius 50
> marker link #4:13,14 color #659cef radius 0.5
> marker #4 position 6919,4342,2982 color yellow radius 50
> marker link #4:14,15 color #659cef radius 0.5
> marker #4 position 6782,4164,2968 color yellow radius 50
> marker link #4:15,16 color #659cef radius 0.5
> marker #4 position 6669,4050,2959 color yellow radius 50
> marker link #4:16,17 color #659cef radius 0.5
> marker #4 position 6518,3929,2947 color yellow radius 50
> marker link #4:17,18 color #659cef radius 0.5
> marker #4 position 6358,3879,2935 color yellow radius 50
> marker link #4:18,19 color #659cef radius 0.5
> marker #4 position 6082,3827,2917 color yellow radius 50
> marker link #4:19,20 color #659cef radius 0.5
> marker #4 position 5927,3832,2908 color yellow radius 50
> marker link #4:20,21 color #659cef radius 0.5
> marker #4 position 5712,3868,2896 color yellow radius 50
> marker link #4:21,22 color #659cef radius 0.5
> marker #4 position 5520,3929,2887 color yellow radius 50
> marker link #4:22,23 color #659cef radius 0.5
> marker #4 position 5360,4025,2880 color yellow radius 50
> marker link #4:23,24 color #659cef radius 0.5
> marker #4 position 5194,4171,2875 color yellow radius 50
> marker link #4:24,25 color #659cef radius 0.5
> marker #4 position 5065,4358,2872 color yellow radius 50
> marker link #4:25,26 color #659cef radius 0.5
> marker #4 position 4985,4601,2873 color yellow radius 50
> marker link #4:26,27 color #659cef radius 0.5
> marker #4 position 4979,4850,2878 color yellow radius 50
> marker link #4:27,28 color #659cef radius 0.5
> marker #4 position 4990,5021,2883 color yellow radius 50
> marker link #4:28,29 color #659cef radius 0.5
> hide #4 models
> select add #4
29 atoms, 28 bonds, 29 residues, 1 model selected
> select subtract #4
Nothing selected
> show #4 models
> hide #4 models
> close #2
> marker #2 position 5214,5028,1743 color yellow radius 50
> marker #2 position 5322,5199,1881 color yellow radius 50
> marker link #2:1,2 color #659cef radius 0.5
> marker #2 position 5508,5412,1966 color yellow radius 50
> marker link #2:2,3 color #659cef radius 0.5
> marker #2 position 5625,5498,2017 color yellow radius 50
> marker link #2:3,4 color #659cef radius 0.5
> marker #2 position 5814,5624,2058 color yellow radius 50
> marker link #2:4,5 color #659cef radius 0.5
> marker #2 position 6038,5642,2092 color yellow radius 50
> marker link #2:5,6 color #659cef radius 0.5
> marker #2 position 6217,5624,2119 color yellow radius 50
> marker link #2:6,7 color #659cef radius 0.5
> marker #2 position 6380,5500,2137 color yellow radius 50
> marker link #2:7,8 color #659cef radius 0.5
> marker #2 position 6548,5350,2151 color yellow radius 50
> marker link #2:8,9 color #659cef radius 0.5
> marker #2 position 6696,5211,2165 color yellow radius 50
> marker link #2:9,10 color #659cef radius 0.5
> marker #2 position 6755,5058,2171 color yellow radius 50
> marker link #2:10,11 color #659cef radius 0.5
> marker #2 position 6819,4821,2173 color yellow radius 50
> marker link #2:11,12 color #659cef radius 0.5
> marker #2 position 6809,4558,2169 color yellow radius 50
> marker link #2:12,13 color #659cef radius 0.5
> marker #2 position 6729,4423,2160 color yellow radius 50
> marker link #2:13,14 color #659cef radius 0.5
> marker #2 position 6620,4229,2150 color yellow radius 50
> marker link #2:14,15 color #659cef radius 0.5
> marker #2 position 6451,4067,2138 color yellow radius 50
> marker link #2:15,16 color #659cef radius 0.5
> marker #2 position 6293,4000,2127 color yellow radius 50
> marker link #2:16,17 color #659cef radius 0.5
> marker #2 position 6106,3896,2116 color yellow radius 50
> marker link #2:17,18 color #659cef radius 0.5
> marker #2 position 5884,3883,2104 color yellow radius 50
> marker link #2:18,19 color #659cef radius 0.5
> marker #2 position 5650,3946,2092 color yellow radius 50
> marker link #2:19,20 color #659cef radius 0.5
> marker #2 position 5489,4063,2085 color yellow radius 50
> marker link #2:20,21 color #659cef radius 0.5
> marker #2 position 5367,4202,2080 color yellow radius 50
> marker link #2:21,22 color #659cef radius 0.5
> marker #2 position 5242,4433,2077 color yellow radius 50
> marker link #2:22,23 color #659cef radius 0.5
> marker #2 position 5179,4648,2078 color yellow radius 50
> marker link #2:23,24 color #659cef radius 0.5
> marker #2 position 5162,4816,2081 color yellow radius 50
> marker link #2:24,25 color #659cef radius 0.5
> marker #2 position 5120,5133,2613 color yellow radius 50
> marker link #2:25,26 color #659cef radius 0.5
> marker #2 position 6203,4914,3452 color yellow radius 50
> marker link #2:26,27 color #659cef radius 0.5
> delete atoms sel
> delete bonds sel
> hide #2 models
> show #2 models
> hide #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> marker #5 position 5184,4565,2943 color yellow radius 50
> marker #5 position 5143,4761,3062 color yellow radius 50
> marker link #5:1,2 color #659cef radius 0.5
> marker #5 position 5137,4954,3122 color yellow radius 50
> marker link #5:2,3 color #659cef radius 0.5
> marker #5 position 5162,5116,3157 color yellow radius 50
> marker link #5:3,4 color #659cef radius 0.5
> marker #5 position 5272,5277,3186 color yellow radius 50
> marker link #5:4,5 color #659cef radius 0.5
> marker #5 position 5429,5436,3219 color yellow radius 50
> marker link #5:5,6 color #659cef radius 0.5
> marker #5 position 5544,5516,3250 color yellow radius 50
> marker link #5:6,7 color #659cef radius 0.5
> marker #5 position 5706,5631,3287 color yellow radius 50
> marker link #5:7,8 color #659cef radius 0.5
> marker #5 position 5841,5584,3318 color yellow radius 50
> marker link #5:8,9 color #659cef radius 0.5
> marker #5 position 6005,5516,3349 color yellow radius 50
> marker link #5:9,10 color #659cef radius 0.5
> marker #5 position 6160,5503,3384 color yellow radius 50
> marker link #5:10,11 color #659cef radius 0.5
> marker #5 position 6294,5482,3419 color yellow radius 50
> marker link #5:11,12 color #659cef radius 0.5
> marker #5 position 6433,5399,3454 color yellow radius 50
> marker link #5:12,13 color #659cef radius 0.5
> marker #5 position 6538,5259,3483 color yellow radius 50
> marker link #5:13,14 color #659cef radius 0.5
> marker #5 position 6641,5120,3510 color yellow radius 50
> marker link #5:14,15 color #659cef radius 0.5
> marker #5 position 6752,4949,3540 color yellow radius 50
> marker link #5:15,16 color #659cef radius 0.5
> marker #5 position 6765,4795,3556 color yellow radius 50
> marker link #5:16,17 color #659cef radius 0.5
> marker #5 position 6745,4659,3561 color yellow radius 50
> marker link #5:17,18 color #659cef radius 0.5
> marker #5 position 6724,4534,3561 color yellow radius 50
> marker link #5:18,19 color #659cef radius 0.5
> marker #5 position 6659,4358,3554 color yellow radius 50
> marker link #5:19,20 color #659cef radius 0.5
> marker #5 position 6565,4253,3542 color yellow radius 50
> marker link #5:20,21 color #659cef radius 0.5
> marker #5 position 6462,4179,3528 color yellow radius 50
> marker link #5:21,22 color #659cef radius 0.5
> marker #5 position 6262,4084,3502 color yellow radius 50
> marker link #5:22,23 color #659cef radius 0.5
> marker #5 position 6111,4068,3482 color yellow radius 50
> marker link #5:23,24 color #659cef radius 0.5
> marker #5 position 5858,4021,3453 color yellow radius 50
> marker link #5:24,25 color #659cef radius 0.5
> marker #5 position 5715,4032,3437 color yellow radius 50
> marker link #5:25,26 color #659cef radius 0.5
> marker #5 position 5578,4120,3419 color yellow radius 50
> marker link #5:26,27 color #659cef radius 0.5
> marker #5 position 5364,4257,3395 color yellow radius 50
> marker link #5:27,28 color #659cef radius 0.5
> marker #5 position 5226,4412,3379 color yellow radius 50
> marker link #5:28,29 color #659cef radius 0.5
> ui mousemode right "link markers"
> marker link #5:29,1 color #659cef radius 0.5
> show #4 models
> show #2 models
> ui tool show "Segment Map"
Must show map in surface style, surface threshold level is needed to segment
> volume #3 region 0,0,0,1023,1023,319 step 4
> volume #3 change image level -33.12,0 level 67.03,0.8 level 146.7,1
> volume #3 level 42.77
> volume #3 step 1
> volume #3 level 46.48
> volume #3 level 59.47
> volume #3 level 64.11
> volume #3 level 74.31
> volume #3 style mesh
> volume #3 style image
> volume #3 region 0,0,159,1023,1023,159 step 1 showOutlineBox true
> volume #3 region 0,0,0,1023,1023,319 step 1
> volume #3 region 0,0,0,1023,1023,319 step 1 maximumIntensityProjection true
> volume #3 maximumIntensityProjection false colorMode opaque8 orthoplanes xyz
> positionPlanes 511,511,159 imageMode orthoplanes
> volume #3 region 0,0,159,1023,1023,159 step 1 colorMode auto8 imageMode
> "full region"
> select add #5
29 atoms, 29 bonds, 29 residues, 1 model selected
> select subtract #5
Nothing selected
> color zone #3 near #2 distance 50
> color zone #3 near #2 distance 50 bondPointSpacing 15
> volume splitbyzone #3
Opened emd_54480.map 0 as #6.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #6.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #6.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6 models
> show #!6 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.2 models
> close #6
> close #4
> close #2
> close #5
> show #!3 models
> ui mousemode right "mark plane"
> marker #2 position 5095,4332,1956 color yellow radius 14.6
> marker #2 position 5199,4145,1956 color yellow radius 14.6
> marker link #2:1,2 color #f24347 radius 7.3
> marker #2 position 5345,4031,1956 color yellow radius 14.6
> marker link #2:2,3 color #f24347 radius 7.3
> marker #2 position 5535,3911,1956 color yellow radius 14.6
> marker link #2:3,4 color #f24347 radius 7.3
> marker change #2:4 radius 100
> marker change #2:4 radius 20
> marker #2 position 5756,3833,1956 color yellow radius 20
> marker link #2:4,5 color #f24347 radius 7.3
> marker #2 position 6012,3782,1956 color yellow radius 20
> marker link #2:5,6 color #e5f771 radius 7.3
> marker #2 position 6279,3828,1956 color yellow radius 20
> marker link #2:6,7 color #e5f771 radius 7.3
> marker #2 position 6479,3885,1956 color yellow radius 20
> marker link #2:7,8 color #e5f771 radius 7.3
> marker #2 position 6679,4008,1956 color yellow radius 20
> marker link #2:8,9 color #e5f771 radius 7.3
> marker #2 position 6847,4161,1956 color yellow radius 20
> marker link #2:9,10 color #e5f771 radius 7.3
> marker #2 position 6928,4309,1956 color yellow radius 20
> marker link #2:10,11 color #e5f771 radius 7.3
> marker #2 position 7002,4421,1956 color yellow radius 20
> marker link #2:11,12 color #e5f771 radius 7.3
> marker #2 position 7058,4624,1956 color yellow radius 20
> marker link #2:12,13 color #e5f771 radius 7.3
> marker #2 position 7066,4869,1956 color yellow radius 20
> marker link #2:13,14 color #e5f771 radius 7.3
> marker #2 position 7030,5058,1956 color yellow radius 20
> marker link #2:14,15 color #e5f771 radius 7.3
> marker #2 position 6953,5242,1956 color yellow radius 20
> marker link #2:15,16 color #e5f771 radius 7.3
> marker #2 position 6829,5385,1956 color yellow radius 20
> marker link #2:16,17 color #e5f771 radius 7.3
> marker #2 position 6699,5496,1956 color yellow radius 20
> marker link #2:17,18 color #e5f771 radius 7.3
> marker #2 position 6513,5613,1956 color yellow radius 20
> marker link #2:18,19 color #e5f771 radius 7.3
> marker #2 position 6371,5647,1956 color yellow radius 20
> marker link #2:19,20 color #e5f771 radius 7.3
> marker #2 position 6148,5716,1956 color yellow radius 20
> marker link #2:20,21 color #e5f771 radius 7.3
> marker #2 position 5986,5715,1956 color yellow radius 20
> marker link #2:21,22 color #e5f771 radius 7.3
> marker #2 position 5798,5715,1956 color yellow radius 20
> marker link #2:22,23 color #e5f771 radius 7.3
> marker #2 position 5604,5655,1956 color yellow radius 20
> marker link #2:23,24 color #e5f771 radius 7.3
> marker #2 position 5432,5560,1956 color yellow radius 20
> marker link #2:24,25 color #e5f771 radius 7.3
> marker #2 position 5284,5423,1956 color yellow radius 20
> marker link #2:25,26 color #e5f771 radius 7.3
> marker #2 position 5133,5294,1956 color yellow radius 20
> marker link #2:26,27 color #e5f771 radius 7.3
> marker #2 position 5054,5132,1956 color yellow radius 20
> marker link #2:27,28 color #e5f771 radius 7.3
> marker #2 position 5005,4960,1956 color yellow radius 20
> marker link #2:28,29 color #e5f771 radius 7.3
> marker #2 position 4977,4764,1956 color yellow radius 20
> marker link #2:29,30 color #e5f771 radius 7.3
> marker #2 position 5006,4562,1956 color yellow radius 20
> marker link #2:30,31 color #e5f771 radius 7.3
> marker #2 position 5047,4417,1956 color yellow radius 20
> marker link #2:31,32 color #e5f771 radius 7.3
> ui mousemode right "link markers"
> marker link #2:32,1 color #e5f771 radius 7.3
> color zone #3 near #2 distance 50
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4.2 models
> show #!4.2 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4 models
> select add #2
32 atoms, 32 bonds, 32 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> show #!4.2 models
> show #2 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> hide #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> hide #2 models
> hide #!4 models
> show #!4 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4.2 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> color #4.2 #ff4238ff models
> color #4.2 #ffe72eff models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> close #4
> show #!3 models
> color zone #3 near #2 distance 50
> color zone #3 near #2 distance 50 bondPointSpacing 15
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4.4 models
> hide #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> show #!4.3 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.3 models
> hide #!4.4 models
> hide #!4.1 models
> hide #!4 models
> show #!4 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> hide #!4.1 models
> hide #!4 models
> show #!4 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.1 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> hide #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.4 models
> hide #!4.4 models
> close #4
> show #!3 models
> show #2 models
> ui mousemode right "mark plane"
> marker #2 position 5485,7071,1956 color #ff2c2e radius 20
> marker #2 position 5472,6840,1956 color #ff2c2e radius 20
> marker link #2:33,34 color #f669e8 radius 7.3
> marker #2 position 5474,6669,1956 color #ff2c2e radius 20
> marker link #2:34,35 color #f669e8 radius 7.3
> marker #2 position 5521,6493,1956 color #ff2c2e radius 20
> marker link #2:35,36 color #f669e8 radius 7.3
> marker #2 position 5612,6330,1956 color #ff2c2e radius 20
> marker link #2:36,37 color #f669e8 radius 7.3
> marker #2 position 5732,6186,1956 color #ff2c2e radius 20
> marker link #2:37,38 color #f669e8 radius 7.3
> marker #2 position 5865,6043,1956 color #ff2c2e radius 20
> marker link #2:38,39 color #f669e8 radius 7.3
> marker #2 position 6045,5956,1956 color #ff2c2e radius 20
> marker link #2:39,40 color #f669e8 radius 7.3
> marker #2 position 6206,5871,1956 color #ff2c2e radius 20
> marker link #2:40,41 color #f669e8 radius 7.3
> marker #2 position 6386,5823,1956 color #ff2c2e radius 20
> marker link #2:41,42 color #f669e8 radius 7.3
> marker #2 position 6546,5791,1956 color #ff2c2e radius 20
> marker link #2:42,43 color #f669e8 radius 7.3
> marker #2 position 6679,5779,1956 color #ff2c2e radius 20
> marker link #2:43,44 color #f669e8 radius 7.3
> marker #2 position 6829,5802,1956 color #ff2c2e radius 20
> marker link #2:44,45 color #f669e8 radius 7.3
> marker #2 position 6944,5813,1956 color #ff2c2e radius 20
> marker link #2:45,46 color #f669e8 radius 7.3
> marker #2 position 7056,5845,1956 color #ff2c2e radius 20
> marker link #2:46,47 color #f669e8 radius 7.3
> marker #2 position 7160,5911,1956 color #ff2c2e radius 20
> marker link #2:47,48 color #f669e8 radius 7.3
> marker #2 position 7249,5957,1956 color #ff2c2e radius 20
> marker link #2:48,49 color #f669e8 radius 7.3
> marker #2 position 7356,6047,1956 color #ff2c2e radius 20
> marker link #2:49,50 color #f669e8 radius 7.3
> marker #2 position 7444,6144,1956 color #ff2c2e radius 20
> marker link #2:50,51 color #f669e8 radius 7.3
> marker #2 position 7517,6273,1956 color #ff2c2e radius 20
> marker link #2:51,52 color #f669e8 radius 7.3
> marker #2 position 7565,6361,1956 color #ff2c2e radius 20
> marker link #2:52,53 color #f669e8 radius 7.3
> marker #2 position 7644,6588,1956 color #ff2c2e radius 20
> marker link #2:53,54 color #f669e8 radius 7.3
> marker #2 position 7665,6745,1956 color #ff2c2e radius 20
> marker link #2:54,55 color #f669e8 radius 7.3
> marker #2 position 7671,6873,1956 color #ff2c2e radius 20
> marker link #2:55,56 color #f669e8 radius 7.3
> marker #2 position 7652,7011,1956 color #ff2c2e radius 20
> marker link #2:56,57 color #f669e8 radius 7.3
> marker #2 position 7609,7156,1956 color #ff2c2e radius 20
> marker link #2:57,58 color #f669e8 radius 7.3
> marker #2 position 7544,7272,1956 color #ff2c2e radius 20
> marker link #2:58,59 color #f669e8 radius 7.3
> marker #2 position 7473,7405,1956 color #ff2c2e radius 20
> marker link #2:59,60 color #f669e8 radius 7.3
> marker #2 position 7383,7480,1956 color #ff2c2e radius 20
> marker link #2:60,61 color #f669e8 radius 7.3
> marker #2 position 7266,7627,1956 color #ff2c2e radius 20
> marker link #2:61,62 color #f669e8 radius 7.3
> marker #2 position 7150,7710,1956 color #ff2c2e radius 20
> marker link #2:62,63 color #f669e8 radius 7.3
> marker #2 position 6977,7781,1956 color #ff2c2e radius 20
> marker link #2:63,64 color #f669e8 radius 7.3
> marker #2 position 6842,7852,1956 color #ff2c2e radius 20
> marker link #2:64,65 color #f669e8 radius 7.3
> marker #2 position 6658,7869,1956 color #ff2c2e radius 20
> marker link #2:65,66 color #f669e8 radius 7.3
> marker #2 position 6550,7880,1956 color #ff2c2e radius 20
> marker link #2:66,67 color #f669e8 radius 7.3
> marker #2 position 6421,7857,1956 color #ff2c2e radius 20
> marker link #2:67,68 color #f669e8 radius 7.3
> marker #2 position 6296,7824,1956 color #ff2c2e radius 20
> marker link #2:68,69 color #f669e8 radius 7.3
> marker #2 position 6176,7797,1956 color #ff2c2e radius 20
> marker link #2:69,70 color #f669e8 radius 7.3
> marker #2 position 6076,7754,1956 color #ff2c2e radius 20
> marker link #2:70,71 color #f669e8 radius 7.3
> marker #2 position 5935,7701,1956 color #ff2c2e radius 20
> marker link #2:71,72 color #f669e8 radius 7.3
> marker #2 position 5851,7633,1956 color #ff2c2e radius 20
> marker link #2:72,73 color #f669e8 radius 7.3
> marker #2 position 5719,7520,1956 color #ff2c2e radius 20
> marker link #2:73,74 color #f669e8 radius 7.3
> marker #2 position 5644,7428,1956 color #ff2c2e radius 20
> marker link #2:74,75 color #f669e8 radius 7.3
> marker #2 position 5565,7266,1956 color #ff2c2e radius 20
> marker link #2:75,76 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:76,33 color #f669e8 radius 7.3
> select #3
3 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> hide #!3 models
> hide #2 models
> show #2 models
> show #!3 models
> select up
76 atoms, 76 bonds, 76 residues, 6 models selected
> select up
76 atoms, 76 bonds, 76 residues, 6 models selected
> select up
76 atoms, 76 bonds, 76 residues, 6 models selected
> select up
76 atoms, 76 bonds, 76 residues, 6 models selected
> select subtract #2
5 models selected
> select subtract #1
3 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> select add #3
3 models selected
> color zone #3 near #2 distance 50
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4 models
> show #!4 models
> hide #!4.2 models
> hide #!4.3 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.1 models
> close #4
> show #!3 models
> select ~sel & ##selected
Nothing selected
> color zone #3 near #2 distance 10
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> close #4
> color #2 #76e8ffff
> show #!3 models
> color zone #3 near #2 distance 5
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> show #!4.2 models
> close #4
> show #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> ui mousemode right "mark plane"
> marker #2 position 5151,5024,2672 color #ff2c2e radius 20
> marker #2 position 5156,4778,2672 color #ff2c2e radius 20
> marker link #2:77,78 color #f669e8 radius 7.3
> marker #2 position 5178,4493,2672 color #ff2c2e radius 20
> marker link #2:78,79 color #f669e8 radius 7.3
> ui mousemode right "mark plane"
> marker #2 position 5111,4835,2672 color #ff2c2e radius 20
> marker link #2:79,80 color #f669e8 radius 7.3
> marker #2 position 5153,4562,2672 color #ff2c2e radius 20
> marker link #2:80,81 color #f669e8 radius 7.3
> marker #2 position 5277,4324,2672 color #ff2c2e radius 20
> marker link #2:81,82 color #f669e8 radius 7.3
> marker change #2:82 radius 30
> marker #2 position 5217,4464,2672 color #ff2c2e radius 30
> marker link #2:82,83 color #f669e8 radius 7.3
> marker #2 position 5361,4212,2672 color #ff2c2e radius 30
> marker link #2:83,84 color #f669e8 radius 7.3
> marker #2 position 5475,4158,2672 color #ff2c2e radius 30
> marker link #2:84,85 color #f669e8 radius 7.3
> marker #2 position 5609,4120,2672 color #ff2c2e radius 30
> marker link #2:85,86 color #f669e8 radius 7.3
> hide #!3 models
> show #!3 models
> ui mousemode right "mark plane"
> marker #2 position 5154,5055,2672 color #ff2c2e radius 30
> marker link #2:86,87 color #f669e8 radius 7.3
> marker #2 position 5136,4891,2672 color #ff2c2e radius 30
> marker link #2:87,88 color #f669e8 radius 7.3
> marker #2 position 5131,4678,2672 color #ff2c2e radius 30
> marker link #2:88,89 color #f669e8 radius 7.3
> ui mousemode right "mark plane"
> marker #2 position 5202,5054,2672 color #ff2c2e radius 30
> marker link #2:89,90 color #f669e8 radius 7.3
> marker #2 position 5150,4863,2672 color #ff2c2e radius 30
> marker link #2:90,91 color #f669e8 radius 7.3
> marker #2 position 5191,4514,2672 color #ff2c2e radius 30
> marker link #2:91,92 color #f669e8 radius 7.3
> show #2 models
> marker #2 position 5292,4311,2672 color #ff2c2e radius 30
> marker link #2:92,93 color #f669e8 radius 7.3
> select /M:83@M
1 atom, 1 residue, 1 model selected
> select /M:92@M
1 atom, 1 residue, 1 model selected
> select add /M:77@M
2 atoms, 1 bond, 2 residues, 3 models selected
> ui mousemode right "delete markers"
> marker delete #2:83
> marker delete #2:92
> marker delete #2:79
> marker delete #2:81,82 linksOnly true
> marker delete #2:84
> marker delete #2:93
> marker delete #2:82
> marker delete #2:85
> marker delete #2:86
> marker delete #2:90
> marker delete #2:77,78 linksOnly true
> marker delete #2:88
> marker delete #2:91
> marker delete #2:80,81 linksOnly true
> marker delete #2:89
> marker delete #2:81
> marker delete #2:78
> marker delete #2:80
> marker delete #2:87
> marker delete #2:77
> ui mousemode right "mark plane"
> marker #2 position 5133,4893,2672 color #ff2c2e radius 30
> marker #2 position 5124,4758,2672 color #ff2c2e radius 30
> marker link #2:94,95 color #f669e8 radius 7.3
> marker #2 position 5130,4645,2672 color #ff2c2e radius 30
> marker link #2:95,96 color #f669e8 radius 7.3
> marker #2 position 5153,4524,2672 color #ff2c2e radius 30
> marker link #2:96,97 color #f669e8 radius 7.3
> marker #2 position 5221,4418,2672 color #ff2c2e radius 30
> marker link #2:97,98 color #f669e8 radius 7.3
> marker #2 position 5307,4288,2672 color #ff2c2e radius 30
> marker link #2:98,99 color #f669e8 radius 7.3
> marker #2 position 5447,4161,2672 color #ff2c2e radius 30
> marker link #2:99,100 color #f669e8 radius 7.3
> marker #2 position 5586,4064,2672 color #ff2c2e radius 30
> marker link #2:100,101 color #f669e8 radius 7.3
> marker #2 position 5774,3987,2672 color #ff2c2e radius 30
> marker link #2:101,102 color #f669e8 radius 7.3
> marker #2 position 5979,3950,2672 color #ff2c2e radius 30
> marker link #2:102,103 color #f669e8 radius 7.3
> marker #2 position 6171,3952,2672 color #ff2c2e radius 30
> marker link #2:103,104 color #f669e8 radius 7.3
> marker #2 position 6303,3974,2672 color #ff2c2e radius 30
> marker link #2:104,105 color #f669e8 radius 7.3
> marker #2 position 6417,4022,2672 color #ff2c2e radius 30
> marker link #2:105,106 color #f669e8 radius 7.3
> marker #2 position 6551,4065,2672 color #ff2c2e radius 30
> marker link #2:106,107 color #f669e8 radius 7.3
> marker #2 position 6641,4153,2672 color #ff2c2e radius 30
> marker link #2:107,108 color #f669e8 radius 7.3
> marker #2 position 6721,4215,2672 color #ff2c2e radius 30
> marker link #2:108,109 color #f669e8 radius 7.3
> marker #2 position 6799,4299,2672 color #ff2c2e radius 30
> marker link #2:109,110 color #f669e8 radius 7.3
> marker #2 position 6865,4398,2672 color #ff2c2e radius 30
> marker link #2:110,111 color #f669e8 radius 7.3
> marker #2 position 6914,4539,2672 color #ff2c2e radius 30
> marker link #2:111,112 color #f669e8 radius 7.3
> marker #2 position 6955,4634,2672 color #ff2c2e radius 30
> marker link #2:112,113 color #f669e8 radius 7.3
> marker #2 position 6965,4779,2672 color #ff2c2e radius 30
> marker link #2:113,114 color #f669e8 radius 7.3
> marker #2 position 6939,4958,2672 color #ff2c2e radius 30
> marker link #2:114,115 color #f669e8 radius 7.3
> marker #2 position 6864,5111,2672 color #ff2c2e radius 30
> marker link #2:115,116 color #f669e8 radius 7.3
> marker #2 position 6826,5207,2672 color #ff2c2e radius 30
> marker link #2:116,117 color #f669e8 radius 7.3
> marker #2 position 6748,5323,2672 color #ff2c2e radius 30
> marker link #2:117,118 color #f669e8 radius 7.3
> marker #2 position 6636,5429,2672 color #ff2c2e radius 30
> marker link #2:118,119 color #f669e8 radius 7.3
> marker #2 position 6556,5530,2672 color #ff2c2e radius 30
> marker link #2:119,120 color #f669e8 radius 7.3
> marker #2 position 6445,5671,2672 color #ff2c2e radius 30
> marker link #2:120,121 color #f669e8 radius 7.3
> marker #2 position 6348,5747,2672 color #ff2c2e radius 30
> marker link #2:121,122 color #f669e8 radius 7.3
> marker #2 position 6224,5802,2672 color #ff2c2e radius 30
> marker link #2:122,123 color #f669e8 radius 7.3
> marker #2 position 6161,5759,2672 color #ff2c2e radius 30
> marker link #2:123,124 color #f669e8 radius 7.3
> marker #2 position 5778,5645,2672 color #ff2c2e radius 30
> marker link #2:124,125 color #f669e8 radius 7.3
> marker #2 position 5655,5590,2672 color #ff2c2e radius 30
> marker link #2:125,126 color #f669e8 radius 7.3
> marker #2 position 5563,5535,2672 color #ff2c2e radius 30
> marker link #2:126,127 color #f669e8 radius 7.3
> marker #2 position 5412,5450,2672 color #ff2c2e radius 30
> marker link #2:127,128 color #f669e8 radius 7.3
> marker #2 position 5289,5356,2672 color #ff2c2e radius 30
> marker link #2:128,129 color #f669e8 radius 7.3
> marker #2 position 5214,5199,2672 color #ff2c2e radius 30
> marker link #2:129,130 color #f669e8 radius 7.3
> marker #2 position 5125,4996,2672 color #ff2c2e radius 30
> marker link #2:130,131 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:131,94 color #f669e8 radius 7.3
> ui mousemode right "mark plane"
> marker #2 position 5760,6750,2672 color #ff2c2e radius 30
> marker link #2:94,132 color #f669e8 radius 7.3
> ui mousemode right "delete markers"
> marker delete #2:94,132 linksOnly true
> ui mousemode right "mark plane"
> marker #2 position 5850,6524,2672 color #ff2c2e radius 30
> marker link #2:132,133 color #f669e8 radius 7.3
> marker #2 position 5964,6362,2672 color #ff2c2e radius 30
> marker link #2:133,134 color #f669e8 radius 7.3
> marker #2 position 6122,6231,2672 color #ff2c2e radius 30
> marker link #2:134,135 color #f669e8 radius 7.3
> marker #2 position 6279,6144,2672 color #ff2c2e radius 30
> marker link #2:135,136 color #f669e8 radius 7.3
> marker #2 position 6495,6093,2672 color #ff2c2e radius 30
> marker link #2:136,137 color #f669e8 radius 7.3
> marker #2 position 6688,6125,2672 color #ff2c2e radius 30
> marker link #2:137,138 color #f669e8 radius 7.3
> marker #2 position 6872,6248,2672 color #ff2c2e radius 30
> marker link #2:138,139 color #f669e8 radius 7.3
> marker #2 position 6993,6323,2672 color #ff2c2e radius 30
> marker link #2:139,140 color #f669e8 radius 7.3
> marker #2 position 5773,6944,2672 color #ff2c2e radius 30
> marker link #2:140,141 color #f669e8 radius 7.3
> ui mousemode right "delete markers"
> marker delete #2:140,141 linksOnly true
> ui mousemode right "mark plane"
> marker #2 position 5797,7116,2672 color #ff2c2e radius 30
> marker link #2:141,142 color #f669e8 radius 7.3
> marker #2 position 5863,7225,2672 color #ff2c2e radius 30
> marker link #2:142,143 color #f669e8 radius 7.3
> marker #2 position 5975,7343,2672 color #ff2c2e radius 30
> marker link #2:143,144 color #f669e8 radius 7.3
> marker #2 position 6086,7448,2672 color #ff2c2e radius 30
> marker link #2:144,145 color #f669e8 radius 7.3
> marker #2 position 6211,7588,2672 color #ff2c2e radius 30
> marker link #2:145,146 color #f669e8 radius 7.3
> marker #2 position 6378,7642,2672 color #ff2c2e radius 30
> marker link #2:146,147 color #f669e8 radius 7.3
> marker #2 position 6536,7642,2672 color #ff2c2e radius 30
> marker link #2:147,148 color #f669e8 radius 7.3
> marker #2 position 6706,7614,2672 color #ff2c2e radius 30
> marker link #2:148,149 color #f669e8 radius 7.3
> marker #2 position 6811,7545,2672 color #ff2c2e radius 30
> marker link #2:149,150 color #f669e8 radius 7.3
> marker #2 position 6913,7460,2672 color #ff2c2e radius 30
> marker link #2:150,151 color #f669e8 radius 7.3
> marker #2 position 6977,7385,2672 color #ff2c2e radius 30
> marker link #2:151,152 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:152,141 color #f669e8 radius 7.3
> ui mousemode right "delete markers"
> marker delete #2:152,141 linksOnly true
> marker delete #2:132
> ui mousemode right "mark plane"
> marker #2 position 5804,6711,2672 color #ff2c2e radius 30
> marker link #2:141,153 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:153,133 color #f669e8 radius 7.3
> color zone #3 near #2 distance 50 bondPointSpacing 15
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.4 models
> hide #!4.3 models
> hide #!4.1 models
> hide #!4.2 models
> hide #!4 models
> show #!4 models
> show #!4.1 models
> show #!4.2 models
> show #!4.3 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.4 models
> show #!4.4 models
> close #4
> show #!2 models
> show #!3 models
> ui mousemode right "mark plane"
> marker #2 position 5205,4813,1533 color #ff2c2e radius 30
> marker link #2:133,154 color #f669e8 radius 7.3
> ui mousemode right "delete markers"
> marker delete #2:154
> ui mousemode right "mark plane"
> marker #2 position 5199,4874,1533 color #ff2c2e radius 30
> marker #2 position 5225,4475,1533 color #ff2c2e radius 30
> marker link #2:155,156 color #f669e8 radius 7.3
> marker #2 position 5428,4206,1533 color #ff2c2e radius 30
> marker link #2:156,157 color #f669e8 radius 7.3
> marker #2 position 5619,4015,1533 color #ff2c2e radius 30
> marker link #2:157,158 color #f669e8 radius 7.3
> marker #2 position 5824,3884,1533 color #ff2c2e radius 30
> marker link #2:158,159 color #f669e8 radius 7.3
> marker #2 position 6213,3870,1533 color #ff2c2e radius 30
> marker link #2:159,160 color #f669e8 radius 7.3
> marker #2 position 6446,3992,1533 color #ff2c2e radius 30
> marker link #2:160,161 color #f669e8 radius 7.3
> marker #2 position 6695,4237,1533 color #ff2c2e radius 30
> marker link #2:161,162 color #f669e8 radius 7.3
> marker #2 position 6845,4461,1533 color #ff2c2e radius 30
> marker link #2:162,163 color #f669e8 radius 7.3
> marker #2 position 6880,4683,1533 color #ff2c2e radius 30
> marker link #2:163,164 color #f669e8 radius 7.3
> marker #2 position 6852,4939,1533 color #ff2c2e radius 30
> marker link #2:164,165 color #f669e8 radius 7.3
> marker #2 position 6803,5147,1533 color #ff2c2e radius 30
> marker link #2:165,166 color #f669e8 radius 7.3
> marker #2 position 6629,5363,1533 color #ff2c2e radius 30
> marker link #2:166,167 color #f669e8 radius 7.3
> marker #2 position 6414,5502,1533 color #ff2c2e radius 30
> marker link #2:167,168 color #f669e8 radius 7.3
> marker #2 position 6197,5564,1533 color #ff2c2e radius 30
> marker link #2:168,169 color #f669e8 radius 7.3
> marker #2 position 5955,5632,1533 color #ff2c2e radius 30
> marker link #2:169,170 color #f669e8 radius 7.3
> marker #2 position 5760,5597,1533 color #ff2c2e radius 30
> marker link #2:170,171 color #f669e8 radius 7.3
> marker #2 position 5492,5359,1533 color #ff2c2e radius 30
> marker link #2:171,172 color #f669e8 radius 7.3
> marker #2 position 5277,5142,1533 color #ff2c2e radius 30
> marker link #2:172,173 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:173,155 color #f669e8 radius 7.3
> select #3
3 models selected
> ui mousemode right "mark plane"
> marker #2 position 5626,7271,1533 color #ff2c2e radius 30
> marker #2 position 5572,6974,1533 color #ff2c2e radius 30
> marker link #2:174,175 color #f669e8 radius 7.3
> marker #2 position 5531,6602,1533 color #ff2c2e radius 30
> marker link #2:175,176 color #f669e8 radius 7.3
> marker #2 position 5574,6457,1533 color #ff2c2e radius 30
> marker link #2:176,177 color #f669e8 radius 7.3
> marker #2 position 5770,6195,1533 color #ff2c2e radius 30
> marker link #2:177,178 color #f669e8 radius 7.3
> marker #2 position 5903,6016,1533 color #ff2c2e radius 30
> marker link #2:178,179 color #f669e8 radius 7.3
> marker #2 position 6148,5896,1533 color #ff2c2e radius 30
> marker link #2:179,180 color #f669e8 radius 7.3
> marker #2 position 6499,5814,1533 color #ff2c2e radius 30
> marker link #2:180,181 color #f669e8 radius 7.3
> marker #2 position 6823,5842,1533 color #ff2c2e radius 30
> marker link #2:181,182 color #f669e8 radius 7.3
> marker #2 position 7166,5956,1533 color #ff2c2e radius 30
> marker link #2:182,183 color #f669e8 radius 7.3
> marker #2 position 7396,6164,1533 color #ff2c2e radius 30
> marker link #2:183,184 color #f669e8 radius 7.3
> marker #2 position 7594,6436,1533 color #ff2c2e radius 30
> marker link #2:184,185 color #f669e8 radius 7.3
> marker #2 position 7580,6665,1533 color #ff2c2e radius 30
> marker link #2:185,186 color #f669e8 radius 7.3
> marker #2 position 7548,6909,1533 color #ff2c2e radius 30
> marker link #2:186,187 color #f669e8 radius 7.3
> marker #2 position 7523,7142,1533 color #ff2c2e radius 30
> marker link #2:187,188 color #f669e8 radius 7.3
> marker #2 position 7361,7428,1533 color #ff2c2e radius 30
> marker link #2:188,189 color #f669e8 radius 7.3
> marker #2 position 7201,7607,1533 color #ff2c2e radius 30
> marker link #2:189,190 color #f669e8 radius 7.3
> marker #2 position 7020,7766,1533 color #ff2c2e radius 30
> marker link #2:190,191 color #f669e8 radius 7.3
> marker #2 position 6769,7885,1533 color #ff2c2e radius 30
> marker link #2:191,192 color #f669e8 radius 7.3
> marker #2 position 6512,7855,1533 color #ff2c2e radius 30
> marker link #2:192,193 color #f669e8 radius 7.3
> marker #2 position 6288,7783,1533 color #ff2c2e radius 30
> marker link #2:193,194 color #f669e8 radius 7.3
> marker #2 position 5973,7671,1533 color #ff2c2e radius 30
> marker link #2:194,195 color #f669e8 radius 7.3
> marker #2 position 5762,7479,1533 color #ff2c2e radius 30
> marker link #2:195,196 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:196,174 color #f669e8 radius 7.3
> select #3
3 models selected
> select up
177 atoms, 176 bonds, 177 residues, 6 models selected
> select subtract #2
5 models selected
> color zone #3 near #2 distance 500 bondPointSpacing 150
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4 models
> hide #!2 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4.2 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.4 models
> show #!4.4 models
> show #!2 models
> hide #!2 models
> show #!4.1 models
> hide #!4.1 models
> show #!3 models
> hide #!3 models
> select add #3
5 models selected
> show #!4.1 models
> show #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.3 models
> hide #!4.4 models
> hide #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.4 models
> show #!4.3 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!2 models
> hide #!4.1 models
> close #4
> color zone #3 near #2 distance 30 bondPointSpacing 15
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> hide #!4.3 models
> hide #!4.4 models
> hide #!4.1 models
> show #!4.2 models
> show #!4.3 models
> show #!4.4 models
> close #4
> color zone #3 near #2 distance 800 bondPointSpacing 200
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4.1 models
> close #4
> color zone #3 near #2 distance 1000 bondPointSpacing 200
> color zone #3 near #2 distance 1000 bondPointSpacing 500
Traceback (most recent call last):
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1380, in color_zone
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color zone #3 near #2 distance 1000 bondPointSpacing 500
Traceback (most recent call last):
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1380, in color_zone
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color zone #3 near #2 distance 1000 bondPointSpacing 300
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4.1 models
> hide #!4.2 models
> hide #!4.3 models
> hide #!4.4 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.2 models
> show #!4.3 models
> show #!4.4 models
> hide #!4 models
> show #!4 models
> volume #4.3 style surface
> volume #4.4 style surface
> volume #4.2 style surface
> volume #4.2 level 30.82
> volume #4.3 level 33.44
> volume #4.4 level 27.31
> volume #4.4 style image
> volume #4.4
> volume #4.3 style image
> volume #4.2 style image
> volume #4.4
> volume #4.4 style surface
> volume #4.4 style image
> volume #4.4 level -33.12,0 level 61.4,0.9538 level 146.7,1
> volume #4.2 style mesh
> volume #4.2 style surface
> volume #4.2 style image
> volume #4.2
> volume #4.2 colorMode opaque8 imageMode "box faces"
> volume #4.2 colorMode auto8 imageMode "tilted slab" tiltedSlabAxis
> 0.1075,0.03071,-0.9937 tiltedSlabOffset -498.2 tiltedSlabSpacing 14.6
> volume #4.2 colorMode opaque8 positionPlanes 511,511,0 imageMode orthoplanes
> volume #4.2 colorMode auto8 imageMode "full region"
> volume #4.2 style surface
> volume #4.2
> volume #4.2 color #ff3531
> volume #4.3 color #fffb57 color #ffffb3 color #ffffb3
> volume #4.3 color #ff65f5 color #ffffb3 color #ffffb3
> volume #4.4 color #ffffb3 color #5a51ff color #ffffb3
> volume #4.4 level -30.31,0 level 61.4,0.9538 level 146.7,1
> volume #4.4 style surface
> volume #4.4 style mesh
> hide #!4 models
> show #!4 models
> show #!4.1 models
> show #4.1.1 models
> hide #4.1.1 models
> show #4.2.2 models
> hide #4.2.2 models
> hide #4.2.1 models
> show #4.2.1 models
> hide #4.2.1 models
> show #4.2.1 models
> show #4.2.2 models
> hide #4.2.2 models
> hide #4.2.1 models
> show #4.2.1 models
> show #4.2.2 models
> show #4.3.1 models
> hide #4.3.1 models
> hide #4.3.2 models
> show #4.3.2 models
> show #4.3.1 models
> hide #4.4.1 models
> show #4.4.2 models
> hide #4.4.2 models
> show #4.4.2 models
> show #4.4.1 models
> hide #4.4.1 models
> hide #4.3.1 models
> hide #4.2.2 models
> show #4.2.2 models
> hide #4.2.1 models
> hide #!4.1 models
> hide #4.2.2 models
> show #4.2.2 models
> hide #4.2.2 models
> show #4.2.2 models
> show #4.3.1 models
> hide #4.3.1 models
> hide #4.4.2 models
> show #4.4.2 models
> hide #4.4.2 models
> show #4.4.2 models
> hide #4.4.2 models
> show #4.4.2 models
> hide #4.4.2 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> hide #4.3.2 models
> show #4.3.2 models
> hide #4.2.2 models
> show #4.2.2 models
> hide #!4.2 models
> show #!4.2 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4 models
> show #!4 models
> close #4
> color zone #3 near #2 distance 1000 bondPointSpacing 300
> volume splitbyzone #3
Opened emd_54480.map 0 as #4.1, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 1 as #4.2, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 2 as #4.3, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
Opened emd_54480.map 3 as #4.4, grid size 1024,1024,1, pixel 14.6,14.6,14.6,
shown at step 1, values float32
> hide #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.4 models
> hide #!4.3 models
> show #!4.3 models
> show #!4.4 models
> show #4.3.1 models
> hide #4.3.1 models
> volume #4.4 level -33.12,0 level 42.38,0.5846 level 146.7,1
> volume #4.4 level -33.12,0 level 42.38,0.5231 level 146.7,1
> volume #4.3 level -33.12,0 level -21.5,0.01538 level 146.7,1
> volume #4.1 level -33.12,0 level 17.32,0.3231 level 146.7,1
> volume #4.1 region 0,0,0,1023,1023,0
> volume #4.1 level -33.12,0 level 40.17,0.2923 level 146.7,1
> volume #4.1 level -33.12,0 level 40.17,0.2923 level 61.52,0.9692
> volume #4.1 level -33.12,0 level 40.17,0.2923 level 60.95,0.4615
> volume #4.3 level -33.12,0 level -21.5,0.01538 level -0.381,0.4615
> hide #!4.4 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.4 models
> show #!4.4 models
> hide #!4.3 models
> show #!4.3 models
> volume #4.4 level -33.12,0 level 60,0.5231 level 146.7,1
> volume #4.4 level -33.12,0 level 150,0.5231 level 146.7,1
> volume #4.4 level -33.12,0 level 100,0.5231 level 146.7,1
> volume #4.4 level -33.12,0 level 97,0.5231 level 146.7,1
> volume #4.4 level -33.12,0 level 30.89,0.7846 level 146.7,1
> volume #4.4 style mesh
> volume #4.4 style surface
> volume #4.4 style image
> volume #4.4
> volume #4.4 level -33.12,0 level 11.85,0.7231 level 146.7,1
> volume #4.3 level -33.12,0 level -21.5,0.01538 level -4.768,0.7077
> hide #!4 models
> show #!4 models
> close #4.4
> close #4
> vop scale #3 factor -1 sd 1
Opened emd_54480.map scaled as #4, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> vop scale #3 factor -1 sd 1
Opened emd_54480.map scaled as #5, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> close #5
> select up
6 models selected
> select add #3
6 models selected
> select add #3
6 models selected
> select subtract #1
4 models selected
> select add #4
5 models selected
> select add #3
5 models selected
> show #!2 models
> hide #!2 models
> show #!2 models
> color zone #4 near #2 distance 50
color zone: No surfaces specified.
> color zone #4 near #2 distance 50
color zone: No surfaces specified.
> hide #!2 models
> show #!3 models
> hide #!3 models
> close #2
> ui mousemode right "mark plane"
> marker #2 position 4976,4901,2000 color #ff2c2e radius 30
> marker #2 position 5014,4570,2000 color #ff2c2e radius 30
> marker link #2:1,2 color #f669e8 radius 7.3
> marker #2 position 5062,4332,2000 color #ff2c2e radius 30
> marker link #2:2,3 color #f669e8 radius 7.3
> marker #2 position 5259,4077,2000 color #ff2c2e radius 30
> marker link #2:3,4 color #f669e8 radius 7.3
> marker #2 position 5481,3945,2000 color #ff2c2e radius 30
> marker link #2:4,5 color #f669e8 radius 7.3
> marker #2 position 5747,3840,2000 color #ff2c2e radius 30
> marker link #2:5,6 color #f669e8 radius 7.3
> marker #2 position 5961,3807,2000 color #ff2c2e radius 30
> marker link #2:6,7 color #f669e8 radius 7.3
> marker #2 position 6201,3809,2000 color #ff2c2e radius 30
> marker link #2:7,8 color #f669e8 radius 7.3
> marker #2 position 6459,3856,2000 color #ff2c2e radius 30
> marker link #2:8,9 color #f669e8 radius 7.3
> marker #2 position 6643,3983,2000 color #ff2c2e radius 30
> marker link #2:9,10 color #f669e8 radius 7.3
> marker #2 position 6805,4080,2000 color #ff2c2e radius 30
> marker link #2:10,11 color #f669e8 radius 7.3
> marker #2 position 6941,4250,2000 color #ff2c2e radius 30
> marker link #2:11,12 color #f669e8 radius 7.3
> marker #2 position 7017,4394,2000 color #ff2c2e radius 30
> marker link #2:12,13 color #f669e8 radius 7.3
> marker #2 position 7049,4555,2000 color #ff2c2e radius 30
> marker link #2:13,14 color #f669e8 radius 7.3
> marker #2 position 7079,4729,2000 color #ff2c2e radius 30
> marker link #2:14,15 color #f669e8 radius 7.3
> marker #2 position 7086,4989,2000 color #ff2c2e radius 30
> marker link #2:15,16 color #f669e8 radius 7.3
> marker #2 position 7005,5154,2000 color #ff2c2e radius 30
> marker link #2:16,17 color #f669e8 radius 7.3
> marker #2 position 6903,5294,2000 color #ff2c2e radius 30
> marker link #2:17,18 color #f669e8 radius 7.3
> marker #2 position 6781,5439,2000 color #ff2c2e radius 30
> marker link #2:18,19 color #f669e8 radius 7.3
> marker #2 position 6622,5556,2000 color #ff2c2e radius 30
> marker link #2:19,20 color #f669e8 radius 7.3
> marker #2 position 6415,5671,2000 color #ff2c2e radius 30
> marker link #2:20,21 color #f669e8 radius 7.3
> marker #2 position 6185,5710,2000 color #ff2c2e radius 30
> marker link #2:21,22 color #f669e8 radius 7.3
> marker #2 position 5984,5732,2000 color #ff2c2e radius 30
> marker link #2:22,23 color #f669e8 radius 7.3
> marker #2 position 5749,5692,2000 color #ff2c2e radius 30
> marker link #2:23,24 color #f669e8 radius 7.3
> marker #2 position 5519,5664,2000 color #ff2c2e radius 30
> marker link #2:24,25 color #f669e8 radius 7.3
> marker #2 position 5381,5562,2000 color #ff2c2e radius 30
> marker link #2:25,26 color #f669e8 radius 7.3
> marker #2 position 5232,5392,2000 color #ff2c2e radius 30
> marker link #2:26,27 color #f669e8 radius 7.3
> marker #2 position 5090,5230,2000 color #ff2c2e radius 30
> marker link #2:27,28 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> select /M:1@M
1 atom, 1 residue, 1 model selected
> select /M:28@M
1 atom, 1 residue, 1 model selected
> select /M:1@M
1 atom, 1 residue, 1 model selected
> ui mousemode right "link markers"
> marker link #2:1,28 color #f669e8 radius 7.3
> select #4
2 models selected
> ui mousemode right "mark plane"
> marker #2 position 5524,6535,2000 color #ff2c2e radius 30
> marker #2 position 5590,6349,2000 color #ff2c2e radius 30
> marker link #2:29,30 color #f669e8 radius 7.3
> marker #2 position 5766,6120,2000 color #ff2c2e radius 30
> marker link #2:30,31 color #f669e8 radius 7.3
> marker #2 position 5949,5997,2000 color #ff2c2e radius 30
> marker link #2:31,32 color #f669e8 radius 7.3
> marker #2 position 6150,5927,2000 color #ff2c2e radius 30
> marker link #2:32,33 color #f669e8 radius 7.3
> marker #2 position 6350,5849,2000 color #ff2c2e radius 30
> marker link #2:33,34 color #f669e8 radius 7.3
> marker #2 position 6619,5789,2000 color #ff2c2e radius 30
> marker link #2:34,35 color #f669e8 radius 7.3
> marker #2 position 6850,5801,2000 color #ff2c2e radius 30
> marker link #2:35,36 color #f669e8 radius 7.3
> marker #2 position 7082,5869,2000 color #ff2c2e radius 30
> marker link #2:36,37 color #f669e8 radius 7.3
> marker #2 position 7244,5951,2000 color #ff2c2e radius 30
> marker link #2:37,38 color #f669e8 radius 7.3
> marker #2 position 7355,6053,2000 color #ff2c2e radius 30
> marker link #2:38,39 color #f669e8 radius 7.3
> marker #2 position 7465,6177,2000 color #ff2c2e radius 30
> marker link #2:39,40 color #f669e8 radius 7.3
> marker #2 position 7562,6338,2000 color #ff2c2e radius 30
> marker link #2:40,41 color #f669e8 radius 7.3
> marker #2 position 7653,6546,2000 color #ff2c2e radius 30
> marker link #2:41,42 color #f669e8 radius 7.3
> marker #2 position 7672,6738,2000 color #ff2c2e radius 30
> marker link #2:42,43 color #f669e8 radius 7.3
> marker #2 position 7675,6884,2000 color #ff2c2e radius 30
> marker link #2:43,44 color #f669e8 radius 7.3
> marker #2 position 7653,7075,2000 color #ff2c2e radius 30
> marker link #2:44,45 color #f669e8 radius 7.3
> marker #2 position 7575,7235,2000 color #ff2c2e radius 30
> marker link #2:45,46 color #f669e8 radius 7.3
> marker #2 position 7463,7433,2000 color #ff2c2e radius 30
> marker link #2:46,47 color #f669e8 radius 7.3
> marker #2 position 7345,7572,2000 color #ff2c2e radius 30
> marker link #2:47,48 color #f669e8 radius 7.3
> marker #2 position 7219,7692,2000 color #ff2c2e radius 30
> marker link #2:48,49 color #f669e8 radius 7.3
> marker #2 position 7017,7785,2000 color #ff2c2e radius 30
> marker link #2:49,50 color #f669e8 radius 7.3
> marker #2 position 6765,7842,2000 color #ff2c2e radius 30
> marker link #2:50,51 color #f669e8 radius 7.3
> marker #2 position 6593,7860,2000 color #ff2c2e radius 30
> marker link #2:51,52 color #f669e8 radius 7.3
> marker #2 position 6368,7841,2000 color #ff2c2e radius 30
> marker link #2:52,53 color #f669e8 radius 7.3
> marker #2 position 6118,7754,2000 color #ff2c2e radius 30
> marker link #2:53,54 color #f669e8 radius 7.3
> marker #2 position 5937,7693,2000 color #ff2c2e radius 30
> marker link #2:54,55 color #f669e8 radius 7.3
> marker #2 position 5734,7510,2000 color #ff2c2e radius 30
> marker link #2:55,56 color #f669e8 radius 7.3
> marker #2 position 5617,7366,2000 color #ff2c2e radius 30
> marker link #2:56,57 color #f669e8 radius 7.3
> marker #2 position 5460,7045,2000 color #ff2c2e radius 30
> marker link #2:57,58 color #f669e8 radius 7.3
> marker #2 position 5445,6795,2000 color #ff2c2e radius 30
> marker link #2:58,59 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #2:59,29 color #f669e8 radius 7.3
> select #4
2 models selected
> color zone #4 near #2 distance 50
color zone: No surfaces specified.
> volume #4 region 0,0,0,1023,1023,319 step 1
> color zone #4 near #2 distance 50
> color zone #4 near #2 distance 50 bondPointSpacing 15
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #5.1, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
Opened emd_54480.map scaled 1 as #5.2, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
Opened emd_54480.map scaled 2 as #5.3, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
> hide #!5 models
> show #!5 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.2 models
> hide #!5.1 models
> hide #!5.3 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.3 models
> hide #!5.3 models
> show #!5.1 models
> hide #!5 models
> show #!5 models
> hide #!5.1 models
> show #!5.1 models
> show #!5.2 models
> show #!5.3 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.3 models
> show #!5.3 models
> show #!5.2 models
> show #!5.1 models
> close #5
> show #!4 models
> volume #4 style image region 0,0,159,1023,1023,159 step 1
> hide #2 models
> ui mousemode right "mark plane"
> marker #5 position 5185,5134,2701 color #ff2c2e radius 30
> marker #5 position 5128,4819,2701 color #ff2c2e radius 30
> marker link #5:1,2 color #f669e8 radius 7.3
> marker #5 position 5169,4491,2701 color #ff2c2e radius 30
> marker link #5:2,3 color #f669e8 radius 7.3
> marker #5 position 5294,4302,2701 color #ff2c2e radius 30
> marker link #5:3,4 color #f669e8 radius 7.3
> marker #5 position 5458,4145,2701 color #ff2c2e radius 30
> marker link #5:4,5 color #f669e8 radius 7.3
> marker #5 position 5680,4034,2701 color #ff2c2e radius 30
> marker link #5:5,6 color #f669e8 radius 7.3
> marker #5 position 5928,3999,2701 color #ff2c2e radius 30
> marker link #5:6,7 color #f669e8 radius 7.3
> marker #5 position 6145,3959,2701 color #ff2c2e radius 30
> marker link #5:7,8 color #f669e8 radius 7.3
> marker #5 position 6347,4016,2701 color #ff2c2e radius 30
> marker link #5:8,9 color #f669e8 radius 7.3
> marker #5 position 6582,4100,2701 color #ff2c2e radius 30
> marker link #5:9,10 color #f669e8 radius 7.3
> marker #5 position 6757,4206,2701 color #ff2c2e radius 30
> marker link #5:10,11 color #f669e8 radius 7.3
> marker #5 position 6875,4393,2701 color #ff2c2e radius 30
> marker link #5:11,12 color #f669e8 radius 7.3
> marker #5 position 6922,4587,2701 color #ff2c2e radius 30
> marker link #5:12,13 color #f669e8 radius 7.3
> marker #5 position 6944,4804,2701 color #ff2c2e radius 30
> marker link #5:13,14 color #f669e8 radius 7.3
> marker #5 position 6909,5012,2701 color #ff2c2e radius 30
> marker link #5:14,15 color #f669e8 radius 7.3
> marker #5 position 6825,5264,2701 color #ff2c2e radius 30
> marker link #5:15,16 color #f669e8 radius 7.3
> marker #5 position 6682,5352,2701 color #ff2c2e radius 30
> marker link #5:16,17 color #f669e8 radius 7.3
> marker #5 position 6554,5511,2701 color #ff2c2e radius 30
> marker link #5:17,18 color #f669e8 radius 7.3
> marker #5 position 5722,5627,2701 color #ff2c2e radius 30
> marker link #5:18,19 color #f669e8 radius 7.3
> marker #5 position 5574,5554,2701 color #ff2c2e radius 30
> marker link #5:19,20 color #f669e8 radius 7.3
> marker #5 position 5437,5449,2701 color #ff2c2e radius 30
> marker link #5:20,21 color #f669e8 radius 7.3
> marker #5 position 5284,5338,2701 color #ff2c2e radius 30
> marker link #5:21,22 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #5:22,1 color #f669e8 radius 7.3
> show #2 models
> hide #2 models
> hide #5 models
> ui mousemode right "mark plane"
> marker #6 position 5077,4846,1664 color #ff2c2e radius 30
> marker #6 position 5128,4502,1664 color #ff2c2e radius 30
> marker link #6:1,2 color #f669e8 radius 7.3
> marker #6 position 5263,4198,1664 color #ff2c2e radius 30
> marker link #6:2,3 color #f669e8 radius 7.3
> marker #6 position 5509,4019,1664 color #ff2c2e radius 30
> marker link #6:3,4 color #f669e8 radius 7.3
> marker #6 position 5921,3866,1664 color #ff2c2e radius 30
> marker link #6:4,5 color #f669e8 radius 7.3
> marker #6 position 6229,3858,1664 color #ff2c2e radius 30
> marker link #6:5,6 color #f669e8 radius 7.3
> marker #6 position 6507,4003,1664 color #ff2c2e radius 30
> marker link #6:6,7 color #f669e8 radius 7.3
> marker #6 position 6751,4160,1664 color #ff2c2e radius 30
> marker link #6:7,8 color #f669e8 radius 7.3
> marker #6 position 6852,4348,1664 color #ff2c2e radius 30
> marker link #6:8,9 color #f669e8 radius 7.3
> marker #6 position 6975,4667,1664 color #ff2c2e radius 30
> marker link #6:9,10 color #f669e8 radius 7.3
> marker #6 position 6962,4864,1664 color #ff2c2e radius 30
> marker link #6:10,11 color #f669e8 radius 7.3
> marker #6 position 6939,5030,1664 color #ff2c2e radius 30
> marker link #6:11,12 color #f669e8 radius 7.3
> marker #6 position 6812,5298,1664 color #ff2c2e radius 30
> marker link #6:12,13 color #f669e8 radius 7.3
> marker #6 position 6636,5419,1664 color #ff2c2e radius 30
> marker link #6:13,14 color #f669e8 radius 7.3
> marker #6 position 6480,5553,1664 color #ff2c2e radius 30
> marker link #6:14,15 color #f669e8 radius 7.3
> marker #6 position 6232,5640,1664 color #ff2c2e radius 30
> marker link #6:15,16 color #f669e8 radius 7.3
> marker #6 position 5983,5730,1664 color #ff2c2e radius 30
> marker link #6:16,17 color #f669e8 radius 7.3
> marker #6 position 5777,5636,1664 color #ff2c2e radius 30
> marker link #6:17,18 color #f669e8 radius 7.3
> marker #6 position 5474,5538,1664 color #ff2c2e radius 30
> marker link #6:18,19 color #f669e8 radius 7.3
> marker #6 position 5306,5393,1664 color #ff2c2e radius 30
> marker link #6:19,20 color #f669e8 radius 7.3
> marker #6 position 5194,5161,1664 color #ff2c2e radius 30
> marker link #6:20,21 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #6:21,1 color #f669e8 radius 7.3
> select add #6
21 atoms, 21 bonds, 21 residues, 1 model selected
> select subtract #6
Nothing selected
> show #2 models
> show #5 models
> color zone #4 near #2 #5 #6 distance 50
> color zone #4 near #2 #5 #6 distance 50 bondPointSpacing 15
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #7.1, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 1 as #7.2, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 2 as #7.3, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #5 models
> hide #6 models
> hide #2 models
> hide #!7 models
> show #!7 models
> hide #!7.1 models
> hide #!7.2 models
> hide #!7.3 models
> show #!7.3 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.1 models
> hide #!7.1 models
> hide #!7.3 models
> show #!7.1 models
> hide #!7.1 models
> show #!7.2 models
> show #!7.3 models
> show #!7.1 models
> hide #!7.1 models
> hide #!7.2 models
> hide #!7.3 models
> show #!7.1 models
> show #!7.2 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.2 models
> hide #!7.3 models
> show #!7.2 models
> show #!7.3 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!7 models
> close #7
> color zone #4 near #2 #5 #6 distance 500
> color zone #4 near #2 #5 #6 distance 500 bondPointSpacing 200
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #7.1, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 1 as #7.2, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 2 as #7.3, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #!7.2 models
> hide #!7.3 models
> hide #!7.1 models
> show #!7.2 models
> show #!7.3 models
> close #7
> color zone #4 near #2 #5 #6 distance 800
> color zone #4 near #2 #5 #6 distance 800 bondPointSpacing 400
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #7.1, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 1 as #7.2, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 2 as #7.3, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> show #!7.1 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.3 models
> hide #!7.1 models
> hide #!7.2 models
> show #!7.1 models
> hide #!7.1 models
> show #!7.2 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> hide #!7.2 models
> close #7
> color zone #4 near #2 #5 #6 distance 1000
> color zone #4 near #2 #5 #6 distance 1000 bondPointSpacing 600
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #7.1, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 1 as #7.2, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
Opened emd_54480.map scaled 2 as #7.3, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #!7.2 models
> hide #!7.3 models
> hide #!7.1 models
> show #!7.2 models
> show #!7.3 models
> hide #!7.3 models
> volume #7.2 style surface
> volume #7.2 style image
> volume #7.2
> volume #7.2 style surface
> volume #7.2 style image
> hide #!7 models
> hide #!7.2 models
> show #!4 models
> volume #4 region 0,0,0,1023,1023,319 step 1
> volume #4 style surface region 0,0,0,1023,1023,319 step 1
> show #!7 models
> hide #!7 models
> close #7
> color zone #4 near #2 #5 #6 distance 1000
> color zone #4 near #2 #5 #6 distance 1000 bondPointSpacing 600
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #7.1, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
Opened emd_54480.map scaled 1 as #7.2, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
Opened emd_54480.map scaled 2 as #7.3, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
> hide #!7 models
> show #!7 models
> hide #!7.2 models
> hide #!7.3 models
> hide #!7.1 models
> show #!7.2 models
> show #!7.3 models
> volume #7.3 level 2.162
> color #7.2 #ffef20ff models
> color #7.2 #f57cffff models
> volume #7.3 level 2.542
> volume #7.3 level 0.2118
> volume #7.3 level 1.607
> volume #7.2 level 1.889
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> color #7.2 #f9ff33ff models
> color #7.2 #e3ffbfff models
> hide #!7.2 models
> hide #!7.3 models
> hide #!7 models
> show #!7.2 models
> hide #!7.2 models
> show #!4 models
> volume #4 style image region 0,0,159,1023,1023,159 step 1
> ui mousemode right "mark plane"
> marker #8 position 1.175e+04,9558,2321 color #ff2c2e radius 30
> marker #8 position 1.171e+04,9213,2321 color #ff2c2e radius 30
> marker link #8:1,2 color #f669e8 radius 7.3
> marker #8 position 1.17e+04,8932,2321 color #ff2c2e radius 30
> marker link #8:2,3 color #f669e8 radius 7.3
> marker #8 position 1.175e+04,8559,2321 color #ff2c2e radius 30
> marker link #8:3,4 color #f669e8 radius 7.3
> marker #8 position 1.187e+04,8277,2321 color #ff2c2e radius 30
> marker link #8:4,5 color #f669e8 radius 7.3
> marker #8 position 1.208e+04,7998,2321 color #ff2c2e radius 30
> marker link #8:5,6 color #f669e8 radius 7.3
> marker #8 position 1.235e+04,7788,2321 color #ff2c2e radius 30
> marker link #8:6,7 color #f669e8 radius 7.3
> marker #8 position 1.268e+04,7639,2321 color #ff2c2e radius 30
> marker link #8:7,8 color #f669e8 radius 7.3
> marker #8 position 1.294e+04,7551,2321 color #ff2c2e radius 30
> marker link #8:8,9 color #f669e8 radius 7.3
> marker #8 position 1.332e+04,7547,2321 color #ff2c2e radius 30
> marker link #8:9,10 color #f669e8 radius 7.3
> marker #8 position 1.356e+04,7589,2321 color #ff2c2e radius 30
> marker link #8:10,11 color #f669e8 radius 7.3
> marker #8 position 1.375e+04,7670,2321 color #ff2c2e radius 30
> marker link #8:11,12 color #f669e8 radius 7.3
> marker #8 position 1.395e+04,7740,2321 color #ff2c2e radius 30
> marker link #8:12,13 color #f669e8 radius 7.3
> marker #8 position 1.414e+04,7840,2321 color #ff2c2e radius 30
> marker link #8:13,14 color #f669e8 radius 7.3
> marker #8 position 1.425e+04,8023,2321 color #ff2c2e radius 30
> marker link #8:14,15 color #f669e8 radius 7.3
> marker #8 position 1.438e+04,8162,2321 color #ff2c2e radius 30
> marker link #8:15,16 color #f669e8 radius 7.3
> marker #8 position 1.451e+04,8319,2321 color #ff2c2e radius 30
> marker link #8:16,17 color #f669e8 radius 7.3
> marker #8 position 1.46e+04,8516,2321 color #ff2c2e radius 30
> marker link #8:17,18 color #f669e8 radius 7.3
> marker #8 position 1.467e+04,8691,2321 color #ff2c2e radius 30
> marker link #8:18,19 color #f669e8 radius 7.3
> marker #8 position 1.47e+04,8923,2321 color #ff2c2e radius 30
> marker link #8:19,20 color #f669e8 radius 7.3
> marker #8 position 1.473e+04,9157,2321 color #ff2c2e radius 30
> marker link #8:20,21 color #f669e8 radius 7.3
> marker #8 position 1.472e+04,9414,2321 color #ff2c2e radius 30
> marker link #8:21,22 color #f669e8 radius 7.3
> marker #8 position 1.466e+04,9653,2321 color #ff2c2e radius 30
> marker link #8:22,23 color #f669e8 radius 7.3
> marker #8 position 1.455e+04,9846,2321 color #ff2c2e radius 30
> marker link #8:23,24 color #f669e8 radius 7.3
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> marker link #8:24,25 color #f669e8 radius 7.3
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> marker link #8:25,26 color #f669e8 radius 7.3
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> marker link #8:26,27 color #f669e8 radius 7.3
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> marker link #8:27,28 color #f669e8 radius 7.3
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> marker link #8:30,31 color #f669e8 radius 7.3
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> marker link #8:31,32 color #f669e8 radius 7.3
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> marker link #8:32,33 color #f669e8 radius 7.3
> marker #8 position 1.265e+04,1.048e+04,2321 color #ff2c2e radius 30
> marker link #8:33,34 color #f669e8 radius 7.3
> marker #8 position 1.247e+04,1.038e+04,2321 color #ff2c2e radius 30
> marker link #8:34,35 color #f669e8 radius 7.3
> marker #8 position 1.231e+04,1.029e+04,2321 color #ff2c2e radius 30
> marker link #8:35,36 color #f669e8 radius 7.3
> marker #8 position 1.21e+04,1.003e+04,2321 color #ff2c2e radius 30
> marker link #8:36,37 color #f669e8 radius 7.3
> marker #8 position 1.194e+04,9859,2321 color #ff2c2e radius 30
> marker link #8:37,38 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #8:38,1 color #f669e8 radius 7.3
> select #4
3 models selected
> hide #8 models
> show #8 models
> hide #8 models
> ui mousemode right "mark plane"
> marker #9 position 1.17e+04,9299,2497 color #ff2c2e radius 30
> marker #9 position 1.168e+04,9022,2497 color #ff2c2e radius 30
> marker link #9:1,2 color #f669e8 radius 7.3
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> marker link #9:2,3 color #f669e8 radius 7.3
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> marker link #9:3,4 color #f669e8 radius 7.3
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> marker link #9:4,5 color #f669e8 radius 7.3
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> marker link #9:16,17 color #f669e8 radius 7.3
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> marker link #9:17,18 color #f669e8 radius 7.3
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> marker link #9:18,19 color #f669e8 radius 7.3
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> marker link #9:19,20 color #f669e8 radius 7.3
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> marker link #9:20,21 color #f669e8 radius 7.3
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> marker link #9:21,22 color #f669e8 radius 7.3
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> marker link #9:22,23 color #f669e8 radius 7.3
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> marker link #9:23,24 color #f669e8 radius 7.3
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> marker link #9:24,25 color #f669e8 radius 7.3
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> marker link #9:25,26 color #f669e8 radius 7.3
> marker #9 position 1.388e+04,1.051e+04,2497 color #ff2c2e radius 30
> marker link #9:26,27 color #f669e8 radius 7.3
> marker #9 position 1.36e+04,1.058e+04,2497 color #ff2c2e radius 30
> marker link #9:27,28 color #f669e8 radius 7.3
> marker #9 position 1.329e+04,1.063e+04,2497 color #ff2c2e radius 30
> marker link #9:28,29 color #f669e8 radius 7.3
> marker #9 position 1.291e+04,1.054e+04,2497 color #ff2c2e radius 30
> marker link #9:29,30 color #f669e8 radius 7.3
> marker #9 position 1.26e+04,1.044e+04,2497 color #ff2c2e radius 30
> marker link #9:30,31 color #f669e8 radius 7.3
> marker #9 position 1.23e+04,1.025e+04,2497 color #ff2c2e radius 30
> marker link #9:31,32 color #f669e8 radius 7.3
> marker #9 position 1.207e+04,1.004e+04,2497 color #ff2c2e radius 30
> marker link #9:32,33 color #f669e8 radius 7.3
> marker #9 position 1.189e+04,9747,2497 color #ff2c2e radius 30
> marker link #9:33,34 color #f669e8 radius 7.3
> marker #9 position 1.177e+04,9578,2497 color #ff2c2e radius 30
> marker link #9:34,35 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #9:35,1 color #f669e8 radius 7.3
> select #4
3 models selected
> hide #9 models
> ui mousemode right "mark plane"
> marker #10 position 1.182e+04,9226,3051 color #ff2c2e radius 30
> marker #10 position 1.181e+04,8961,3051 color #ff2c2e radius 30
> marker link #10:1,2 color #f669e8 radius 7.3
> marker #10 position 1.181e+04,8729,3051 color #ff2c2e radius 30
> marker link #10:2,3 color #f669e8 radius 7.3
> marker #10 position 1.188e+04,8476,3051 color #ff2c2e radius 30
> marker link #10:3,4 color #f669e8 radius 7.3
> marker #10 position 1.2e+04,8253,3051 color #ff2c2e radius 30
> marker link #10:4,5 color #f669e8 radius 7.3
> marker #10 position 1.217e+04,8068,3051 color #ff2c2e radius 30
> marker link #10:5,6 color #f669e8 radius 7.3
> marker #10 position 1.235e+04,7890,3051 color #ff2c2e radius 30
> marker link #10:6,7 color #f669e8 radius 7.3
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> marker link #10:7,8 color #f669e8 radius 7.3
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> marker link #10:25,26 color #f669e8 radius 7.3
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> marker link #10:26,27 color #f669e8 radius 7.3
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> marker link #10:27,28 color #f669e8 radius 7.3
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> marker link #10:28,29 color #f669e8 radius 7.3
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> marker link #10:29,30 color #f669e8 radius 7.3
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> marker link #10:30,31 color #f669e8 radius 7.3
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> marker link #10:31,32 color #f669e8 radius 7.3
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> marker link #10:32,33 color #f669e8 radius 7.3
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> marker link #10:33,34 color #f669e8 radius 7.3
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> marker link #10:34,35 color #f669e8 radius 7.3
> marker #10 position 1.212e+04,9944,3051 color #ff2c2e radius 30
> marker link #10:35,36 color #f669e8 radius 7.3
> marker #10 position 1.197e+04,9691,3051 color #ff2c2e radius 30
> marker link #10:36,37 color #f669e8 radius 7.3
> marker #10 position 1.186e+04,9484,3051 color #ff2c2e radius 30
> marker link #10:37,38 color #f669e8 radius 7.3
> ui mousemode right "link markers"
> marker link #10:38,1 color #f669e8 radius 7.3
> hide #10 models
> select add #10
38 atoms, 38 bonds, 38 residues, 1 model selected
> select subtract #10
Nothing selected
> color zone #4 near #8 #9 #10 distance 1000
> color zone #4 near #8 #9 #10 distance 1000 bondPointSpacing 600
Traceback (most recent call last):
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1380, in color_zone
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> volume #4 region 0,0,0,1023,1023,319 step 1
> volume #4 style surface region 0,0,0,1023,1023,319 step 1
> color zone #4 near #8 #9 #10 distance 1000
> color zone #4 near #8 #9 #10 distance 1000 bondPointSpacing 400
Traceback (most recent call last):
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1380, in color_zone
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color zone #4 near #8 #9 #10 distance 800 bondPointSpacing 400
Traceback (most recent call last):
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1380, in color_zone
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color zone #4 near #8 #9 #10 distance 600 bondPointSpacing 400
Traceback (most recent call last):
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 322, in execute
cmd.run(cmd_text)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1380, in color_zone
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
ValueError: all the input arrays must have same number of dimensions, but the
array at index 0 has 2 dimension(s) and the array at index 1 has 1
dimension(s)
File
"/Users/guodongxie/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 60, in points_and_colors
colors = concatenate((colors, bcolors))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color zone #4 near #8 #9 #10 distance 600 bondPointSpacing 200
> volume splitbyzone #4
Opened emd_54480.map scaled 0 as #11.1, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
Opened emd_54480.map scaled 1 as #11.2, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
Opened emd_54480.map scaled 2 as #11.3, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at level 2.46, step 1, values float32
> hide #!11 models
> show #!11 models
> hide #!11.1 models
> hide #!11.2 models
> hide #!11.3 models
> show #!11.1 models
> hide #!11.1 models
> show #!11.2 models
> show #!11.3 models
> hide #!11.3 models
> volume #11.2 level 0.04262
> show #!11.3 models
> hide #!11.3 models
> volume #11.2 level 0.1226
> color #11.2 #fcff6dff models
> show #!7.2 models
> show #!4 models
> color #11.2 #fc2019ff models
> color #7.2 #12fd0fff models
> volume #4 change image level -1.346,0 level 2.656,0.8 level 5.601,1
> volume #4 level 4.306
> volume #4 level 2.711
> hide #!7.2 models
> hide #!11.2 models
> hide #!4 models
> show #!4 models
> hide #!7 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!3 models
> volume #4 style image region 0,0,159,1023,1023,159 step 1
> elipsoid radius 200,500,700
Unknown command: shape elipsoid radius 200,500,700
> shape ellipsoid radius 200,500,700
> hide #12 models
> show #12 models
> volume onemask #12 ongird #4 fullmap true valuetype float32
Expected a density maps specifier or a keyword
> volume onesmask #12 ongird #4 fullmap true valuetype float32
Expected a keyword
> volume onesmask #12 onGrid #4 fullMap true valueType float32
Opened emd_54480.map scaled masked as #13, grid size 1024,1024,1, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #!11 models
> hide #!13 models
> show #!13 models
> close #13
> show #!4 models
> select add #12
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,4905.5,0,1,0,4335.1,0,0,1,499.61
> view matrix models #12,1,0,0,6354.8,0,1,0,4845,0,0,1,688.84
> view matrix models #12,1,0,0,6841.1,0,1,0,5008.8,0,0,1,1413.1
> view matrix models #12,1,0,0,6954.3,0,1,0,4911.8,0,0,1,1479.8
> view matrix models #12,1,0,0,6920.5,0,1,0,4946.5,0,0,1,1867.2
> volume #4 region 0,0,0,1023,1023,319 step 1
> volume #4 level 0.7094,0 level 2.656,0.8 level 5.601,1
> volume #4 level 0.7094,0 level 4.18,0.7077 level 5.601,1
> volume #4 level -0.1766,0.01538 level 4.18,0.7077 level 5.601,1
> volume #4 style surface
> volume #4 step 4
> volume #4 level 1.784
> volume #4 step 2
> volume #4 level 1.218
> volume #4 level 2.098
> volume #!4 showOutlineBox false
> volume #!4 showOutlineBox true
> view matrix models #12,1,0,0,-3121.6,0,1,0,3806.4,0,0,1,1825
> ui mousemode right "crop volume"
> volume #4 region 0,0,0,1023,826,319
> volume #4 region 0,0,0,1023,643,319
> volume #4 region 341,0,0,1023,643,319
> volume #4 region 341,0,0,566,643,319
> volume #4 region 341,298,0,566,643,319
> volume #4 level 1.584
> volume #4 level 1.864
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,2973.4,0,1,0,6717.6,0,0,1,2550.5
> view matrix models #12,1,0,0,6531.4,0,1,0,6933.8,0,0,1,2739.3
> shape ellipsoid radius 1000,500,700
> shape ellipsoid radius 4000,5000,7000
> close #14
> shape ellipsoid radius 4000,1000,1000
> shape ellipsoid radius 800,1000,1000
> close #15
> close #14
> close #13
> shape ellipsoid radius 800,1000,1000
> view matrix models #12,1,0,0,6248.1,0,1,0,8456.7,0,0,1,2909.6
> view matrix models #12,1,0,0,3749.7,0,1,0,9148.7,0,0,1,4069.4
> close #12
> shape ellipsoid radius 1500,1000,1000
> shape ellipsoid radius 1500,1500,1500
> close #13
> close #12
> select add #14
1 model selected
> view matrix models #14,1,0,0,932.59,0,1,0,2807.1,0,0,1,2331.6
> view matrix models #14,1,0,0,1129.8,0,1,0,6073.5,0,0,1,38.173
> view matrix models #14,1,0,0,6641.6,0,1,0,7768.9,0,0,1,1456.6
> view matrix models #14,1,0,0,6675.9,0,1,0,7239.7,0,0,1,1916.6
> volume onesmask #14 onGrid #4 fullMap true valueType float32
Opened emd_54480.map scaled masked as #12, grid size 226,346,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> volume subtract #4 #14
volume subtract operation requires exactly two volumes
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> select subtract #14
Nothing selected
> hide #14 models
> hide #!12 models
> show #!12 models
> volume subtract #4 #12
Opened volume difference as #13, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> show #14 models
> hide #14 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> volume onesmask #14 onGrid #4 fullMap true valueType float32 invertMask true
Opened emd_54480.map scaled masked as #15, grid size 226,346,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #!15 models
> show #!15 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> close #13
> volume subtract #4 #15
Opened volume difference as #13, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> show #!15 models
> hide #!15 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #14 models
> hide #14 models
> show #!15 models
> show #!12 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!12 models
> show #!15 models
> hide #!15 models
> show #!12 models
> show #!13 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!15 models
> hide #!15 models
> close #15
> close #12
> close #13
> show #14 models
> shape ellipsoid radius 1000,1000,1000
> hide #12 models
> show #12 models
> hide #14 models
> shape ellipsoid radius 1100,1100,1100
> hide #12 models
> hide #13 models
> show #14 models
> close #14
> show #12 models
> hide #12 models
> show #13 models
> close #12
> select add #13
1 model selected
> view matrix models #13,1,0,0,1212.4,0,1,0,5714.9,0,0,1,5685
> view matrix models #13,1,0,0,9326.8,0,1,0,5174.6,0,0,1,9078.2
> view matrix models #13,1,0,0,4683.8,0,1,0,5706.7,0,0,1,8208.4
> view matrix models #13,1,0,0,2564.3,0,1,0,6807.7,0,0,1,4432.8
> view matrix models #13,1,0,0,6868.8,0,1,0,6429.8,0,0,1,2772.8
> view matrix models #13,1,0,0,6968.9,0,1,0,6496.8,0,0,1,2425.2
> view matrix models #13,1,0,0,6471,0,1,0,6793.9,0,0,1,2364.8
> view matrix models #13,1,0,0,6386.8,0,1,0,6810.2,0,0,1,2238.3
> volume onesmask #13 onGrid #4 fullMap true valueType float32
Opened emd_54480.map scaled masked as #12, grid size 226,346,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> select subtract #13
Nothing selected
> hide #13 models
> hide #!12 models
> show #!12 models
> volume subtract #4 #12
Opened volume difference as #14, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #13 models
> hide #13 models
> volume onesmask #13 onGrid #4 fullMap true valueType float32 invertMask true
Opened emd_54480.map scaled masked as #15, grid size 226,346,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> show #13 models
> hide #!15 models
> show #!15 models
> hide #13 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> volume subtract #4 #15
Opened volume difference as #16, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> ui mousemode right "crop volume"
> volume #16 region 0,0,0,1023,678,319
> volume #16 region 290,0,0,1023,678,319
> volume #16 region 290,0,0,609,678,319
> volume #16 region 290,344,0,609,678,319
> volume #16 region 290,344,0,609,605,319
> volume #16 region 290,344,0,558,605,319
> volume #16 region 290,344,42,558,605,319
> volume #16 region 343,344,42,558,605,319
> volume #!16 showOutlineBox false
> hide #!16 models
> show #!4 models
> volume #4 region 0,298,0,566,643,319
> volume #4 region 0,298,0,566,718,319
> volume #4 region 0,298,0,870,718,319
> volume #4 region 0,0,0,870,718,319
> volume #4 region 0,0,0,870,1023,319
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 0,0,286,1023,1023,319
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 655,0,0,1023,1023,319
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 1,0,0,1023,1023,319
> volume #4 region 28,0,0,1023,1023,319
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 0,609,0,1023,1023,319
> volume #4 region 0,0,0,1023,1023,319
> show #13 models
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 0,0,297,1023,1023,319
> volume #4 region 0,0,0,1023,1023,319
> color #16 #d52c22ff models
> color #16 #d523a7ff models
> color #16 #7bd576ff models
> show #!16 models
> hide #13 models
> volume #16 level 1.54
> hide #!4 models
> volume #16 level 1.515
> show #!4 models
> shape ellipsoid radius 1700,1400,1800
> select add #17
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,-7065.7,0,1,0,9359.9,0,0,1,561.91
> view matrix models #17,1,0,0,-4123.3,0,1,0,13510,0,0,1,823.78
> view matrix models #17,1,0,0,2163.5,0,1,0,14862,0,0,1,-302.5
> view matrix models #17,1,0,0,2909.2,0,1,0,13918,0,0,1,2128.6
> view matrix models #17,1,0,0,4053.8,0,1,0,13823,0,0,1,1681.4
> view matrix models #17,1,0,0,3616.5,0,1,0,13153,0,0,1,2257.6
> view matrix models #17,1,0,0,3742.7,0,1,0,13257,0,0,1,2292.9
> view matrix models #17,1,0,0,-3965.5,0,1,0,15252,0,0,1,3622.9
> shape ellipsoid radius 2700,2400,1800
> close #17
> select add #18
1 model selected
> view matrix models #18,1,0,0,-7478.6,0,1,0,15363,0,0,1,2977.4
> view matrix models #18,1,0,0,-1308.6,0,1,0,12258,0,0,1,2993.2
> view matrix models #18,1,0,0,2569.6,0,1,0,14281,0,0,1,1465.6
> view matrix models #18,1,0,0,3808.9,0,1,0,13601,0,0,1,1209.1
> shape ellipsoid radius 2000,2000,1800
> close #18
> select add #16
2 models selected
> view matrix models #16,1,0,0,-5982.6,0,1,0,9157.6,0,0,1,-3842.7
> view matrix models #16,1,0,0,-17922,0,1,0,1926.8,0,0,1,-8787.8
> view matrix models #16,1,0,0,-284.3,0,1,0,627.82,0,0,1,-9964.4
> view matrix models #16,1,0,0,1392.7,0,1,0,-504.08,0,0,1,-168.26
> view matrix models #16,1,0,0,1075.1,0,1,0,-560.95,0,0,1,-108.96
> select subtract #16
Nothing selected
> select add #17
1 model selected
> view matrix models #17,1,0,0,-1363.7,0,1,0,10219,0,0,1,70.97
> select subtract #17
Nothing selected
> select add #16
2 models selected
> select subtract #16
Nothing selected
> select add #16
2 models selected
> view matrix models #16,1,0,0,-11151,0,1,0,-2085,0,0,1,-641.98
> ui mousemode right "crop volume"
> select subtract #16
Nothing selected
> volume #16 region 343,371,42,558,605,319
> volume #16 region 343,371,42,558,605,264
> volume #16 region 355,371,42,558,605,264
> volume #16 region 355,371,42,558,605,232
> volume #16 region 355,371,42,523,605,232
> volume #16 region 355,371,42,523,554,232
> volume #16 region 355,371,56,523,554,232
> volume #16 level 1.274
> volume #16 region 355,378,56,523,554,232
> volume #16 region 355,378,56,523,554,201
> volume #16 region 355,378,83,523,554,201
> volume #16 region 355,378,83,517,554,201
> volume #16 region 355,378,83,517,554,196
> volume #16 region 355,378,83,517,554,248
> select add #16
2 models selected
> volume sel showOutlineBox true
> volume sel showOutlineBox false
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> select add #16
3 models selected
> volume sel showOutlineBox true
> select add #16
3 models selected
> select add #16
3 models selected
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> volume sel region all imageMode "full region"
> volume unzone sel
> mousemode rightMode "crop volume"
> volume #16 orthoplanes xyz positionPlanes 512,512,160 style image region all
> mousemode rightMode "move planes"
> volume #16 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 2336 tiltedSlabSpacing 14.6 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume sel planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume sel showOutlineBox false
> volume #16 region 0,0,0,1023,1023,319 step 2
> volume #16 style surface region 0,0,0,1023,1023,319 step 2
> volume #16 region 0,0,0,1023,1023,319
> ui mousemode right "crop volume"
> volume #16 region 0,233,0,1023,1023,319
> volume sel showOutlineBox true
> volume #4 region 0,0,0,1023,1023,1
> volume #16 region 363,233,0,1023,1023,319
> volume #16 region 363,233,0,624,1023,319
> volume #4 region 0,0,0,1023,1023,118
> volume #16 region 0,233,0,1,1023,319
> hide #!16 models
> select add #16
3 models selected
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 0,0,0,1019,1023,319
> volume #4 region 0,0,0,1023,1023,319
> volume #4 region 471,0,0,1023,1023,319
> volume #4 region 0,0,0,1023,1023,319
> select add #17
4 models selected
> select add #16
4 models selected
> show #!16 models
> hide #!16 models
> volume #4 region 0,0,0,1023,1023,319
> ui mousemode right "translate selected models"
> view matrix models
> #16,1,0,0,-6703.3,0,1,0,1275.7,0,0,1,1073.2,#17,1,0,0,3084.2,0,1,0,13580,0,0,1,1786.2
> view matrix models
> #16,1,0,0,-6332.4,0,1,0,427.94,0,0,1,1018.3,#17,1,0,0,3455.1,0,1,0,12732,0,0,1,1731.2
> view matrix models
> #16,1,0,0,-6091.4,0,1,0,370.86,0,0,1,996.97,#17,1,0,0,3696.1,0,1,0,12675,0,0,1,1709.9
> volume onesmask #17 onGrid #4 fullMap true valueType float32 invertMask true
Opened emd_54480.map scaled masked as #18, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> volume subtract #4 #18
Opened volume difference as #19, grid size 1024,1024,320, pixel
14.6,14.6,14.6, shown at step 1, values float32
> hide #17 models
> select subtract #17
3 models selected
> show #!4 models
> volume #19 level -0.6517
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac16,10
Model Number: Z1CF000BULL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 23 days, 17 hours, 3 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
KA270H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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