![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 weeks ago
Closed 12 days ago
#19024 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003168ab000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031589f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000314893000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000313887000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031287b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031186f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000310863000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030f857000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030e84b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030d83f000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030c833000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030b827000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030a81b000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000020a2220c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.segment._segment (total: 60)
{"app_name":"ChimeraX","timestamp":"2025-09-29 00:48:47.00 -0400","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6 (24G84)","roots_installed":0,"name":"ChimeraX","incident_id":"3DFF73CF-CAB3-464F-96E1-BB5B914A8C18"}
{
"uptime" : 4300000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 13198,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2025-09-29 00:48:45.0676 -0400",
"codeSigningMonitor" : 1,
"incident" : "3DFF73CF-CAB3-464F-96E1-BB5B914A8C18",
"pid" : 8848,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-28 17:22:33.1110 -0400",
"procStartAbsTime" : 104623720205176,
"procExitAbsTime" : 105266245235486,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F5319B2A-99FE-5DFC-A089-2820E639FE6C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "216F332D-5F24-FDDF-13EF-8C5782DCD983",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "C7B9956A-D635-442A-9D14-EA5F4A39739A",
"wakeTime" : 4381149,
"sleepWakeUUID" : "33DCD15E-AB4C-4937-83CB-3B0726637761",
"sip" : "enabled",
"vmRegionInfo" : "0x62d9cd21b5a8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e2d9cd21b5a8","rawCodes":[1,249425077319080],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e2d9cd21b5a8 -> 0x000062d9cd21b5a8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":8848},
"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3bcc001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
"vmregioninfo" : "0x62d9cd21b5a8 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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fault"},"pc":{"value":6914878316},"far":{"value":0}}},{"id":43463127,"frames":[{"imageOffset":7020,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":158}],"threadState":{"x":[{"value":13495857152},{"value":0},{"value":13495320576},{"value":13495856000},{"value":5062658},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13495855984},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6914878316},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6910230528,
"size" : 5040898048,
"uuid" : "032c7bce-a479-35b8-97bc-ce7f8f80ccab"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "21fd85c95149e325a0547644f6eb7c1d938de282",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64c17a9925d75a7281053d4c",
"factorPackIds" : {
"SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
},
"deploymentId" : 240000002
},
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : {
},
"deploymentId" : 240000011
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09262025/New Images/Composition-before-JMB-color.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Sat Sep 27 12:14:37 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Manuscript/09202025/Composition-with-color.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
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Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
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Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
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Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
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Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
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Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Sat Sep 20 19:10:23 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project
> files/C.jejuni/2nd_paper/For-2nd-manuscript/After-
> review/Updated_Figures/09122025/For_Composition-
> maps/Building_Whole_Model_09102025_Backup.cxs"
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
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Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
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Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
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Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
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Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
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Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
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Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
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Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
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Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
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Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
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pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
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pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #188, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #189, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #190, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #191, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened Single-MotA-ring.mrc gaussian as #192, grid size 200,200,200, pixel
2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #193, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #194, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #195, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #196, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #197, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #198, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #199, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #200, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #201, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #202, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #203, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #204, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #205, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #206, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #207, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened Single-MotA-ring.mrc gaussian copy as #208, grid size 200,200,200,
pixel 2.14, shown at level 0.000997, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #214, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #215, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #216, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #217, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #218, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #219, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #220, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #221, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #222, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #223, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #224, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #225, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #226, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #227, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #228, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #229, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened PflAB_wout_FlgYoverlap.mrc copy gaussian copy as #230, grid size
200,200,200, pixel 2.14, shown at level 0.00045, step 1, values float32
Opened C17-FlgY_New.mrc gaussian as #231, grid size 256,256,256, pixel 2.14,
shown at level 0.0112, step 1, values float32
Opened MS-ring_New_polished.mrc gaussian as #232, grid size 256,256,256, pixel
2.14, shown at level 0.00974, step 1, values float32
Opened Basal_disk.mrc as #209, grid size 250,250,250, pixel 4.3, shown at
level 0.157, step 1, values float32
Opened C-Vrings.mrc as #4, grid size 250,250,250, pixel 4.3, shown at level
0.0283, step 1, values float32
Opened 1unit_PflABCD.mrc as #5, grid size 200,200,200, pixel 2.14, shown at
level 0.00404, step 1, values float32
Log from Wed Sep 10 10:46:36 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/shoichi/Desktop/For_Composition-
> maps/Building_Whole_Model_09102025.cxs
Opened C17_proximal-disk.mrc as #1, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened Rod.mrc as #3, grid size 250,250,250, pixel 4.3, shown at level 0.0137,
step 1, values float32
Opened Exp_ATP.mrc gaussian as #82, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened LP-ring.mrc gaussian as #83, grid size 250,250,250, pixel 4.3, shown at
level 0.0137, step 1, values float32
Opened OM.mrc gaussian as #88, grid size 250,250,250, pixel 4.3, shown at
level 0.027, step 1, values float32
Opened IM.mrc as #87, grid size 250,250,250, pixel 4.3, shown at level 0.0881,
step 1, values float32
Opened IM.mrc gaussian as #89, grid size 250,250,250, pixel 4.3, shown at
level 0.0166, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #107, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #108, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #109, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #110, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #111, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #112, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #113, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #114, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #115, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #116, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #117, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #118, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #119, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #120, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #121, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #122, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened Single_Cage_unit.mrc gaussian copy as #123, grid size 200,200,200,
pixel 2.14, shown at level 0.000576, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #124, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #125, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #126, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #127, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #128, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #129, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #130, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #131, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #132, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #133, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #134, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #135, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #136, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #137, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #138, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #139, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xMotBpg-09092025.mrc gaussian copy as #140, grid size 200,200,200,
pixel 2.14, shown at level 0.000793, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #141, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #142, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #143, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #144, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #145, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #146, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #147, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #148, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #149, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #150, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #151, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #152, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #153, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #154, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #155, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #156, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflD.mrc gaussian copy as #157, grid size 200,200,200, pixel 2.14,
shown at level 0.000785, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #158, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #159, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #160, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #161, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #162, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #163, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #164, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #165, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #166, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #167, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #168, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #169, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #170, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #171, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #172, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #173, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xPflC.mrc gaussian copy as #174, grid size 200,200,200, pixel 2.14,
shown at level 0.00107, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #175, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #176, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #177, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #178, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #179, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #180, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #181, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #182, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #183, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #184, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #185, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #186, grid size 200,200,200, pixel 2.14,
shown at level 0.000848, step 1, values float32
Opened 1xFliL.mrc gaussian copy as #187, grid size 200,200,200, pixel 2.14,
[deleted to fit within ticket limits]
> hide #!34 models
> volume #33 level 0.0282
> color #33 #42424233 models
> select clear
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/6rwy.pdb1
6rwy.pdb1 title:
Export apparatus core and inner rod of the shigella type 3 secretion system
[more info...]
Chain information for 6rwy.pdb1 #35
---
Chain | Description
A G H I J K | No description available
B C D E F | No description available
L M N O P Q R S T U V | No description available
a b c d e | No description available
f | No description available
g h i j k | No description available
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> view matrix models #35,1,0,0,-4.6654,0,1,0,-2.1689,0,0,1,2.2084
> view matrix models #35,1,0,0,-91.196,0,1,0,-40.005,0,0,1,205.21
> view matrix models #35,1,0,0,-75.528,0,1,0,-74.953,0,0,1,205.52
> fitmap #35 inMap #33
Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms
average map value = 0.03909, steps = 60
shifted from previous position = 10.9
rotated from previous position = 3.76 degrees
atoms outside contour = 11081, contour level = 0.0282
Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.99741760 -0.03266759 -0.06396064 -43.37423719
0.03327497 0.99941048 0.00845379 -87.59819848
0.06364677 -0.01056025 0.99791661 -187.77700704
Axis -0.13122930 -0.88070887 0.45511620
Axis point 2905.35176727 0.00000000 -800.81795837
Rotation angle (degrees) 4.15448090
Shift along axis -2.61987781
> fitmap #35 inMap #33
Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms
average map value = 0.03909, steps = 24
shifted from previous position = 0.00687
rotated from previous position = 0.126 degrees
atoms outside contour = 11085, contour level = 0.0282
Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.99749474 -0.03046883 -0.06384280 -44.16910568
0.03108711 0.99947870 0.00871326 -86.97208983
0.06354403 -0.01067612 0.99792193 -187.70382242
Axis -0.13577780 -0.89205051 0.43105716
Axis point 2945.80706779 0.00000000 -801.76090259
Rotation angle (degrees) 4.09446743
Shift along axis 2.66960472
> hide sel atoms
> show sel cartoons
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #35,0.99788,0.012764,-0.063768,-59.237,-0.01212,0.99987,0.010477,-74.276,0.063894,-0.0096822,0.99791,195.83
> fitmap #35 inMap #33
Fit molecule 6rwy.pdb1 (#35) to map Exp.mrc (#33) using 22743 atoms
average map value = 0.03909, steps = 60
shifted from previous position = 18.5
rotated from previous position = 0.279 degrees
atoms outside contour = 11083, contour level = 0.0282
Position of 6rwy.pdb1 (#35) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.99763100 -0.02561100 -0.06384716 -45.85770181
0.02625088 0.99961302 0.00920332 -85.57822793
0.06358675 -0.01085756 0.99791725 -187.65065701
Axis -0.14428373 -0.91654180 0.37300580
Axis point 3013.35399803 0.00000000 -796.02195102
Rotation angle (degrees) 3.98635331
Shift along axis 15.05776032
> split #35
Split 6rwy.pdb1 (#35) into 33 models
Chain information for 6rwy.pdb1 A #35.1
---
Chain | Description
A | No description available
Chain information for 6rwy.pdb1 B #35.2
---
Chain | Description
B | No description available
Chain information for 6rwy.pdb1 C #35.3
---
Chain | Description
C | No description available
Chain information for 6rwy.pdb1 D #35.4
---
Chain | Description
D | No description available
Chain information for 6rwy.pdb1 E #35.5
---
Chain | Description
E | No description available
Chain information for 6rwy.pdb1 F #35.6
---
Chain | Description
F | No description available
Chain information for 6rwy.pdb1 G #35.7
---
Chain | Description
G | No description available
Chain information for 6rwy.pdb1 H #35.8
---
Chain | Description
H | No description available
Chain information for 6rwy.pdb1 I #35.9
---
Chain | Description
I | No description available
Chain information for 6rwy.pdb1 J #35.10
---
Chain | Description
J | No description available
Chain information for 6rwy.pdb1 K #35.11
---
Chain | Description
K | No description available
Chain information for 6rwy.pdb1 L #35.12
---
Chain | Description
L | No description available
Chain information for 6rwy.pdb1 M #35.13
---
Chain | Description
M | No description available
Chain information for 6rwy.pdb1 N #35.14
---
Chain | Description
N | No description available
Chain information for 6rwy.pdb1 O #35.15
---
Chain | Description
O | No description available
Chain information for 6rwy.pdb1 P #35.16
---
Chain | Description
P | No description available
Chain information for 6rwy.pdb1 Q #35.17
---
Chain | Description
Q | No description available
Chain information for 6rwy.pdb1 R #35.18
---
Chain | Description
R | No description available
Chain information for 6rwy.pdb1 S #35.19
---
Chain | Description
S | No description available
Chain information for 6rwy.pdb1 T #35.20
---
Chain | Description
T | No description available
Chain information for 6rwy.pdb1 U #35.21
---
Chain | Description
U | No description available
Chain information for 6rwy.pdb1 V #35.22
---
Chain | Description
V | No description available
Chain information for 6rwy.pdb1 a #35.23
---
Chain | Description
a | No description available
Chain information for 6rwy.pdb1 b #35.24
---
Chain | Description
b | No description available
Chain information for 6rwy.pdb1 c #35.25
---
Chain | Description
c | No description available
Chain information for 6rwy.pdb1 d #35.26
---
Chain | Description
d | No description available
Chain information for 6rwy.pdb1 e #35.27
---
Chain | Description
e | No description available
Chain information for 6rwy.pdb1 f #35.28
---
Chain | Description
f | No description available
Chain information for 6rwy.pdb1 g #35.29
---
Chain | Description
g | No description available
Chain information for 6rwy.pdb1 h #35.30
---
Chain | Description
h | No description available
Chain information for 6rwy.pdb1 i #35.31
---
Chain | Description
i | No description available
Chain information for 6rwy.pdb1 j #35.32
---
Chain | Description
j | No description available
Chain information for 6rwy.pdb1 k #35.33
---
Chain | Description
k | No description available
> hide #!20 models
> hide #35.12 models
> hide #35.13 models
> hide #35.14 models
> hide #35.15 models
> hide #35.16 models
> hide #35.17 models
> hide #35.18 models
> hide #35.19 models
> hide #35.20 models
> hide #35.21 models
> hide #35.22 models
> hide #35.7 models
> hide #35.8 models
> hide #35.9 models
> hide #35.10 models
> hide #35.11 models
> hide #35.2 models
> hide #35.3 models
> hide #35.4 models
> hide #35.6 models
> hide #35.5 models
> hide #35.1 models
> select add #35.23
1643 atoms, 1678 bonds, 208 residues, 1 model selected
> select add #35.24
3286 atoms, 3356 bonds, 416 residues, 2 models selected
> select add #35.25
4929 atoms, 5034 bonds, 624 residues, 3 models selected
> select add #35.26
6572 atoms, 6712 bonds, 832 residues, 4 models selected
> select add #35.28
8453 atoms, 8641 bonds, 1072 residues, 5 models selected
> select add #35.27
10096 atoms, 10319 bonds, 1280 residues, 6 models selected
> select add #35.30
10759 atoms, 10995 bonds, 1366 residues, 7 models selected
> select add #35.29
11422 atoms, 11671 bonds, 1452 residues, 8 models selected
> select add #35.31
11996 atoms, 12257 bonds, 1 pseudobond, 1527 residues, 10 models selected
> select add #35.32
12524 atoms, 12797 bonds, 2 pseudobonds, 1595 residues, 12 models selected
> select add #35.33
12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 14 models selected
> save /Users/shoichi/Desktop/Exp_6rwy.pdb selectedOnly true
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/Exp_6rwy.pdb
Summary of feedback from opening /Users/shoichi/Library/CloudStorage/OneDrive-
YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-Projects/Project-
with-Bill/MxiA-project/Model-PDB-AlphaFolds/Exp_6rwy.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 11 THR A 23 1 13
Start residue of secondary structure not found: HELIX 2 2 GLN A 24 ASN A 40 1
17
Start residue of secondary structure not found: HELIX 3 3 ASN A 43 ASN A 81 1
39
Start residue of secondary structure not found: HELIX 4 4 THR B 11 THR B 23 1
13
Start residue of secondary structure not found: HELIX 5 5 GLN B 24 ASN B 40 1
17
754 messages similar to the above omitted
Chain information for Exp_6rwy.pdb
---
Chain | Description
36.1/a 36.2/b 36.3/c 36.4/d 36.5/e | No description available
36.6/f | No description available
36.7/g 36.8/h | No description available
36.9/i | No description available
36.10/j | No description available
36.11/k | No description available
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 37 models selected
> select subtract #35
Nothing selected
> hide #!35 models
> select add #36
12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 15 models selected
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models #36,1,0,0,1.8402,0,1,0,-7.3614e-15,0,0,1,22.102
> combine #36
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 316
shifted from previous position = 14.7
rotated from previous position = 20.6 degrees
atoms outside contour = 2517, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.97215783 0.23225297 -0.03110797 -36.48471750
-0.21917028 0.94819832 0.22996594 -39.18940239
0.08290680 -0.21674525 0.97270137 -310.80580561
Axis -0.69231910 -0.17670165 -0.69962190
Axis point 156.75641938 -568.23716310 0.00000000
Rotation angle (degrees) 18.82141158
Shift along axis 249.63044579
> select subtract #36
Nothing selected
> hide #!36 models
> show #!35 models
> hide #!35 models
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 44
shifted from previous position = 0.0237
rotated from previous position = 0.537 degrees
atoms outside contour = 2518, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.97005550 0.24114627 -0.02899658 -39.23648975
-0.22826290 0.94593773 0.23042975 -36.50652393
0.08299623 -0.21691080 0.97265684 -310.77604186
Axis -0.67981987 -0.17019457 -0.71335738
Axis point 156.72094753 -535.52573200 0.00000000
Rotation angle (degrees) 19.20894193
Shift along axis 254.58134139
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 44
shifted from previous position = 0.0162
rotated from previous position = 0.248 degrees
atoms outside contour = 2519, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96904395 0.24527257 -0.02819900 -40.42088046
-0.23247603 0.94495711 0.23024108 -35.07248352
0.08311866 -0.21655813 0.97272497 -310.93483988
Axis -0.67337250 -0.16776719 -0.72001642
Axis point 157.89194862 -520.78803134 0.00000000
Rotation angle (degrees) 19.37577446
Shift along axis 256.98051248
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0648
rotated from previous position = 0.0971 degrees
atoms outside contour = 2509, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96863326 0.24682847 -0.02872841 -40.40134866
-0.23388087 0.94461726 0.23021288 -34.59326791
0.08396044 -0.21627282 0.97271615 -311.22221523
Axis -0.67072132 -0.16928384 -0.72213288
Axis point 160.83362397 -516.13702243 0.00000000
Rotation angle (degrees) 19.44123990
Shift along axis 257.69792107
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 40
shifted from previous position = 0.0997
rotated from previous position = 1.18 degrees
atoms outside contour = 2519, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96366431 0.26609641 -0.02331951 -46.71349923
-0.25378087 0.93929856 0.23089713 -28.45567455
0.08334488 -0.21658928 0.97269868 -310.98516898
Axis -0.64462062 -0.15365398 -0.74890234
Axis point 157.55723427 -450.67017193 0.00000000
Rotation angle (degrees) 20.30960300
Shift along axis 267.38233255
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 28
shifted from previous position = 0.0588
rotated from previous position = 0.0884 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96394851 0.26497357 -0.02433681 -45.95977070
-0.25246266 0.93964523 0.23093169 -28.89301795
0.08405877 -0.21646213 0.97266555 -311.18545152
Axis -0.64599219 -0.15651244 -0.74712646
Axis point 159.68219339 -455.04109604 0.00000000
Rotation angle (degrees) 20.26021000
Shift along axis 266.70665549
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 36
shifted from previous position = 0.059
rotated from previous position = 0.834 degrees
atoms outside contour = 2517, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96020555 0.27853448 -0.02058754 -50.30086275
-0.26646024 0.93567851 0.23131074 -24.47016918
0.08369134 -0.21662010 0.97266206 -311.05082031
Axis -0.62813123 -0.14622976 -0.76424343
Axis point 157.45642500 -412.32042966 0.00000000
Rotation angle (degrees) 20.88898113
Shift along axis 272.89235505
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 28
shifted from previous position = 0.0572
rotated from previous position = 0.201 degrees
atoms outside contour = 2501, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.96102174 0.27557271 -0.02229133 -48.89154354
-0.26321841 0.93663567 0.23114862 -25.45689706
0.08457710 -0.21627137 0.97266305 -311.36854755
Axis -0.63154775 -0.15084823 -0.76052104
Axis point 160.51258554 -422.13786937 -0.00000000
Rotation angle (degrees) 20.74595341
Shift along axis 271.51980439
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 40
shifted from previous position = 0.114
rotated from previous position = 0.934 degrees
atoms outside contour = 2516, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95677138 0.29034963 -0.01690027 -54.24303291
-0.27874957 0.93202561 0.23157490 -20.51184159
0.08298917 -0.21685329 0.97267027 -310.81188942
Axis -0.61311299 -0.13657373 -0.77810030
Axis point 154.50693313 -377.00324123 0.00000000
Rotation angle (degrees) 21.45053528
Shift along axis 277.90131068
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06746, steps = 28
shifted from previous position = 0.0915
rotated from previous position = 0.405 degrees
atoms outside contour = 2500, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95862930 0.28399751 -0.01937193 -51.83607203
-0.27204105 0.93405344 0.23138247 -22.64444243
0.08380646 -0.21654005 0.97266998 -311.10230759
Axis -0.62088266 -0.14301955 -0.77074647
Axis point 157.48594051 -396.19307279 0.00000000
Rotation angle (degrees) 21.14407053
Shift along axis 275.20372299
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0325
rotated from previous position = 0.935 degrees
atoms outside contour = 2497, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95402487 0.29929815 -0.01603642 -56.17567245
-0.28767749 0.92937671 0.23130194 -17.37440552
0.08413212 -0.21605449 0.97274984 -311.34959895
Axis -0.60065328 -0.13449356 -0.78811619
Axis point 157.82962251 -352.91585473 0.00000000
Rotation angle (degrees) 21.86318717
Shift along axis 281.45850608
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0938
rotated from previous position = 0.597 degrees
atoms outside contour = 2503, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95112319 0.30856628 -0.01230992 -59.65431835
-0.29745493 0.92612763 0.23196590 -14.37103207
0.08297741 -0.21696650 0.97264602 -310.76314943
Axis -0.59055654 -0.12534750 -0.79720197
Axis point 153.01157515 -327.45218791 0.00000000
Rotation angle (degrees) 22.33942125
Shift along axis 284.77161490
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0668
rotated from previous position = 0.454 degrees
atoms outside contour = 2498, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.95337543 0.30141874 -0.01490093 -57.11152235
-0.28994531 0.92854514 0.23180951 -16.84120644
0.08370792 -0.21668104 0.97264706 -311.02884295
Axis -0.59901117 -0.13170356 -0.78983530
Axis point 155.58109502 -347.05758758 0.00000000
Rotation angle (degrees) 21.98470642
Shift along axis 282.09004500
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06748, steps = 40
shifted from previous position = 0.0247
rotated from previous position = 1.12 degrees
atoms outside contour = 2497, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.94755539 0.31943266 -0.01007796 -62.53011616
-0.30846488 0.92235933 0.23259983 -10.88040410
0.08359549 -0.21729252 0.97252031 -310.77431451
Axis -0.57819656 -0.12038806 -0.80696682
Axis point 152.95845016 -300.88561926 0.00000000
Rotation angle (degrees) 22.89527177
Shift along axis 288.24912922
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06748, steps = 196
shifted from previous position = 0.275
rotated from previous position = 6.03 degrees
atoms outside contour = 2516, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.91061366 0.41271950 0.02110411 -91.92267912
-0.40571723 0.88311805 0.23557598 22.71238621
0.07858938 -0.22308101 0.97162677 -307.49389271
Axis -0.48795796 -0.06115768 -0.87072198
Axis point 136.22711377 -115.71161571 0.00000000
Rotation angle (degrees) 28.03273362
Shift along axis 311.20705701
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0948
rotated from previous position = 0.898 degrees
atoms outside contour = 2512, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90430007 0.42608641 0.02630122 -96.27299907
-0.41984476 0.87651820 0.23547022 28.07916406
0.07727716 -0.22397816 0.97152562 -306.86169323
Axis -0.47660751 -0.05287975 -0.87752436
Axis point 134.26059045 -94.76874164 0.00000000
Rotation angle (degrees) 28.81602027
Shift along axis 313.67822778
> select add #37
12867 atoms, 13147 bonds, 3 pseudobonds, 1638 residues, 2 models selected
> view orient
> turn x 90
[Repeated 2 time(s)]
> view matrix models
> #37,0.88528,0.46366,0.036102,-106.56,-0.45862,0.8575,0.23315,43.037,0.077144,-0.22296,0.97177,79.067
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 72
shifted from previous position = 20.8
rotated from previous position = 0.481 degrees
atoms outside contour = 2511, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90079049 0.43330196 0.02873850 -98.32308247
-0.42743077 0.87300777 0.23486244 31.19999943
0.07667743 -0.22384557 0.97160369 -306.76491610
Axis -0.46974220 -0.04909210 -0.88143759
Axis point 134.11253872 -83.92177367 0.00000000
Rotation angle (degrees) 29.22595638
Shift along axis 315.04895705
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0881
rotated from previous position = 0.69 degrees
atoms outside contour = 2506, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89556547 0.44382392 0.03134996 -100.99634174
-0.43819349 0.86759990 0.23506782 35.26655153
0.07712950 -0.22425597 0.97147326 -306.70958011
Axis -0.46139810 -0.04598628 -0.88600060
Axis point 134.86180551 -69.97063128 0.00000000
Rotation angle (degrees) 29.85139496
Shift along axis 316.72261334
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.113
rotated from previous position = 0.92 degrees
atoms outside contour = 2514, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90246639 0.42989237 0.02733078 -97.18986602
-0.42378755 0.87469951 0.23516987 29.70709181
0.07719151 -0.22381535 0.97156995 -306.89335347
Axis -0.47292364 -0.05137489 -0.87960437
Axis point 134.59471718 -89.23458408 0.00000000
Rotation angle (degrees) 29.02974247
Shift along axis 314.38192225
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0358
rotated from previous position = 0.539 degrees
atoms outside contour = 2508, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89842276 0.43815904 0.02920975 -99.19110537
-0.43221066 0.87054189 0.23526742 32.88583296
0.07765624 -0.22399437 0.97149165 -306.92433299
Axis -0.46611467 -0.04916939 -0.88335694
Axis point 135.40426879 -78.11433990 0.00000000
Rotation angle (degrees) 29.51483713
Shift along axis 315.74119313
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.105
rotated from previous position = 0.62 degrees
atoms outside contour = 2504, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89393780 0.44692368 0.03368125 -102.50135810
-0.44172928 0.86584329 0.23492687 36.69464322
0.07583170 -0.22488801 0.97142933 -306.18633286
Axis -0.45914720 -0.04208924 -0.88736258
Axis point 133.02904390 -64.97443284 0.00000000
Rotation angle (degrees) 30.04811532
Shift along axis 317.21705560
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.115
rotated from previous position = 0.804 degrees
atoms outside contour = 2510, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89992272 0.43507607 0.02911888 -98.73409564
-0.42922052 0.87207973 0.23504615 31.83387789
0.07686897 -0.22402179 0.97154794 -306.74154948
Axis -0.46852644 -0.04873392 -0.88210429
Axis point 134.31242573 -81.69650868 0.00000000
Rotation angle (degrees) 29.33441145
Shift along axis 315.28618152
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 36
shifted from previous position = 0.0953
rotated from previous position = 0.448 degrees
atoms outside contour = 2504, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89659216 0.44173645 0.03148658 -100.79748505
-0.43619417 0.86858072 0.23516415 34.45417341
0.07653194 -0.22458060 0.97144553 -306.45943993
Axis -0.46343059 -0.04540649 -0.88496912
Axis point 133.73323211 -72.40106826 0.00000000
Rotation angle (degrees) 29.73725103
Shift along axis 316.35533473
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.11
rotated from previous position = 0.771 degrees
atoms outside contour = 2513, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90230337 0.43022137 0.02753538 -97.33949968
-0.42415013 0.87451703 0.23519489 29.83327906
0.07710571 -0.22389628 0.97155811 -306.84469626
Axis -0.47271932 -0.05104183 -0.87973358
Axis point 134.42082336 -88.71395964 0.00000000
Rotation angle (degrees) 29.05083100
Shift along axis 314.43310092
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0181
rotated from previous position = 0.511 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89844147 0.43814279 0.02887597 -99.02578382
-0.43210877 0.87055337 0.23541205 32.78427291
0.07800602 -0.22398151 0.97146659 -307.00647837
Axis -0.46625270 -0.04986361 -0.88324517
Axis point 135.80530966 -78.46119855 0.00000000
Rotation angle (degrees) 29.51453840
Shift along axis 315.69828774
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 36
shifted from previous position = 0.101
rotated from previous position = 0.522 degrees
atoms outside contour = 2506, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89466699 0.44554139 0.03261660 -101.81955415
-0.44014180 0.86661685 0.23505410 36.02578634
0.07646023 -0.22465108 0.97143488 -306.41395689
Axis -0.46023802 -0.04389445 -0.88670979
Axis point 133.84591683 -67.26281795 0.00000000
Rotation angle (degrees) 29.96170923
Shift along axis 316.98015163
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.101
rotated from previous position = 0.826 degrees
atoms outside contour = 2512, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90086803 0.43314603 0.02865865 -98.26801868
-0.42723813 0.87302139 0.23516215 31.02573130
0.07683994 -0.22409412 0.97153355 -306.71089778
Axis -0.47032174 -0.04934219 -0.88111453
Axis point 134.07806725 -84.40785637 0.00000000
Rotation angle (degrees) 29.22472317
Shift along axis 314.93413586
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 36
shifted from previous position = 0.0873
rotated from previous position = 0.516 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89702346 0.44087858 0.03122484 -100.56014533
-0.43530634 0.86903240 0.23514055 34.12334041
0.07653303 -0.22451896 0.97145969 -306.48305045
Axis -0.46408011 -0.04574392 -0.88461130
Axis point 133.74442886 -73.53778176 0.00000000
Rotation angle (degrees) 29.68539583
Shift along axis 316.22539615
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.115
rotated from previous position = 0.831 degrees
atoms outside contour = 2513, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.90315769 0.42846252 0.02694538 -96.81966205
-0.42230950 0.87539339 0.23524690 29.11132680
0.07720667 -0.22384433 0.97156206 -306.88791911
Axis -0.47424756 -0.05192061 -0.87885921
Axis point 134.49541167 -91.31340629 0.00000000
Rotation angle (degrees) 28.94832832
Shift along axis 314.11628340
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0364
rotated from previous position = 0.588 degrees
atoms outside contour = 2509, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89875096 0.43749997 0.02899116 -99.00445363
-0.43152127 0.87087727 0.23529168 32.61101453
0.07769236 -0.22397892 0.97149233 -306.93891595
Axis -0.46667981 -0.04948688 -0.88304077
Axis point 135.42086570 -79.04471548 0.00000000
Rotation angle (degrees) 29.47618687
Shift along axis 315.62913969
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 40
shifted from previous position = 0.0995
rotated from previous position = 0.601 degrees
atoms outside contour = 2507, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89441850 0.44598789 0.03332197 -102.20916020
-0.44078288 0.86646626 0.23440704 36.55563001
0.07567034 -0.22434575 0.97156728 -306.34974761
Axis -0.45907197 -0.04237783 -0.88738776
Axis point 133.36087951 -65.78360653 0.00000000
Rotation angle (degrees) 29.97700279
Shift along axis 317.22322991
> fitmap #37 inMap #33
Fit molecule combination (#37) to map Exp.mrc (#33) using 12867 atoms
average map value = 0.06747, steps = 28
shifted from previous position = 0.0922
rotated from previous position = 0.746 degrees
atoms outside contour = 2514, contour level = 0.0282
Position of combination (#37) relative to Exp.mrc (#33) coordinates:
Matrix rotation and translation
0.89997567 0.43495953 0.02922328 -98.78534713
-0.42911600 0.87208028 0.23523485 31.71397404
0.07683259 -0.22424582 0.97149913 -306.65274386
Axis -0.46895168 -0.04859065 -0.88188620
Axis point 134.01873267 -81.91850950 0.00000000
Rotation angle (degrees) 29.33413674
Shift along axis 315.21737538
> close #35-36
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiA-project/Model-PDB-AlphaFolds/6rwy.pdb1
6rwy.pdb1 title:
Export apparatus core and inner rod of the shigella type 3 secretion system
[more info...]
Chain information for 6rwy.pdb1 #35
---
Chain | Description
A G H I J K | No description available
B C D E F | No description available
L M N O P Q R S T U V | No description available
a b c d e | No description available
f | No description available
g h i j k | No description available
> matchmaker #37 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6rwy.pdb1, chain f (#35) with combination, chain f (#37), sequence
alignment score = 1227.8
RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs:
0.001)
> matchmaker #35 to #37
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain f (#37) with 6rwy.pdb1, chain f (#35), sequence
alignment score = 1227.8
RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs:
0.001)
> show #!7 models
> hide #!7 models
> show #!12 models
> hide #!37 models
> hide #!35 models
> hide #!33 models
> show #!35 models
> fitmap #35 inMap #12
Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743
atoms
average map value = 0.05154, steps = 76
shifted from previous position = 11.5
rotated from previous position = 15 degrees
atoms outside contour = 4533, contour level = 0.012281
Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.87803641 0.47858703 -0.00255505 -192.64047971
-0.47852090 0.87798327 0.01277250 119.46473498
0.00835605 -0.00999207 0.99991516 209.09071995
Axis -0.02377648 -0.01139611 -0.99965234
Axis point 130.99637747 446.12669410 0.00000000
Rotation angle (degrees) 28.60186207
Shift along axis -205.79914853
> fitmap #35 inMap #12
Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743
atoms
average map value = 0.05154, steps = 24
shifted from previous position = 0.027
rotated from previous position = 0.102 degrees
atoms outside contour = 4531, contour level = 0.012281
Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.87884036 0.47710585 -0.00310138 -192.24835410
-0.47703354 0.87879083 0.01287176 118.65116797
0.00886666 -0.00983277 0.99991235 208.88473927
Axis -0.02378722 -0.01253874 -0.99963841
Axis point 129.94428451 446.20277398 0.00000000
Rotation angle (degrees) 28.50544415
Shift along axis -205.72389102
> fitmap #35 inMap #12
Fit molecule 6rwy.pdb1 (#35) to map Needle.mrc gaussian (#12) using 22743
atoms
average map value = 0.05154, steps = 24
shifted from previous position = 0.00171
rotated from previous position = 0.102 degrees
atoms outside contour = 4529, contour level = 0.012281
Position of 6rwy.pdb1 (#35) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
0.87967555 0.47556249 -0.00335195 -191.93472314
-0.47548863 0.87962901 0.01278152 117.88941222
0.00902689 -0.00964978 0.99991269 208.77241920
Axis -0.02357725 -0.01301123 -0.99963734
Axis point 129.27153288 446.50117910 0.00000000
Rotation angle (degrees) 28.40481137
Shift along axis -205.70530071
> matchmaker #37 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6rwy.pdb1, chain f (#35) with combination, chain f (#37), sequence
alignment score = 1227.8
RMSD between 240 pruned atom pairs is 0.001 angstroms; (across all 240 pairs:
0.001)
> hide #!35 models
> show #!35 models
> select subtract #37
Nothing selected
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> hide sel atoms
> show sel cartoons
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 35/f
Alignment identifier is 5
> select #35/A,G-K:59
30 atoms, 24 bonds, 6 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> select #35/f:210-256
387 atoms, 397 bonds, 47 residues, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> color sel #e34affff
> color sel #e34bffff
> color sel #e44dffff
> color sel #e34effff
> color sel #e24effff
> color sel #e04fffff
> color sel #de56ffff
> color sel #df61ffff
> color sel #e46fffff
> color sel #e572ffff
> color sel #e473ffff
> color sel #ce73ffff
> color sel #cd73ffff
> color sel #ca72ffff
> color sel #c773ffff
> color sel #bd73ffff
> color sel #b472ffff
> color sel #ab6effff
> color sel #9d6affff
> color sel #7c5effff
> color sel #6c5affff
> color sel #6960ffff
> color sel #6b65ffff
> color sel #7771ffff
> color sel #7c77ffff
> color sel #8079ffff
> color sel #9081ffff
> color sel #9686ffff
> color sel #ab96ffff
> color sel #bb9effff
> color sel #c4a6ffff
> color sel #cdb0ffff
> color sel #ccb0ffff
> color sel #c4adffff
> color sel #b6a7ffff
> color sel #b2a5ffff
> color sel #aba0ffff
> color sel #a69cffff
> color sel #a199ffff
> color sel #9d96ffff
> color sel #9c95ffff
> color sel #9c94ffff
> color sel #9994ffff
> color sel #9093ffff
> color sel #8e93ffff
> color sel #8e94ffff
> color sel #9097ffff
> color sel #979dffff
> color sel #999effff
> color sel #9ca0ffff
> color sel #e5c7ffff
> color sel #ffc5e7ff
> color sel #ff9da2ff
> color sel #ff9596ff
> color sel #ff9494ff
> color sel #ff9790ff
> color sel #ff998dff
> color sel #ffa184ff
> color sel #ffa27cff
> color sel #ff9e75ff
> color sel #ff9667ff
> color sel #ff8e5cff
> color sel #ff8c59ff
> color sel #ff7d54ff
> color sel #ff7255ff
> color sel #ff5e50ff
> color sel #ff364cff
[Repeated 1 time(s)]
> color sel #ff3950ff
> color sel #ff3d53ff
> color sel #ff475cff
> color sel #ff5364ff
> color sel #ff5b68ff
> color sel #ff616bff
> color sel #ff646aff
> color sel #ff6469ff
> color sel #ff6966ff
> color sel #ff7167ff
> color sel #ff7767ff
> color sel #ff7e66ff
> color sel #ff7e65ff
> color sel #ff7d64ff
> color sel #ff7a61ff
> color sel #ff7a60ff
> color sel #ff624cff
> color sel #ff5c49ff
> color sel #ff5747ff
> color sel #ff5647ff
> select #35/f:256
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> color sel #ff5647ff
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> color sel #ff5647ff
> select clear
> show #!20 models
> hide #!20 models
> show #!37 models
> close #37
> show #!27 models
> hide #!27 models
> show #!26 models
> hide #!26 models
> show #21 models
> hide #21 models
> show #21 models
> matchmaker #21 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6rwy.pdb1, chain M (#35) with 6zni.pdb, chain A (#21), sequence
alignment score = 471.3
RMSD between 68 pruned atom pairs is 0.800 angstroms; (across all 73 pairs:
1.078)
> select add #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,518.01,-0.93631,0.35116,0.003362,377.64,0.007299,0.029031,-0.99955,873.02
> open /Users/shoichi/Library/CloudStorage/OneDrive-
> YaleUniversity/Jun_Lab_documents/Project-documents/Shigella-
> Projects/Project-with-Bill/MxiG_Linker/Manuscript-
> start-2023/Newest_ver/Figures-maps/PDB/6zni.pdb
6zni.pdb title:
Structure of the shigella mxih needle filament attached to the basal body
[more info...]
Chain information for 6zni.pdb #36
---
Chain | Description | UniProt
A B C D E F G H I J K L M N O P Q R S T U V W | protein mxih | MXIH_SHIFL 1-83
> matchmaker #36 to #21
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6zni.pdb, chain A (#21) with 6zni.pdb, chain A (#36), sequence
alignment score = 488.1
RMSD between 82 pruned atom pairs is 0.000 angstroms; (across all 82 pairs:
0.000)
> select add #36
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,513.47,-0.93631,0.35116,0.003362,379.08,0.007299,0.029031,-0.99955,909.24,#36,-0.3511,-0.93587,-0.029745,513.47,-0.93631,0.35116,0.0033619,379.08,0.007299,0.029031,-0.99955,909.24
> undo
> select subtract #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #36,-0.3511,-0.93587,-0.029745,503.75,-0.93631,0.35116,0.0033619,377.16,0.007299,0.029031,-0.99955,987.31
> select add #21
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> combine #21,36
Remapping chain ID 'A' in 6zni.pdb #36 to 'X'
Remapping chain ID 'B' in 6zni.pdb #36 to 'Y'
Remapping chain ID 'C' in 6zni.pdb #36 to 'Z'
Remapping chain ID 'D' in 6zni.pdb #36 to 'a'
Remapping chain ID 'E' in 6zni.pdb #36 to 'b'
Remapping chain ID 'F' in 6zni.pdb #36 to 'c'
Remapping chain ID 'G' in 6zni.pdb #36 to 'd'
Remapping chain ID 'H' in 6zni.pdb #36 to 'e'
Remapping chain ID 'I' in 6zni.pdb #36 to 'f'
Remapping chain ID 'J' in 6zni.pdb #36 to 'g'
Remapping chain ID 'K' in 6zni.pdb #36 to 'h'
Remapping chain ID 'L' in 6zni.pdb #36 to 'i'
Remapping chain ID 'M' in 6zni.pdb #36 to 'j'
Remapping chain ID 'N' in 6zni.pdb #36 to 'k'
Remapping chain ID 'O' in 6zni.pdb #36 to 'l'
Remapping chain ID 'P' in 6zni.pdb #36 to 'm'
Remapping chain ID 'Q' in 6zni.pdb #36 to 'n'
Remapping chain ID 'R' in 6zni.pdb #36 to 'o'
Remapping chain ID 'S' in 6zni.pdb #36 to 'p'
Remapping chain ID 'T' in 6zni.pdb #36 to 'q'
Remapping chain ID 'U' in 6zni.pdb #36 to 'r'
Remapping chain ID 'V' in 6zni.pdb #36 to 's'
Remapping chain ID 'W' in 6zni.pdb #36 to 't'
> select subtract #36
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> hide #36 models
> hide #21 models
> select subtract #21
Nothing selected
> color #37 #ffcdc1ff
> color #37 #fff0b9ff
> color #37 #fffab8ff
> color #37 #cdca94ff
> select add #37
29624 atoms, 30038 bonds, 3772 residues, 1 model selected
> color sel #ff5647ff
> color #37 #cdca94ff
> select #35/B-F:33-73
1025 atoms, 1020 bonds, 205 residues, 1 model selected
> select #35/B-F:11-73
1575 atoms, 1570 bonds, 315 residues, 1 model selected
> color sel #cdca94ff
> select #35/A,G-K:59
30 atoms, 24 bonds, 6 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> color sel #cdca94ff
> select #35/L-V:39-83
4004 atoms, 4059 bonds, 495 residues, 1 model selected
> select #35/L-V
6281 atoms, 6347 bonds, 803 residues, 1 model selected
> color sel #cdca94ff
> select clear
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> select #35/B-F:73
25 atoms, 20 bonds, 5 residues, 1 model selected
> select #35/B-F:11-73
1575 atoms, 1570 bonds, 315 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> select #35/L-V:83
121 atoms, 110 bonds, 11 residues, 1 model selected
> select #35/L-V
6281 atoms, 6347 bonds, 803 residues, 1 model selected
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> select #35/f:214-256
355 atoms, 364 bonds, 43 residues, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> select subtract #35
Nothing selected
> hide #!35 models
> show #!35 models
> fitmap #37 inMap #12
Fit molecule combination (#37) to map Needle.mrc gaussian (#12) using 29624
atoms
average map value = 0.06417, steps = 548
shifted from previous position = 70.3
rotated from previous position = 11.1 degrees
atoms outside contour = 8428, contour level = 0.012281
Position of combination (#37) relative to Needle.mrc gaussian (#12)
coordinates:
Matrix rotation and translation
-0.49153012 -0.85972065 -0.13884720 566.36821533
-0.86955619 0.49323881 0.02423863 329.40732755
0.04764637 0.13264946 -0.99001714 908.59071574
Axis 0.50204458 -0.86364149 -0.04554785
Axis point 350.50708701 0.00000000 464.01580445
Rotation angle (degrees) 173.80173096
Shift along axis -41.53209647
> fitmap #37 inMap #12
Fit molecule combination (#37) to map Needle.mrc gaussian (#12) using 29624
atoms
average map value = 0.06423, steps = 48
shifted from previous position = 0.0821
rotated from previous position = 1.4 degrees
atoms outside contour = 8424, contour level = 0.012281
Position of combination (#37) relative to Needle.mrc gaussian (#12)
coordinates:
Matrix rotation and translation
-0.51261344 -0.84748446 -0.13783161 568.00591214
-0.85732198 0.51402279 0.02792129 321.77742772
0.04718573 0.13247890 -0.99006204 908.81302700
Axis 0.49146888 -0.86966667 -0.04624087
Axis point 347.11623201 0.00000000 463.91377007
Rotation angle (degrees) 173.89374851
Shift along axis -42.70617861
> view orient
> turn x 90
[Repeated 2 time(s)]
> select add #37
29624 atoms, 30038 bonds, 3772 residues, 1 model selected
> view matrix models
> #37,-0.51261,-0.84748,-0.13783,569.7,-0.85732,0.51402,0.027921,321.78,0.047186,0.13248,-0.99006,856.35
> close #37
> show #36 models
> show #21 models
> fitmap #36 inMap #12
Fit molecule 6zni.pdb (#36) to map Needle.mrc gaussian (#12) using 14812 atoms
average map value = 0.0782, steps = 132
shifted from previous position = 32.5
rotated from previous position = 1.92 degrees
atoms outside contour = 571, contour level = 0.012281
Position of 6zni.pdb (#36) relative to Needle.mrc gaussian (#12) coordinates:
Matrix rotation and translation
-0.33643885 -0.94170519 -0.00049053 521.74293397
-0.94170368 0.33643919 -0.00169149 382.53410278
0.00175792 -0.00010715 -0.99999845 975.28376338
Axis 0.57600370 -0.81744690 0.00055009
Axis point 395.23518164 0.00000000 487.99286048
Rotation angle (degrees) 179.92120163
Shift along axis -11.63896146
> view orient
> turn x 90
[Repeated 2 time(s)]
> select add #36
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #36,-0.33644,-0.94171,-0.00049053,521.99,-0.9417,0.33644,-0.0016915,382.53,0.0017579,-0.00010715,-1,1003.3
> select subtract #36
Nothing selected
> select add #21
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,531.02,-0.93631,0.35116,0.003362,377.64,0.007299,0.029031,-0.99955,883.73
> turn y 10
[Repeated 47 time(s)]
> select add #36
29624 atoms, 30038 bonds, 3772 residues, 2 models selected
> view matrix models
> #21,-0.3511,-0.93587,-0.029745,530.99,-0.93631,0.35116,0.003362,377.58,0.007299,0.029031,-0.99955,877.32,#36,-0.33644,-0.94171,-0.00049053,521.96,-0.9417,0.33644,-0.0016915,382.48,0.0017579,-0.00010715,-1,996.86
> turn y 10
[Repeated 40 time(s)]
> select clear
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> hide #!35 models
> show #!35 models
> select #35/A,G-K:58-59
60 atoms, 54 bonds, 12 residues, 1 model selected
> select #35/A,G-K:25-59
1050 atoms, 1044 bonds, 210 residues, 1 model selected
> hide sel cartoons
> select #35/B-F:73
25 atoms, 20 bonds, 5 residues, 1 model selected
> select #35/B-F:11-73
1575 atoms, 1570 bonds, 315 residues, 1 model selected
> hide sel cartoons
> select #35/L-V:40-83
3905 atoms, 3960 bonds, 484 residues, 1 model selected
> select #35/L-V
6281 atoms, 6347 bonds, 803 residues, 1 model selected
> hide sel cartoons
> select clear
> select #35/a-e
8215 atoms, 8390 bonds, 1040 residues, 1 model selected
> hide sel cartoons
> select #35/f:209-256
396 atoms, 406 bonds, 48 residues, 1 model selected
> select #35/f
1881 atoms, 1929 bonds, 240 residues, 1 model selected
> hide sel cartoons
> select #35/g-k:86
35 atoms, 30 bonds, 5 residues, 1 model selected
> select #35/g-k
2771 atoms, 2828 bonds, 3 pseudobonds, 358 residues, 2 models selected
> hide sel cartoons
> select clear
> hide #21 models
> hide #!12 models
Drag select of 194 residues
> color sel #cdca94ff
> select clear
> select add #35
22743 atoms, 23078 bonds, 3 pseudobonds, 3160 residues, 2 models selected
> show sel cartoons
> select subtract #35
Nothing selected
> select add #36
14812 atoms, 15019 bonds, 1886 residues, 1 model selected
> show #21 models
> show sel surfaces
> select add #21
29624 atoms, 30038 bonds, 3772 residues, 25 models selected
> show sel surfaces
> show sel cartoons
> combine #21,36
Remapping chain ID 'A' in 6zni.pdb #36 to 'X'
Remapping chain ID 'B' in 6zni.pdb #36 to 'Y'
Remapping chain ID 'C' in 6zni.pdb #36 to 'Z'
Remapping chain ID 'D' in 6zni.pdb #36 to 'a'
Remapping chain ID 'E' in 6zni.pdb #36 to 'b'
Remapping chain ID 'F' in 6zni.pdb #36 to 'c'
Remapping chain ID 'G' in 6zni.pdb #36 to 'd'
Remapping chain ID 'H' in 6zni.pdb #36 to 'e'
Remapping chain ID 'I' in 6zni.pdb #36 to 'f'
Remapping chain ID 'J' in 6zni.pdb #36 to 'g'
Remapping chain ID 'K' in 6zni.pdb #36 to 'h'
Remapping chain ID 'L' in 6zni.pdb #36 to 'i'
Remapping chain ID 'M' in 6zni.pdb #36 to 'j'
Remapping chain ID 'N' in 6zni.pdb #36 to 'k'
Remapping chain ID 'O' in 6zni.pdb #36 to 'l'
Remapping chain ID 'P' in 6zni.pdb #36 to 'm'
Remapping chain ID 'Q' in 6zni.pdb #36 to 'n'
Remapping chain ID 'R' in 6zni.pdb #36 to 'o'
Remapping chain ID 'S' in 6zni.pdb #36 to 'p'
Remapping chain ID 'T' in 6zni.pdb #36 to 'q'
Remapping chain ID 'U' in 6zni.pdb #36 to 'r'
Remapping chain ID 'V' in 6zni.pdb #36 to 's'
Remapping chain ID 'W' in 6zni.pdb #36 to 't'
> select subtract #36
14812 atoms, 15019 bonds, 1886 residues, 47 models selected
> select subtract #21
23 models selected
> hide #!21 models
> hide #!36 models
> select add #37
29624 atoms, 30038 bonds, 3772 residues, 1 model selected
> color sel #cdca94ff
> show sel surfaces
> select add #35
52367 atoms, 53116 bonds, 3 pseudobonds, 6932 residues, 49 models selected
> show sel surfaces
> select clear
> show #!36 models
> hide #!36 models
> close #36
> close #34
> show #!33 models
> hide #!33 models
> show #!33 models
> show #!32 models
> show #!31 models
> hide #!31 models
> hide #!32 models
> hide #!33 models
> hide #!35 models
> show #!35 models
> show #!26 models
> hide #!26 models
> close #26
> show #!27 models
> save /Users/shoichi/Desktop/Shigella-ipaDnull-bin2-06252025.cxs includeMaps
> true
——— End of log from Wed Jun 25 10:52:06 2025 ———
opened ChimeraX session
> hide #!37 models
> show #!37 models
> show #!33 models
> hide #!33 models
> show #!33 models
> show #!32 models
> show #!28 models
> hide #!13 models
> show #!15 models
> hide #!15 models
> show #!16 models
> show #!15 models
> color #16 #42424208 models
> color #16 #4242421e models
> color #16 #42424240 models
> hide #!15 models
> color #14 #5e5e5eff models
> color #14 #5e5e5e81 models
> set bgColor black
> color #14 #5e5e5e80 models
> color #14 #5e5e5e67 models
> color #14 darkgrey models
> color #14 #a9a9a95b models
> color #14 #a9a9a967 models
> color #9 #a9a9a967 models
> show #!20 models
> show #!23 models
> select add #23
124488 atoms, 126648 bonds, 15424 residues, 3 models selected
> show sel surfaces
> select clear
> hide #!27 models
> hide #!23 models
> show #!23 models
> hide #!37 models
> hide #!35 models
> show #!7 models
> hide #!7 models
> show #!12 models
> view orient
> turn x 90
[Repeated 2 time(s)]
> view name P1
> save /Users/shoichitachiyama/Desktop/IMring.png supersample 2
> transparentBackground true
> color #9 darkgrey models
> color #9 #a9a9a980 models
> color #10 #a9a9a980 models
> color #12 #a9a9a980 models
> color #16 #a9a9a980 models
> color #28 #a9a9a980 models
> color #32 #a9a9a980 models
> color #33 #a9a9a980 models
> save /Users/shoichitachiyama/Desktop/IMring.png supersample 2
> transparentBackground true
> turn x 90
> ui tool show "Side View"
> hide #!9 models
> save /Users/shoichitachiyama/Desktop/IMring-2.png supersample 2
> transparentBackground true
> view P1
> show #!9 models
> show #!22 models
> show #!24 models
> show #!21 models
> hide #!21 models
> color #22 #009193ff
> color #22 #005493ff
> color #22 #009193ff
> color #22 #005759ff
> color #22 #005051ff
> color #24 #bfa292ff models
> color #24 #bf6943ff models
> color #24 #bf726cff models
> color #24 #bf746eff models
> color #24 #bf7570ff models
> color #24 #bf713aff models
> color #24 #bf5e32ff models
> show #!29 models
> color #29 #b6bfb4ff models
> color #29 #afbfbaff models
> color #29 #abaebfff models
> color #29 #92a0bfff models
> color #29 #99a9bfff models
> color #29 #94a0bfff models
> show #!30 models
> color #30 #bcbfa6ff models
> color #30 #bfb590ff models
> save /Users/shoichitachiyama/Desktop/Sorting_platform.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
> includeMaps true
> turn x 90
[Repeated 2 time(s)]
> save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2
> transparentBackground true
> hide #!9 models
> save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2
> transparentBackground true
> hide #!14 models
> save /Users/shoichitachiyama/Desktop/Sorting3_platform.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Sorting2_platform.png supersample 2
> transparentBackground true
> turn x 90
> show #!21 models
> hide #!21 models
> show #!37 models
> show #!35 models
> show #!31 models
> hide #!31 models
> show #!27 models
> color #27 #d27473ff
> color #27 #d26969ff
> color #27 #d26968ff
> show #!9 models
> show #!14 models
> volume #312 region 60,0,0,120,120,200
No volumes specified
> volume #9 region 60,0,0,120,120,200
> volume #9 region 0,60,0,120,120,200
> volume #14 region 0,60,0,120,120,200
> volume #14 region 0,0,0,120,120,200
> volume #9 region 0,0,0,120,120,200
> save /Users/shoichitachiyama/Desktop/Overall.png supersample 2
> transparentBackground true
> volume #14 region 0,60,0,120,120,200
> volume #9 region 0,60,0,120,120,200
> hide #!24.6 models
> show #!24.6 models
> hide #!24.5 models
> show #!24.5 models
> hide #!24 models
> show #!24 models
> hide #!24.1 models
> show #!24.1 models
> hide #!24.2 models
> hide #!24.3 models
> hide #!29.2 models
> show #!29.2 models
> hide #!29.5 models
> hide #!29.6 models
> hide #!29.4 models
> hide #!29.3 models
> hide #!30.2 models
> show #!30.2 models
> hide #!30 models
> show #!30 models
> hide #!30.5 models
> show #!30.5 models
> hide #!30.6 models
> hide #!30.1 models
> hide #!10 models
> hide #!12 models
> hide #!16 models
> show #!24.3 models
> hide #!24.3 models
> show #!24.2 models
> show #!29.3 models
> show #!29.4 models
> show #!30.6 models
> show #!21 models
> hide #!21 models
> hide #!28 models
> hide #!32 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!29.6 models
> show #!29.5 models
> show #!30.1 models
> show #!24.3 models
> save /Users/shoichitachiyama/Desktop/Overall2.png supersample 2
> transparentBackground true
> hide #!24.3 models
> hide #!29.5 models
> hide #!29.6 models
> hide #!30.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #23.1.1 models
> show #23.1.1 models
> hide #23.1.13 models
> show #23.1.13 models
> hide #23.1.20 models
> show #23.1.20 models
> hide #23.1.48 models
> show #23.1.48 models
> hide #23.1.44 models
> show #23.1.44 models
> hide #23.1.36 models
> hide #23.1.35 models
> show #23.1.35 models
> show #23.1.36 models
> hide #23.1.34 models
> hide #23.1.33 models
> hide #23.1.32 models
> hide #23.1.31 models
> hide #23.1.30 models
> hide #23.1.29 models
> hide #23.1.28 models
> show #23.1.28 models
> select add #23.1.29
2766 atoms, 340 residues, 1 model selected
> select add #23.1.30
5532 atoms, 680 residues, 2 models selected
> select add #23.1.31
8298 atoms, 1020 residues, 3 models selected
> select add #23.1.32
11064 atoms, 1360 residues, 4 models selected
> select add #23.1.33
13830 atoms, 1700 residues, 5 models selected
> select add #23.1.34
16596 atoms, 2040 residues, 6 models selected
> hide sel cartoons
> select subtract #23.1.29
13830 atoms, 1700 residues, 7 models selected
> select subtract #23.1.30
11064 atoms, 1360 residues, 6 models selected
> select subtract #23.1.31
8298 atoms, 1020 residues, 5 models selected
> select subtract #23.1.32
5532 atoms, 680 residues, 4 models selected
> select subtract #23.1.33
2766 atoms, 340 residues, 3 models selected
> select subtract #23.1.34
1 model selected
> hide #23.1.7 models
> show #23.1.7 models
> hide #23.1.4 models
> hide #23.1.3 models
> hide #23.1.5 models
> hide #23.1.2 models
> hide #23.1.1 models
> hide #!23.1 models
> show #!23.1 models
> hide #23.1.48 models
> show #23.1.48 models
> hide #23.1.6 models
> hide #23.1.18 models
> show #23.1.18 models
> hide #23.1.17 models
> show #23.1.17 models
> hide #23.1.15 models
> show #23.1.15 models
> hide #23.1.12 models
> show #23.1.12 models
> hide #23.1.13 models
> show #23.1.13 models
> hide #23.1.8 models
> show #23.1.8 models
> hide #23.1.7 models
> show #23.1.7 models
> hide #23.1.24 models
> show #23.1.24 models
> hide #23.1.22 models
> show #23.1.22 models
> hide #23.1.21 models
> hide #23.1.22 models
> hide #23.1.20 models
> hide #23.1.23 models
> show #23.1.22 models
> hide #23.1.22 models
> select add #23.1.23
1403 atoms, 177 residues, 1 model selected
> select add #23.1.22
2806 atoms, 354 residues, 2 models selected
> select add #23.1.21
4209 atoms, 531 residues, 3 models selected
> select add #23.1.20
5612 atoms, 708 residues, 4 models selected
> hide sel cartoons
> select add #23.1.6
7015 atoms, 885 residues, 5 models selected
> select add #23.1.5
8418 atoms, 1062 residues, 6 models selected
> select add #23.1.4
9821 atoms, 1239 residues, 7 models selected
> select add #23.1.3
11224 atoms, 1416 residues, 8 models selected
> select add #23.1.2
12627 atoms, 1593 residues, 9 models selected
> select add #23.1.1
14030 atoms, 1770 residues, 10 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide #!23 models
> show #!23 models
> select clear
> hide #!33 models
> save /Users/shoichitachiyama/Desktop/Overall3.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
> includeMaps true
——— End of log from Mon Jul 7 21:04:45 2025 ———
opened ChimeraX session
> hide #!37 models
> hide #!30 models
> hide #!29 models
> hide #!35 models
> hide #!24 models
> hide #!23 models
> hide #!22 models
> hide #!20 models
> hide #!14 models
> hide #!9 models
> select add #27
22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> select clear
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA-
> project/Data_Images/07072025/fold_2025_05_14_18_58mxia1/fold_2025_05_14_18_58mxia1_model_0.cif"
Chain information for fold_2025_05_14_18_58mxia1_model_0.cif #26
---
Chain | Description
A | .
> hide #26 models
> show #26 models
> ui tool show "Side View"
> select add #26
5358 atoms, 5438 bonds, 686 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #26,1,0,0,135.58,0,1,0,-2.256e-13,0,0,1,290.29
> view P1
> view matrix models #26,1,0,0,224.75,0,1,0,201.52,0,0,1,332.43
> view matrix models #26,1,0,0,227.1,0,1,0,185.42,0,0,1,351.22
> hide #27.1 models
> hide #27.2 models
> hide #27.3 models
> hide #27.4 models
> hide #27.5 models
> hide #27.9 models
> hide #27.8 models
> hide #27.7 models
> hide #27.6 models
> hide #27.10 models
> hide #!27 models
> show #!27 models
> show #27.1 models
> hide #27.1 models
> show #27.2 models
> hide #!27 models
> show #!27 models
> matchmaker #26 to #27
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain A (#27) with
fold_2025_05_14_18_58mxia1_model_0.cif, chain A (#26), sequence alignment
score = 1659.8
RMSD between 262 pruned atom pairs is 0.900 angstroms; (across all 295 pairs:
1.890)
> close #26
> select add #27
22242 atoms, 22458 bonds, 33 pseudobonds, 2745 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> select #27/A-C:363
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #27/A-C:363-365
72 atoms, 69 bonds, 9 residues, 1 model selected
> select #27/F,I:686
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #27/F,I:675-686
196 atoms, 196 bonds, 24 residues, 1 model selected
> select #27/F,I:356
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #27/F,I:356-358
40 atoms, 38 bonds, 6 residues, 1 model selected
> select #27/F,I:356
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #27/F,I:356-366
164 atoms, 164 bonds, 22 residues, 1 model selected
> select #27/E,H:357
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #27/E,H:357-363
100 atoms, 100 bonds, 14 residues, 1 model selected
> open "/Volumes/Lab Backup/Jun Liu Lab 2025/Project files/Shigella/MxiA-
> project/Data_Images/07072025/fold_2025_06_25_11_12mxian9/fold_2025_06_25_11_12mxian9_model_0.cif"
Chain information for fold_2025_06_25_11_12mxian9_model_0.cif #26
---
Chain | Description
A B C D E F G H I | .
> select clear
> select add #26
23454 atoms, 23841 bonds, 3096 residues, 1 model selected
> view matrix models #26,1,0,0,146.86,0,1,0,151.64,0,0,1,307.37
> hide sel atoms
> show sel cartoons
> view matrix models #26,1,0,0,251.22,0,1,0,311.07,0,0,1,372.74
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.88671,-0.1247,0.4452,254.1,0.36009,0.79023,-0.49585,304.06,-0.28998,0.59999,0.7456,376.86
> matchmaker #26 to #27
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain A (#27) with
fold_2025_06_25_11_12mxian9_model_0.cif, chain A (#26), sequence alignment
score = 81.9
Fewer than 3 residues aligned; cannot match combination, chain A with
fold_2025_06_25_11_12mxian9_model_0.cif, chain A
> view matrix models
> #26,0.60949,-0.15384,0.77772,257.26,0.74455,0.44806,-0.49486,300.01,-0.27233,0.88067,0.38763,376.41
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.60949,-0.15384,0.77772,285.96,0.74455,0.44806,-0.49486,246.82,-0.27233,0.88067,0.38763,406.33
> view matrix models
> #26,0.60949,-0.15384,0.77772,274.92,0.74455,0.44806,-0.49486,246.93,-0.27233,0.88067,0.38763,406.52
> view matrix models
> #26,0.60949,-0.15384,0.77772,273.03,0.74455,0.44806,-0.49486,246.95,-0.27233,0.88067,0.38763,406.94
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.62253,-0.2226,0.75027,272.12,0.73187,0.50512,-0.4574,247.84,-0.27716,0.83385,0.47737,407.28
> view matrix models
> #26,0.9126,0.08348,0.40023,271.4,0.25148,0.65721,-0.71051,248.11,-0.32235,0.74907,0.57878,407.44
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.9126,0.08348,0.40023,271.28,0.25148,0.65721,-0.71051,250.69,-0.32235,0.74907,0.57878,407.22
> view matrix models
> #26,0.9126,0.08348,0.40023,265.43,0.25148,0.65721,-0.71051,250.09,-0.32235,0.74907,0.57878,407.91
> view matrix models
> #26,0.9126,0.08348,0.40023,260.97,0.25148,0.65721,-0.71051,250.94,-0.32235,0.74907,0.57878,408.4
> mlp sel
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_A SES
surface": minimum -27.73, mean -0.7528, maximum 23.91
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_B SES
surface": minimum -27.06, mean -0.7287, maximum 23.08
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_C SES
surface": minimum -27.17, mean -0.7259, maximum 23.76
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_D SES
surface": minimum -27.79, mean -0.6774, maximum 23.47
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_E SES
surface": minimum -27.83, mean -0.6658, maximum 23.42
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_F SES
surface": minimum -27.05, mean -0.7118, maximum 23.14
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_G SES
surface": minimum -28.03, mean -0.7055, maximum 23.34
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_H SES
surface": minimum -28.28, mean -0.728, maximum 23.46
Map values for surface "fold_2025_06_25_11_12mxian9_model_0.cif_I SES
surface": minimum -27.24, mean -0.7021, maximum 23.39
To also show corresponding color key, enter the above mlp command and add key
true
> show #!9 models
> view P1
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.93635,0.02058,0.35046,259.9,0.25148,0.65721,-0.71051,250.94,-0.24495,0.75342,0.61021,408.47
> view matrix models
> #26,0.93421,0.014723,0.35641,259.9,0.24097,0.71067,-0.66097,251.88,-0.26303,0.70337,0.66037,408.47
> ui mousemode right "translate selected models"
> view matrix models
> #26,0.93421,0.014723,0.35641,258.25,0.24097,0.71067,-0.66097,251.88,-0.26303,0.70337,0.66037,412.5
> turn x 90
> view matrix models
> #26,0.93421,0.014723,0.35641,256.64,0.24097,0.71067,-0.66097,262.97,-0.26303,0.70337,0.66037,412.5
> volume #312 region 0,0,0,120,120,200
No volumes specified
> volume #9 region 0,0,0,120,120,200
> view matrix models
> #26,0.93421,0.014723,0.35641,255.67,0.24097,0.71067,-0.66097,257.12,-0.26303,0.70337,0.66037,412.5
> show #!35 models
> view orient
> view matrix models
> #26,0.93421,0.014723,0.35641,255.72,0.24097,0.71067,-0.66097,257.87,-0.26303,0.70337,0.66037,412.5
> volume #9 region 0,60,0,120,120,200
> view P1
> color #26 #d26968ff
> select add #27
45696 atoms, 46299 bonds, 33 pseudobonds, 5841 residues, 12 models selected
> show sel surfaces
> save /Users/shoichitachiyama/Desktop/Shigella-ipaDnull-bin2-07072025.cxs
> includeMaps true
——— End of log from Tue Jul 8 20:43:49 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac13,1
Model Number: Z14J000E1LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 2 days, 6 hours
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Q24i-10:
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
ASUS PA279:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 12 days ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 12 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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