![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Last modified 11 months ago
#16460 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-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
Current thread 0x00000001d8069ec0 (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, chimerax.segment._segment, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, psutil._psutil_osx, psutil._psutil_posix (total: 65)
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{
"uptime" : 3300000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac13,1",
"coalitionID" : 1402,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2024-12-12 01:21:38.6496 -0500",
"codeSigningMonitor" : 1,
"incident" : "3F9A7BFA-F695-4E8A-91C4-57D7CF78D9CE",
"pid" : 31661,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-11 20:22:55.3917 -0500",
"procStartAbsTime" : 78825843324655,
"procExitAbsTime" : 79256000981915,
"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",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sip" : "enabled",
"vmRegionInfo" : "0x3a646d6379cb is not in any region. Bytes after previous region: 63664793287116 Bytes before following region: 41350109890101\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_MEDIUM 7d48000000-7d50000000 [128.0M] rw-\/rwx SM=PRV \n---> GAP OF 0x5f82b0000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x706f3a646d6379cb","rawCodes":[1,8101758457669188043],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x706f3a646d6379cb -> 0x00003a646d6379cb (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":31661},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x3a646d6379cb is not in any region. Bytes after previous region: 63664793287116 Bytes before following region: 41350109890101\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_MEDIUM 7d48000000-7d50000000 [128.0M] rw-\/rwx SM=PRV \n---> GAP OF 0x5f82b0000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review2.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.0379, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32
Opened 1xPflAB-New.mrc as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 1xPflAB-New-no-cyt-cage.mrc as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 2xFliL.mrc as #21, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits_imasked as #24, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 3xOnly-PflAB.mrc as #25, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 3xOnly-PflAB.mrc as #26, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 1xOnly-PflAB.mrc as #27, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened Rod.mrc as #31, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened PflA-2.1A-230911_imasked as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 3xOnly-PflAB.mrc as #34, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 2xMotB.mrc as #37, grid size 240,240,240, pixel 2.1, shown at level
0.000313, step 1, values float32
opened ChimeraX session
Showing PflA-2.seg - 27 regions, 27 surfaces
> close session
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/For_Fig4FG_After-cleaned.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in restore
data = fdeserialize(stream)
^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 81, in msgpack_deserialize
return next(stream)
^^^^^^^^^^^^
File "msgpack/_unpacker.pyx", line 540, in msgpack._cmsgpack.Unpacker.__next__
File "msgpack/_unpacker.pyx", line 474, in msgpack._cmsgpack.Unpacker._unpack
File "msgpack/_unpacker.pyx", line 448, in
msgpack._cmsgpack.Unpacker.read_from_file
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 668, in read
return self._buffer.read(size)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_compression.py",
line 68, in readinto
data = self.read(len(byte_view))
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_compression.py",
line 103, in read
data = self._decompressor.decompress(rawblock, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 414, in decompress
decompressed, bytes_read, eoframe = decompress_chunk(
^^^^^^^^^^^^^^^^^
RuntimeError: LZ4F_decompress failed with code: ERROR_decompressionFailed
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/For_Fig4FG.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in restore
data = fdeserialize(stream)
^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 81, in msgpack_deserialize
return next(stream)
^^^^^^^^^^^^
File "msgpack/_unpacker.pyx", line 540, in msgpack._cmsgpack.Unpacker.__next__
File "msgpack/_unpacker.pyx", line 474, in msgpack._cmsgpack.Unpacker._unpack
File "msgpack/_unpacker.pyx", line 448, in
msgpack._cmsgpack.Unpacker.read_from_file
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 668, in read
return self._buffer.read(size)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_compression.py",
line 68, in readinto
data = self.read(len(byte_view))
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/_compression.py",
line 103, in read
data = self._decompressor.decompress(rawblock, size)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 414, in decompress
decompressed, bytes_read, eoframe = decompress_chunk(
^^^^^^^^^^^^^^^^^
RuntimeError: LZ4F_decompress failed with code: ERROR_decompressionFailed
opened ChimeraX session
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Final-ver_side-
> view4top-09042024.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Single-MotA-truncated.mrc copy as #281, grid size 110,110,140, pixel
4.3,4.3,4.3, shown at level 0.00853, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #282, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #283, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #284, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #285, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #286, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #287, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #288, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #289, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #290, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #291, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #292, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #293, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #294, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #295, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #296, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #297, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #298, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened Cage-bottom.mrc as #356, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #357, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #358, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #359, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #360, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #361, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #362, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #363, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #364, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #365, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #366, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #367, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #368, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #369, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #370, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #371, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #372, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #373, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened PilM-region.mrc gaussian as #377, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #378, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #379, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #380, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #381, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #382, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #383, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #384, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #385, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #386, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #387, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #388, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #389, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #390, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #391, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #415, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #416, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #417, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #418, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PflA.mrc as #424, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00712, step 1, values float32
Opened PflA.mrc copy as #425, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #426, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #427, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #428, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #429, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #430, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #431, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #432, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #433, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #434, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #435, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #436, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #437, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #438, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #439, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #440, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #441, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc as #442, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #443, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #444, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #445, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #446, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #447, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #448, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #449, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #450, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #451, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #452, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #453, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #454, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #455, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #456, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #457, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #458, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #459, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened MotB_PG.mrc as #460, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #461, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #462, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #463, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #464, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #465, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #466, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #467, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #468, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #469, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #470, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #471, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #472, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #473, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #474, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #475, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #476, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #477, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
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Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened MotB_new.mrc copy as #124, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #125, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #126, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #127, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #128, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #129, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #130, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #131, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #132, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #133, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #134, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #135, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #136, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #137, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #138, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #139, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #140, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #141, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened PilM-region.mrc gaussian copy as #146, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #147, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #148, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #149, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #150, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #151, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #152, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #153, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #154, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #155, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #156, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #157, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #158, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #159, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #160, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #161, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #162, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #163, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #164, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
opened ChimeraX session
> hide #!20 models
> lighting soft
> lighting simple
> hide #!20-514 models
> show #!501 models
> show #!502 models
> show #!356 models
> hide #!356 models
> show #!195 models
> ui tool show "Side View"
> color #195 #797979ff models
> color #195 #7979793f models
> color #195 #79797940 models
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/2xCage_Dec112024.pdb
Chain information for 2xCage_Dec112024.pdb
---
Chain | Description
180.1/A 180.2/A | No description available
180.1/B 180.2/B | No description available
> select add #180
5540 atoms, 5658 bonds, 672 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #180,1,0,0,496.07,0,1,0,299.96,0,0,1,537.23
> view matrix models #180,1,0,0,443.22,0,1,0,98.18,0,0,1,500.89
> view matrix models #180,1,0,0,520.63,0,1,0,120.03,0,0,1,535.46
> ui mousemode right "rotate selected models"
> view matrix models
> #180,0.55567,-0.82363,-0.11343,580.11,0.77037,0.56137,-0.30231,5.4369,0.31267,0.080607,0.94644,490.54
> view matrix models
> #180,0.35687,0.93008,0.087107,589.69,-0.93401,0.35362,0.050816,249.07,0.01646,-0.099493,0.9949,534.41
> view matrix models
> #180,0.22903,0.96621,0.11823,607.76,-0.97322,0.22484,0.047827,256.15,0.019629,-0.12602,0.99183,534.24
> view matrix models
> #180,0.27284,0.95404,-0.12392,578.65,-0.96192,0.27272,-0.018312,247.25,0.016326,0.1242,0.99212,529.63
> ui mousemode right "translate selected models"
> view matrix models
> #180,0.27284,0.95404,-0.12392,572.44,-0.96192,0.27272,-0.018312,245.2,0.016326,0.1242,0.99212,527.9
> view matrix models
> #180,0.27284,0.95404,-0.12392,569.5,-0.96192,0.27272,-0.018312,271.7,0.016326,0.1242,0.99212,532.06
> ui mousemode right "rotate selected models"
> view matrix models
> #180,0.27086,0.95799,-0.094261,572.61,-0.96246,0.2713,-0.008322,272.78,0.017601,0.092976,0.99551,532.86
> ui mousemode right "translate selected models"
> view matrix models
> #180,0.27086,0.95799,-0.094261,569.7,-0.96246,0.2713,-0.008322,271.76,0.017601,0.092976,0.99551,532
> ui mousemode right "rotate selected models"
> view matrix models
> #180,0.27551,0.95778,-0.082193,570.33,-0.96096,0.27666,0.0027414,272.56,0.025365,0.078229,0.99661,531.45
> view matrix models
> #180,0.27322,0.95749,-0.092486,569.59,-0.96162,0.2744,1.6436e-05,272.42,0.025394,0.088932,0.99571,531.14
> ui mousemode right "translate selected models"
> view matrix models
> #180,0.27322,0.95749,-0.092486,570.28,-0.96162,0.2744,1.6436e-05,272.9,0.025394,0.088932,0.99571,529.72
> ui mousemode right "rotate selected models"
> view matrix models
> #180,0.27248,0.95713,-0.098256,569.81,-0.96184,0.2736,-0.0022305,272.72,0.024747,0.095115,0.99516,529.62
> select subtract #180
Nothing selected
> select add #180.1
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #180.1,1,-2.7539e-16,3.4694e-17,-0.14513,4.2978e-16,1,-4.1633e-17,4.5622,-4.5103e-17,-2.7756e-17,1,1.0106
> view matrix models
> #180.1,1,-3.0835e-16,3.8164e-17,-10.33,7.7672e-16,1,-4.1633e-17,4.447,-1.5959e-16,-4.1633e-17,1,2.5051
> ui mousemode right "rotate selected models"
> view matrix models
> #180.1,0.98051,-0.19315,0.035856,-6.7204,0.19409,0.98067,-0.024798,-21.608,-0.030373,0.031274,0.99905,6.4385
> select clear
> select add #180.1
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> view matrix models
> #180.1,0.97877,-0.20494,0.0043171,-9.5704,0.20483,0.97862,0.018706,-18.884,-0.0080584,-0.017425,0.99982,3.2767
> select clear
> select add #180
5540 atoms, 5658 bonds, 672 residues, 3 models selected
> view matrix models
> #180,0.28017,0.95685,-0.07715,570.97,-0.95885,0.28279,0.02523,274.86,0.045958,0.066906,0.9967,527.85
> select clear
> undo
> select clear
> select add #180
5540 atoms, 5658 bonds, 672 residues, 3 models selected
> save /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/Fixed_2xCage_Dec112024.pdb selectedOnly true
> combine #180 modelId #515 name Fixed_Cage_Dec112024
Remapping chain ID 'A' in 2xCage_Dec112024.pdb #180.2 to 'C'
Remapping chain ID 'B' in 2xCage_Dec112024.pdb #180.2 to 'D'
> select clear
> show #!113 models
> view orient
> sym #515 C18 copies true center #113
Made 18 copies for Fixed_Cage_Dec112024 symmetry C18
> color #188 #4a9ed2ff models
> hide #!180 models
> select add #188
99720 atoms, 101844 bonds, 12096 residues, 19 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> hide #180.1 models
> hide #180.2 models
> hide #!188 models
> hide #!195 models
> hide #!501 models
> hide #!502 models
> show #!183 models
> show #!184 models
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/1xPflB-1xPflAn.pdb
Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-
reviewer-response/1xPflB-1xPflAn.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3
33 messages similar to the above omitted
Chain information for 1xPflB-1xPflAn.pdb
---
Chain | Description
189.1/Cj | No description available
189.2/Ck | No description available
> select add #189
7938 atoms, 8108 bonds, 980 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #189,1,0,0,114.53,0,1,0,189.93,0,0,1,-65.109
> combine #189 modelId #516 name 1xPflB1xPflAn_Dec112024
> select subtract #189
Nothing selected
> hide #!189 models
> select add #516
7938 atoms, 8108 bonds, 980 residues, 1 model selected
> hide #!183.2 models
> hide #!183.3 models
> hide #!183.18 models
> view matrix models #516,1,0,0,62.759,0,1,0,212.35,0,0,1,-42.958
> matchmaker #516 to #183.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker New_PflB.pdb, chain CJ (#183.1) with 1xPflB1xPflAn_Dec112024, chain
Cj (#516), sequence alignment score = 4391.6
RMSD between 843 pruned atom pairs is 0.001 angstroms; (across all 843 pairs:
0.001)
> hide #!183.1 models
> hide #!184.19 models
> show #!184.19 models
> hide #!184.19 models
> view orient
> sym #516 C18 copies true center #113
Made 18 copies for 1xPflB1xPflAn_Dec112024 symmetry C18
> hide #!184.20 models
> hide #!184.21 models
> hide #!184.22 models
> hide #!184.23 models
> hide #!184.24 models
> hide #!184.25 models
> hide #!184.26 models
> hide #!184.27 models
> hide #!184.28 models
> hide #!184.29 models
> hide #!184.30 models
> hide #!184.31 models
> hide #!184.32 models
> hide #!184.34 models
> hide #!184.33 models
> hide #!184.35 models
> hide #!184.36 models
> hide #190.1 models
> show #190.1 models
> split #190
Split 1xPflB1xPflAn_Dec112024 (#190.1) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.2) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.3) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.4) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.5) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.6) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.7) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.8) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.9) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.10) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.11) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.12) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.13) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.14) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.15) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.16) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.17) into 2 models
Split 1xPflB1xPflAn_Dec112024 (#190.18) into 2 models
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.1.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.1.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.2.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.2.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.3.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.3.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.4.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.4.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.5.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.5.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.6.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.6.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.7.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.7.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.8.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.8.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.9.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.9.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.10.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.10.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.11.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.11.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.12.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.12.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.13.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.13.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.14.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.14.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.15.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.15.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.16.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.16.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.17.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.17.2
---
Chain | Description
Ck | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Cj #190.18.1
---
Chain | Description
Cj | No description available
Chain information for 1xPflB1xPflAn_Dec112024 Ck #190.18.2
---
Chain | Description
Ck | No description available
> save /Users/shoichitachiyama/Desktop/For-Fig4FG-1_Dec112024.cxs includeMaps
> true
> close #184.19-36
> close #190.1.1
> close #190.3.1
> close #190.2.1
> close #190.4.1
> close #190.5.1
> close #190.6.1
> close #190.7.1
> close #190.8.1
> close #190.9.1
> close #190.10.1
> close #190.11.1
> close #190.12.1
> close #190.13.1
> close #190.14.1
> close #190.15.1
> close #190.17.1
> close #190.18.1
Cell requested for row 0 is out of bounds for table with 421 rows! Resizing
table model.
> color #184.18 #e22d2ede
> color #184.18 #e22d2eff
> color #190 #e22d2eff
> select add #190
34729 atoms, 35528 bonds, 4289 residues, 39 models selected
> select clear
Drag select of 3 residues
> close #190.16.1
> show #!183.18 models
> show #!183.1 models
> show #!183.2 models
> show #!183.3 models
> select add #190
19962 atoms, 20448 bonds, 2466 residues, 37 models selected
> hide sel cartoons
> show sel surfaces
Cell requested for row 225 is out of bounds for table with 420 rows! Resizing
table model.
> select clear
> save /Users/shoichitachiyama/Desktop/For-Fig4FG-2_Dec112024.cxs includeMaps
> true
> hide #!183 models
> hide #!184 models
> hide #!190 models
Cell requested for row 166 is out of bounds for table with 366 rows! Resizing
table model.
> show #!169 models
> show #!168 models
> show #!167 models
> show #!101 models
> show #!124 models
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/Stator.pdb
Chain information for Stator.pdb
---
Chain | Description
191.1/? | No description available
191.2/C 191.3/D 191.4/E 191.5/F 191.6/G 191.7/H 191.8/I 191.9/J 191.10/K 191.11/L | No description available
191.12/K | No description available
191.12/L | No description available
> select add #191
21694 atoms, 22006 bonds, 2748 residues, 13 models selected
> view matrix models #191,1,0,0,522.33,0,1,0,92.81,0,0,1,487.79
> hide #!167 models
> hide #!168 models
> hide #!169 models
> view matrix models #191,1,0,0,561.26,0,1,0,129.1,0,0,1,534.06
> color #124 #905d122e models
> view matrix models #191,1,0,0,553.47,0,1,0,135.94,0,0,1,533.41
> ui mousemode right "rotate selected models"
> view matrix models
> #191,-0.16916,0.98404,0.055218,500.71,-0.98224,-0.17294,0.072784,279.06,0.081171,-0.041925,0.99582,534.64
> view matrix models
> #191,-0.17323,0.98376,0.046981,500.2,-0.98271,-0.17582,0.057991,278.17,0.065309,-0.036123,0.99721,534.7
> view matrix models
> #191,-0.16793,0.98403,0.059066,500.97,-0.98197,-0.17225,0.077845,279.39,0.086776,-0.044928,0.99521,534.7
> ui mousemode right "translate selected models"
> view matrix models
> #191,-0.16793,0.98403,0.059066,501.76,-0.98197,-0.17225,0.077845,279.4,0.086776,-0.044928,0.99521,534.56
> ui mousemode right "rotate selected models"
> view matrix models
> #191,-0.046867,0.99707,0.06053,497.05,-0.99665,-0.050739,0.064113,267.78,0.066996,-0.057323,0.99611,536.35
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #191,-0.047835,0.99882,-0.0083394,491.49,-0.9977,-0.047376,0.048494,266.28,0.048042,0.01064,0.99879,531.06
> show #!189 models
> hide #!189 models
> show #!183 models
> show #!184 models
> view matrix models
> #191,-0.5852,-0.80685,0.080823,685.38,0.81083,-0.58347,0.045971,261.23,0.010067,0.092435,0.99567,524.26
> view matrix models
> #191,-0.58192,-0.80859,0.086911,685.94,0.81266,-0.58224,0.024234,259.34,0.031007,0.084731,0.99592,524.43
> hide #!113 models
> view matrix models
> #191,0.76116,0.63831,-0.11485,509.03,-0.56227,0.73771,0.37368,211.56,0.32325,-0.21985,0.92042,536.55
> ui mousemode right "translate selected models"
> view matrix models
> #191,0.76116,0.63831,-0.11485,492.91,-0.56227,0.73771,0.37368,205.39,0.32325,-0.21985,0.92042,538.05
> view matrix models
> #191,0.76116,0.63831,-0.11485,496.22,-0.56227,0.73771,0.37368,201.31,0.32325,-0.21985,0.92042,539.44
> ui mousemode right "rotate selected models"
> view matrix models
> #191,0.75354,0.65736,0.0077807,504.87,-0.65657,0.75193,0.05932,177.33,0.033144,-0.049809,0.99821,540.4
> ui mousemode right "translate selected models"
> view matrix models
> #191,0.75354,0.65736,0.0077807,502.46,-0.65657,0.75193,0.05932,184.08,0.033144,-0.049809,0.99821,540.33
> show #!113 models
> hide #!113 models
> ui mousemode right "rotate selected models"
> view matrix models
> #191,0.49492,0.86877,0.016893,491.47,-0.86222,0.48859,0.13366,219.94,0.10786,-0.080716,0.99088,540.38
> view matrix models
> #191,0.46832,0.88251,-0.042972,486.28,-0.88319,0.46898,0.0061661,212.3,0.025595,0.035065,0.99906,532.82
> ui mousemode right "translate selected models"
> view matrix models
> #191,0.46832,0.88251,-0.042972,486.56,-0.88319,0.46898,0.0061661,212.95,0.025595,0.035065,0.99906,527.23
> view matrix models
> #191,0.46832,0.88251,-0.042972,486.6,-0.88319,0.46898,0.0061661,212.74,0.025595,0.035065,0.99906,529.43
> view matrix models
> #191,0.46832,0.88251,-0.042972,484.81,-0.88319,0.46898,0.0061661,212.11,0.025595,0.035065,0.99906,529.56
> ui mousemode right "rotate selected models"
> view matrix models
> #191,0.46461,0.88443,-0.043781,484.68,-0.88515,0.46527,0.0058092,212.49,0.025508,0.036053,0.99902,529.46
> view matrix models
> #191,0.4501,0.89175,-0.046933,484.16,-0.89263,0.45078,0.0044555,213.96,0.02513,0.039889,0.99889,529.1
> undo
> view matrix models
> #191,0.4553,0.88916,-0.045804,484.34,-0.88998,0.45597,0.0049336,213.44,0.025272,0.038518,0.99894,529.23
> view matrix models
> #191,0.45443,0.88961,-0.04558,484.34,-0.89002,0.45557,0.018149,214.51,0.03691,0.03232,0.9988,529.46
> select clear
> view orient
> show #!113 models
> sym #191 C18 copies true center #113
Made 18 copies for Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb,
Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb,
Stator.pdb symmetry C18
> hide #!192.1 models
> show #!192.1 models
> close #192
> show #191.1 models
> hide #191.1 models
> show #191.2 models
> hide #191.2 models
> show #191.12 models
> show #191.11 models
> hide #191.11 models
> color #191.12 #dfba68ff
> color #191.12 #90c5d9ff
> color #191.12 #dfba68ff
> show #191.1 models
> color #191.1 #e5ea15ff
> show #!168 models
> hide #!168.1 models
> show #!168.1 models
> hide #!168 models
> color #191.2 #d5720eff
Cell requested for row 0 is out of bounds for table with 379 rows! Resizing
table model.
> show #191.2 models
> color #191.3 #d5720eff
> color #191.4 #d5720eff
> color #191.5 #d5720eff
> color #191.6 #d5720eff
> color #191.7 #d5720eff
> color #191.8 #d5720eff
> color #191.9 #d5720eff
> color #191.10 #d5720eff
> color #191.11 #d5720eff
> show #191.3 models
> show #191.4 models
> show #191.5 models
> show #191.6 models
> show #191.7 models
> show #191.8 models
> show #191.9 models
> show #191.10 models
> show #191.11 models
> hide #!101 models
> view orient
> sym #191 C18 copies true center #113
Made 18 copies for Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb,
Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb, Stator.pdb,
Stator.pdb symmetry C18
> select add #192
390492 atoms, 396108 bonds, 49464 residues, 235 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> save /Users/shoichitachiyama/Desktop/For-Fig4FG-3_Dec112024.cxs includeMaps
> true
> show #!188 models
> show #!190 models
> hide #!113 models
> show #!501 models
> show #!502 models
> lighting soft
> save /Users/shoichitachiyama/Desktop/Fig4F.png supersample 2
> transparentBackground true
> show #!38 models
> show #!39 models
> show #!39-51 models
> show #!354-57 models
> show #!54-57 models
> hide #!54-57 models
> hide #!38-51 models
> turnx 45
Unknown command: turnx 45
> turn x 45
> turn x -45
> save /Users/shoichitachiyama/Desktop/Fig4G.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/For-Fig4FG-3_Dec112024.cxs includeMaps
> true
> close session
> open /Users/shoichitachiyama/Desktop/For-Fig4FG-3_Dec112024.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Single-MotA-truncated.mrc copy as #281, grid size 110,110,140, pixel
4.3,4.3,4.3, shown at level 0.00853, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #282, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #283, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #284, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #285, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #286, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #287, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #288, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #289, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #290, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #291, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #292, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #293, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #294, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #295, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #296, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #297, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #298, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened Cage-bottom.mrc as #356, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #357, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #358, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #359, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #360, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #361, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #362, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #363, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #364, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #365, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #366, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #367, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #368, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #369, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #370, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #371, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #372, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #373, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened PilM-region.mrc gaussian as #377, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #378, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #379, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #380, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #381, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #382, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #383, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #384, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #385, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #386, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #387, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #388, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #389, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #390, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #391, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #415, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #416, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #417, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #418, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PflA.mrc as #424, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00712, step 1, values float32
Opened PflA.mrc copy as #425, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #426, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #427, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #428, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #429, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #430, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #431, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #432, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #433, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #434, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #435, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #436, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #437, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #438, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #439, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #440, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #441, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc as #442, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
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Opened PflA_new.mrc copy as #15, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #17, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #18, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.15, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #21, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #22, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #23, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #24, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #25, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #26, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #27, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #28, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #31, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #32, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #33, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #34, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #35, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #36, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened Unknown_near_PflA.mrc copy as #37, grid size 240,240,240, pixel 2.1,
shown at level 0.127, step 1, values float32
Opened PflB_new.mrc copy as #38, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #39, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #40, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #41, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #42, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #43, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #44, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #45, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #46, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #47, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #48, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #49, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #50, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #51, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #54, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #55, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #56, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened PflB_new.mrc copy as #57, grid size 240,240,240, pixel 2.1, shown at
level 0.0467, step 1, values float32
Opened Top-cage.mrc copy as #58, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #59, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #73, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #74, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #75, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #76, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #77, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #78, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #79, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #80, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #81, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #82, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #83, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #84, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #86, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #121, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #122, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened Top-cage.mrc copy as #123, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened MotB_new.mrc copy as #124, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #125, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #126, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #127, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #128, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #129, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #130, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #131, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #132, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #133, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #134, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #135, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #136, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #137, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #138, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #139, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #140, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #141, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened PilM-region.mrc gaussian copy as #146, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #147, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #148, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #149, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #150, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #151, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #152, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #153, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #154, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #155, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #156, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #157, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #158, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #159, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #160, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #161, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #162, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #163, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #164, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close session
> open /Users/shoichitachiyama/Desktop/Chimera-Dec11_2024/Hp-C1-4.296A-msk.mrc
Opened Hp-C1-4.296A-msk.mrc as #1, grid size 220,220,220, pixel 4.3, shown at
level 0.151, step 1, values float32
> volume #1 level 0.02312
> volume #1 level 0.008419
> volume #1 level 0.005152
> ui tool show "Segment Map"
Segmenting Hp-C1-4.296A-msk.mrc, density threshold 0.005152
Showing 457 region surfaces
17934 watershed regions, grouped to 457 regions
Showing Hp-C1-4.296A-msk.seg - 457 regions, 457 surfaces
Drag select of 24638, 24560, 37313 of 55572 triangles, 24529, 24661, 24663,
34868 of 47056 triangles, 24523, 37743 of 45972 triangles, 24649, 24678,
24634, 4034 of 38580 triangles, 24528, 24681, 24605, 24602, 31449 of 40636
triangles, 24677, 33004 of 41320 triangles, 24334, 24530, 24647, 32629 of
32716 triangles, 24621, 26333 of 35044 triangles, 24660, 24656, 24693, 24590,
24626, 24582, 36444 of 36824 triangles, 24126, 23903 of 29260 triangles,
24641, 9935 of 29812 triangles, 24579, 31722 of 32292 triangles, 24490, 24495,
25572 of 28600 triangles, 24673, 28368 of 28440 triangles, 24557, 24581,
24269, 24520, 5261 of 25348 triangles, 24324, 6 of 24896 triangles, 24651,
24586, 24082, 21451 of 28596 triangles, 24675, 30980 of 32432 triangles,
24549, 13178 of 27088 triangles, 24669, 1682 of 23744 triangles, 24694, 8344
of 26812 triangles, 24179, 24418, 25608 of 25756 triangles, 24050, 10157 of
25148 triangles, 24601, 5393 of 26152 triangles, 24534, 202 of 24276
triangles, 24600, 34 of 26064 triangles, 24482, 24577, 24688, 24684, 10848 of
24728 triangles, 24637, 18350 of 24824 triangles, 24076, 24604, 24689, 24683,
24655, 24821 of 25220 triangles, 24594, 3760 of 23800 triangles, 24680, 24646,
24521, 19056 of 22648 triangles, 24658, 614 of 21252 triangles, 24152, 2747 of
20828 triangles, 24526, 21218 of 23420 triangles, 24336, 323 of 20752
triangles, 24652, 24472, 9560 of 20488 triangles, 24619, 5642 of 22676
triangles, 24692, 10081 of 19764 triangles, 24288, 24691, 24566, 24398, 24695,
18692 of 20148 triangles, 24617, 24629, 989 of 19584 triangles, 24554, 5973 of
16800 triangles, 24627, 16181 of 16708 triangles, 24476, 24259, 7371 of 16148
triangles, 24576, 6716 of 19764 triangles, 24329, 2502 of 17328 triangles,
24653, 24140, 11891 of 16152 triangles, 24232, 15528 of 15976 triangles,
24265, 24671, 10670 of 15956 triangles, 24603, 24588, 1219 of 17320 triangles,
24299, 7867 of 16324 triangles, 24665, 24210, 24484, 14978 of 16848 triangles,
24130, 3344 of 15144 triangles, 24136, 9592 of 15196 triangles, 24431, 24363,
24648, 16157 of 16376 triangles, 22667, 11505 of 13856 triangles, 24589, 9505
of 14000 triangles, 24417, 15271 of 16264 triangles, 24609, 7359 of 16956
triangles, 24518, 14689 of 15232 triangles, 24049, 24209, 24538, 3109 of 12560
triangles, 24416, 7727 of 15380 triangles, 24093, 24222, 24262, 13160 of 13284
triangles, 22438, 9363 of 13116 triangles, 24147, 9024 of 13724 triangles,
24552, 10318 of 12548 triangles, 24399, 8152 of 13188 triangles, 24442, 24123,
11806 of 12376 triangles, 24286, 566 of 13040 triangles, 24112, 24359, 11332
of 12572 triangles, 24507, 6839 of 11816 triangles, 24682, 24376, 24131, 12913
of 12988 triangles, 24696, 10279 of 11768 triangles, 24411, 11958 of 12136
triangles, 24051, 11150 of 11996 triangles, 24461, 12398 of 12448 triangles,
24300, 24067, 24498, 11843 of 11888 triangles, 24555, 11982 of 12224
triangles, 24148, 24264, 7652 of 10676 triangles, 24276, 10656 of 11096
triangles, 24100, 24486, 6105 of 10544 triangles, 24290, 24311, 24077, 24483,
24491, 24407, 22523, 9883 of 10872 triangles, 23003, 24487, 23656, 24471, 5930
of 9836 triangles, 24516, 24139, 23426, 7371 of 8908 triangles, 24181, 1549 of
7796 triangles, 24447, 22950, 8202 of 9020 triangles, 24278, 24250, 24464, 4
of 6788 triangles, 24193, 24356, 23138, 851 of 6336 triangles, 22799, 23352,
831 of 5976 triangles, 24514, 22563, 23024, 23337, 1362 of 5656 triangles,
24553, 669 of 5764 triangles, 23158, 1712 of 4988 triangles, 22647, 20075,
1567 of 5072 triangles, 23786, 22800, 1142 of 4712 triangles, 1
Hp-C1-4.296A-msk.mrc
> hide #!1 models
> select subtract #1
172 models selected
> select add #2.30
173 models selected
> select add #2.105
174 models selected
> select add #2.403
175 models selected
> select add #2.113
176 models selected
> select add #2.48
177 models selected
> select add #2.198
178 models selected
> select add #2.67
179 models selected
> select add #2.313
180 models selected
> select add #2.169
181 models selected
> select add #2.356
182 models selected
> select add #2.110
183 models selected
> select add #2.248
184 models selected
> select add #2.119
185 models selected
> select add #2.94
186 models selected
> select add #2.382
187 models selected
> select add #2.118
188 models selected
> select add #2.125
189 models selected
> select add #2.443
190 models selected
> select add #2.269
191 models selected
> select add #2.311
192 models selected
> select add #2.320
193 models selected
> select add #2.267
194 models selected
> select add #2.331
195 models selected
> select add #2.207
196 models selected
> select add #2.181
197 models selected
> select add #2.221
198 models selected
> select add #2.308
199 models selected
> select add #2.314
200 models selected
Drag select of 24613, 27 of 55436 triangles, 24606, 11466 of 31892 triangles,
24598, 24522, 24550, 24404, 4748 of 21872 triangles, 24224, 7596 of 21712
triangles, 24124, 3174 of 22112 triangles, 24622, 7230 of 18152 triangles,
24341, 3824 of 19724 triangles, 24261, 3639 of 17728 triangles, 24570, 24068,
6147 of 18756 triangles, 24481, 6693 of 21232 triangles, 24241, 2336 of 17984
triangles, 24475, 19491 of 19520 triangles, 24161, 4970 of 17368 triangles,
24318, 1530 of 19672 triangles, 24234, 1832 of 17496 triangles, 24378, 4485 of
14856 triangles, 24640, 24470, 22467, 2349 of 14348 triangles, 23932, 145 of
12660 triangles, 24187, 24129, 2524 of 10888 triangles, 24456, 1919 of 13652
triangles, 22471, 1021 of 11840 triangles, 22821, 4957 of 10728 triangles,
24349, 4476 of 11444 triangles, 24335, 1018 of 12380 triangles, 22804, 332 of
12340 triangles, 24572, 24666, 2398 of 12384 triangles, 24558, 24292, 2019 of
11300 triangles, 24326, 5246 of 10060 triangles, 24002, 737 of 7864 triangles,
23935, 9 of 7160 triangles, 24393, 4372 of 9524 triangles, 24672, 2249 of 9512
triangles, 24668, 24165, 24543, 7358 of 9132 triangles, 23912, 4043 of 5592
triangles, 24578, 24041, 24676, 23037, 5864 of 6072 triangles, 22990, 22512,
5250 of 5760 triangles, 22501, 24257, 4740 of 5064 triangles, 24391, 24040,
22421, 4903 of 5464 triangles, 24667, 22672, 4609 of 4652 triangles, 24285,
23723, 23917, 415 of 4364 triangles, 22592, 23065, 3753 of 3872 triangles,
23356, 24 of 3808 triangles, 20711, 19 of 3960 triangles, 23185, 3232 of 3260
triangles, 23978, 21602, 23826, 23162, 21874, 23055, 1295 of 2332 triangles,
21210, 2212 of 2240 triangles, 23402, 23979, 23762, 21466, 23395, 22970, 2106
of 2168 triangles, 21159, 22121, 23731, 23892, 1667 of 1980 triangles, 23746,
23743, 22169, 22959, 1536 of 1652 triangles, 181, 22114, 406, 874, 488 of 1348
triangles, 22215, 24018
> select add #2.279
294 models selected
> select add #2.360
295 models selected
> select add #2.228
296 models selected
> select add #2.401
297 models selected
> select add #2.323
298 models selected
Drag select of 24277, 5 of 12492 triangles, 24573, 6 of 10928 triangles,
24192, 11 of 6272 triangles
> select add #2.392
302 models selected
> select add #2.410
303 models selected
> select add #2.240
304 models selected
> select add #2.247
305 models selected
> select add #2.399
306 models selected
> select add #2.229
307 models selected
> select subtract #2.369
306 models selected
> select add #2.235
307 models selected
> select add #2.385
308 models selected
> select add #2.340
309 models selected
> select add #2.343
310 models selected
> select add #2.390
311 models selected
> select add #2.366
312 models selected
> select add #2.412
313 models selected
> select subtract #2.130
312 models selected
> select clear
Drag select of 24638, 53626 of 58216 triangles, 24560, 54988 of 55572
triangles, 24529, 41561 of 49176 triangles, 24661, 24663, 47029 of 47056
triangles, 24523, 24649, 24678, 42159 of 51000 triangles, 24528, 24681, 38581
of 45512 triangles, 24605, 40287 of 40532 triangles, 24602, 40292 of 40636
triangles, 24677, 24334, 31334 of 41080 triangles, 24597, 15 of 31868
triangles, 24530, 24647, 32538 of 32716 triangles, 24621, 24660, 37249 of
44624 triangles, 24656, 24693, 24590, 29164 of 33036 triangles, 24626, 24582,
36818 of 36824 triangles, 24547, 1951 of 27756 triangles, 24126, 24641, 1053
of 29812 triangles, 24579, 24490, 24495, 24673, 28157 of 28440 triangles,
24557, 27712 of 32384 triangles, 24581, 23062 of 26724 triangles, 24269, 31168
of 32232 triangles, 24639, 705 of 26012 triangles, 24324, 6530 of 24896
triangles, 24651, 32203 of 33976 triangles, 24586, 24082, 24675, 24549, 39 of
27088 triangles, 24694, 1179 of 26812 triangles, 24179, 24418, 24050, 1044 of
25148 triangles, 24601, 1393 of 26152 triangles, 24534, 22 of 24276 triangles,
24600, 8568 of 26064 triangles, 24482, 24712 of 25604 triangles, 24577, 24688,
25714 of 25960 triangles, 24684, 240 of 24728 triangles, 24616, 11319 of 25564
triangles, 24637, 24076, 26132 of 29592 triangles, 24604, 19886 of 23308
triangles, 24689, 22537 of 24428 triangles, 24683, 24655, 24594, 5189 of 23800
triangles, 24541, 1140 of 21380 triangles, 24680, 24646, 24568, 8206 of 22464
triangles, 24521, 17212 of 22648 triangles, 24615, 662 of 18792 triangles,
24658, 855 of 21252 triangles, 24152, 3392 of 20828 triangles, 24526, 24625,
6642 of 20968 triangles, 24330, 7827 of 19792 triangles, 24336, 2873 of 20752
triangles, 24652, 21128 of 22412 triangles, 24472, 120 of 20488 triangles,
24692, 19210 of 19764 triangles, 24473, 5505 of 19256 triangles, 24288, 24691,
24566, 24398, 24695, 24617, 24554, 3256 of 16800 triangles, 24627, 10651 of
16708 triangles, 24476, 24576, 28 of 19764 triangles, 24329, 1319 of 17328
triangles, 24044, 4003 of 16100 triangles, 24653, 24140, 14417 of 16152
triangles, 24232, 24265, 24671, 14162 of 15956 triangles, 24603, 8558 of 15428
triangles, 24588, 5236 of 17320 triangles, 24299, 346 of 16324 triangles,
24665, 24210, 24484, 24130, 1473 of 15144 triangles, 24136, 14471 of 15196
triangles, 24431, 24434, 444 of 15768 triangles, 24363, 24648, 12526 of 16376
triangles, 22667, 10251 of 13856 triangles, 24589, 9124 of 14000 triangles,
24417, 24518, 24049, 24209, 24538, 3232 of 12560 triangles, 24093, 24222,
24610, 4719 of 13772 triangles, 24262, 7999 of 13284 triangles, 22438, 11155
of 13116 triangles, 24147, 13656 of 13724 triangles, 24552, 10415 of 12548
triangles, 24399, 13010 of 13188 triangles, 24442, 12318 of 12796 triangles,
24123, 24286, 2335 of 13040 triangles, 24112, 24359, 24507, 11207 of 11816
triangles, 24682, 24376, 24131, 12964 of 12988 triangles, 24696, 9976 of 11768
triangles, 24411, 24051, 8833 of 11996 triangles, 24461, 12124 of 12448
triangles, 24300, 11486 of 11580 triangles, 24067, 7474 of 11968 triangles,
24498, 11886 of 11888 triangles, 24555, 12103 of 12224 triangles, 24148, 10441
of 11064 triangles, 24264, 7782 of 10676 triangles, 24276, 11077 of 11096
triangles, 24100, 7795 of 11468 triangles, 24486, 10387 of 10544 triangles,
24290, 24311, 24077, 7909 of 11344 triangles, 24483, 7348 of 11528 triangles,
24491, 24551, 30 of 8792 triangles, 24611, 3321 of 12560 triangles, 24407,
8095 of 11308 triangles, 22523, 10866 of 10872 triangles, 23003, 24487, 8410
of 9132 triangles, 23656, 8694 of 9504 triangles, 24471, 9269 of 9836
triangles, 24516, 24139, 8776 of 9312 triangles, 23426, 7771 of 8908
triangles, 24181, 2248 of 7796 triangles, 24447, 22950, 24278, 22965, 2715 of
7980 triangles, 24250, 24193, 24356, 23138, 1806 of 6336 triangles, 22799,
23352, 1895 of 5976 triangles, 24514, 22563, 23024, 23673, 822 of 5652
triangles, 23337, 1403 of 5656 triangles, 24553, 571 of 5764 triangles, 23158,
831 of 4988 triangles, 22647, 23786
> select add #2.181
179 models selected
> select add #2.207
180 models selected
> select add #2.311
181 models selected
> select add #2.269
182 models selected
> select add #2.308
183 models selected
> select add #2.221
184 models selected
> select add #2.78
185 models selected
> select add #2.145
186 models selected
> select add #2.68
187 models selected
> select add #2.123
188 models selected
> select add #2.15
189 models selected
> select add #2.363
190 models selected
> select add #2.403
191 models selected
> select add #2.331
192 models selected
> select add #2.267
193 models selected
> select add #2.320
194 models selected
> select add #2.237
195 models selected
> select add #2.159
196 models selected
> select add #2.393
197 models selected
> select add #2.216
198 models selected
> select add #2.398
199 models selected
> select add #2.350
200 models selected
> select add #2.364
201 models selected
> select add #2.443
202 models selected
Grouped 202 regions
> select clear
Drag select of 24598, 25442 of 28812 triangles, 24522, 32545 of 32668
triangles, 24550, 24404, 2167 of 21872 triangles, 24124, 141 of 22112
triangles, 24341, 1982 of 19724 triangles, 24261, 3508 of 17728 triangles,
24570, 24438 of 25068 triangles, 24481, 24 of 21232 triangles, 24241, 1592 of
17984 triangles, 24475, 19472 of 19520 triangles, 24318, 1759 of 19672
triangles, 24234, 1777 of 17496 triangles, 24378, 214 of 14856 triangles,
24640, 24470, 22467, 1776 of 14348 triangles, 24187, 13607 of 14156 triangles,
24129, 2607 of 10888 triangles, 24456, 186 of 13652 triangles, 24349, 1394 of
11444 triangles, 24572, 24666, 74 of 12384 triangles, 24558, 24672, 566 of
9512 triangles, 24668, 24165, 24543, 2536 of 9132 triangles, 23912, 320 of
5592 triangles, 24578, 24041, 24676, 23037, 2944 of 6072 triangles, 22990,
22512, 1504 of 5760 triangles, 22501, 24257, 2229 of 5064 triangles, 24391,
24040, 22421, 2878 of 5464 triangles, 24667, 22672, 3127 of 4652 triangles,
24285, 1606 of 4664 triangles, 23723, 22592, 23065, 1469 of 3872 triangles,
23185, 1046 of 3260 triangles, 23978, 21602, 23826, 23162, 1139 of 2800
triangles, 21874, 23055, 21210, 2212 of 2240 triangles, 23402, 23979, 23762,
1095 of 1972 triangles, 23395, 22970, 22121, 23731, 1163 of 1872 triangles,
23746, 23743, 22169, 22959, 1548 of 1652 triangles, 181, 22114, 406, 874, 955
of 1348 triangles, 21098, 593 of 1532 triangles, 22215, 24018
> select add #2.183
73 models selected
> select add #2.285
74 models selected
> select add #2.60
75 models selected
> select add #2.158
76 models selected
> select add #2.133
77 models selected
> select add #2.114
78 models selected
> select add #2.290
79 models selected
> select add #2.345
80 models selected
> select add #2.421
81 models selected
> select add #2.361
82 models selected
> select add #2.273
83 models selected
> select add #2.353
84 models selected
> select add #2.283
85 models selected
> select add #2.298
86 models selected
> select add #2.423
87 models selected
> select add #2.362
88 models selected
> select add #2.351
89 models selected
> select add #2.417
90 models selected
> select add #2.340
91 models selected
> select add #2.385
92 models selected
> select add #2.235
93 models selected
> select add #2.229
94 models selected
> select add #2.247
95 models selected
> select add #2.240
96 models selected
> select add #2.399
97 models selected
> select add #2.410
98 models selected
> select add #2.392
99 models selected
> select add #2.323
100 models selected
> select add #2.369
101 models selected
> select add #2.228
102 models selected
> select add #2.401
103 models selected
> select add #2.360
104 models selected
> select add #2.279
105 models selected
> select add #2.412
106 models selected
> select add #2.343
107 models selected
> select add #2.390
108 models selected
> select add #2.366
109 models selected
Grouped 109 regions
> select add #2.3
2 models selected
Grouped 2 regions
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened Hp-C1-4.296A-msk_imasked as #3, grid size 220,220,220, pixel 4.3, shown
at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Segmenting Hp-C1-4.296A-msk_imasked, density threshold 0.005152
Showing 146 region surfaces
6635 watershed regions, grouped to 146 regions
Showing Hp-C1-4.seg - 146 regions, 146 surfaces
> select #2.4
1 model selected
> select add #2.21
2 models selected
> select add #2.27
3 models selected
> select add #2.2
4 models selected
> select add #2.17
5 models selected
> select add #2.5
6 models selected
> select add #2.11
7 models selected
> select subtract #2.11
6 models selected
> select add #2.3
7 models selected
> select add #2.11
8 models selected
> select add #2.39
9 models selected
> select add #2.109
10 models selected
> select add #2.23
11 models selected
> select add #2.31
12 models selected
> select add #2.8
13 models selected
> select add #2.19
14 models selected
> select add #2.10
15 models selected
> select add #2.7
16 models selected
> select add #2.1
17 models selected
> select add #2.13
18 models selected
> select add #2.25
19 models selected
> select add #2.20
20 models selected
> select add #2.35
21 models selected
> select add #2.15
22 models selected
> select add #2.14
23 models selected
> select add #2.18
24 models selected
> select add #2.6
25 models selected
> select add #2.9
26 models selected
> select add #2.38
27 models selected
> select add #2.22
28 models selected
> select add #2.34
29 models selected
> select add #2.59
30 models selected
> select add #2.29
31 models selected
> select add #2.16
32 models selected
> hide #!3 models
> select add #2.36
33 models selected
> select add #2.62
34 models selected
> select add #2.142
35 models selected
> select add #2.143
36 models selected
> select add #2.141
37 models selected
> select add #2.24
38 models selected
> select add #2.30
39 models selected
> select add #2.37
40 models selected
> select add #2.33
41 models selected
> select add #2.26
42 models selected
> select add #2.55
43 models selected
> select add #2.52
44 models selected
> select add #2.82
45 models selected
> select add #2.28
46 models selected
> select add #2.84
47 models selected
> select add #2.56
48 models selected
> select add #2.49
49 models selected
> select add #2.98
50 models selected
> select add #2.66
51 models selected
> select add #2.105
52 models selected
> select add #2.92
53 models selected
> select add #2.103
54 models selected
> select add #2.88
55 models selected
> select add #2.100
56 models selected
> select add #2.67
57 models selected
> select add #2.97
58 models selected
> select add #2.93
59 models selected
> select add #2.71
60 models selected
> select add #2.104
61 models selected
> select add #2.99
62 models selected
> select add #2.94
63 models selected
> select add #2.68
64 models selected
> select add #2.69
65 models selected
> select add #2.129
66 models selected
> select add #2.90
67 models selected
> select add #2.101
68 models selected
> select add #2.127
69 models selected
> select add #2.12
70 models selected
> select add #2.65
71 models selected
> select add #2.63
72 models selected
> select add #2.108
73 models selected
> select add #2.115
74 models selected
> select add #2.135
75 models selected
> select add #2.118
76 models selected
> select add #2.144
77 models selected
> select add #2.146
78 models selected
Grouped 78 regions
> select add #2.32
2 models selected
> select add #2.138
3 models selected
> select add #2.134
4 models selected
> select add #2.122
5 models selected
> select add #2.137
6 models selected
> select add #2.136
7 models selected
> select add #2.132
8 models selected
> select add #2.128
9 models selected
> select add #2.139
10 models selected
> select add #2.123
11 models selected
> select add #2.133
12 models selected
> select add #2.125
13 models selected
> select add #2.140
14 models selected
> select add #2.119
15 models selected
> select add #2.131
16 models selected
> select add #2.96
17 models selected
> select add #2.126
18 models selected
> select add #2.107
19 models selected
Grouped 19 regions
Opened Hp-C1-4_imasked as #4, grid size 220,220,220, pixel 4.3, shown at step
1, values float32
Segmenting Hp-C1-4_imasked, density threshold 0.005152
Showing 50 region surfaces
884 watershed regions, grouped to 50 regions
Showing Hp-C1-4_imasked.seg - 50 regions, 50 surfaces
> hide #!2 models
> hide #!4 models
> show #!2 models
> select #2.1
1 model selected
> select add #2.17
2 models selected
> select add #2.4
3 models selected
> select add #2.3
4 models selected
> select add #2.15
5 models selected
> select add #2.11
6 models selected
> select add #2.12
7 models selected
> select add #2.5
8 models selected
> select add #2.16
9 models selected
> select add #2.2
10 models selected
> select add #2.7
11 models selected
> select add #2.10
12 models selected
> select add #2.13
13 models selected
> select add #2.8
14 models selected
> select add #2.14
15 models selected
> show #!3 models
Segmenting Hp-C1-4.296A-msk_imasked, density threshold 0.005152
Showing 146 region surfaces
6635 watershed regions, grouped to 146 regions
Showing Hp-C1-4.seg - 146 regions, 146 surfaces
> close #4
> select #2.63
1 model selected
> select add #2.12
2 models selected
> select add #2.65
3 models selected
> select #2.20
1 model selected
> select add #2.14
2 models selected
> select add #2.15
3 models selected
> select add #2.18
4 models selected
> select add #2.6
5 models selected
> select add #2.9
6 models selected
> select add #2.38
7 models selected
> select add #2.22
8 models selected
Drag select of 9185, 21 of 34272 triangles, 9174, 43 of 35160 triangles
> select add #2.59
9 models selected
> select add #2.29
10 models selected
> select add #2.16
11 models selected
> select add #2.4
12 models selected
> select add #2.21
13 models selected
> select add #2.27
14 models selected
> select add #2.2
15 models selected
> select add #2.17
16 models selected
> select add #2.5
17 models selected
> select add #2.11
18 models selected
> select add #2.3
19 models selected
> select add #2.39
20 models selected
> select add #2.109
21 models selected
> select add #2.31
22 models selected
> select add #2.8
23 models selected
> select add #2.19
24 models selected
> select add #2.10
25 models selected
> select add #2.7
26 models selected
> select add #2.1
27 models selected
> select add #2.13
28 models selected
> select add #2.25
29 models selected
> select add #2.35
30 models selected
> select subtract #2.20
29 models selected
> select add #2.20
30 models selected
> select subtract #2.14
29 models selected
> select add #2.14
30 models selected
> hide #!3 models
> select add #2.23
31 models selected
> select add #2.28
32 models selected
> select add #2.52
33 models selected
> select add #2.55
34 models selected
> select add #2.26
35 models selected
> select add #2.33
36 models selected
> select add #2.22
37 models selected
> select add #2.30
38 models selected
> select add #2.24
39 models selected
> select add #2.36
40 models selected
> select add #2.62
41 models selected
> select add #2.103
42 models selected
> select add #2.88
43 models selected
> select add #2.100
44 models selected
> select add #2.67
45 models selected
> select add #2.97
46 models selected
> select add #2.93
47 models selected
> select add #2.37
48 models selected
> select add #2.71
49 models selected
> select add #2.104
50 models selected
> select add #2.99
51 models selected
> select add #2.94
52 models selected
> select add #2.68
53 models selected
> select subtract #2.68
52 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2.69
53 models selected
> select add #2.68
54 models selected
> select add #2.12
55 models selected
> select add #2.115
56 models selected
> select add #2.135
57 models selected
> select add #2.108
58 models selected
> select add #2.63
59 models selected
> select add #2.65
60 models selected
> select add #2.101
61 models selected
> select add #2.105
62 models selected
> select add #2.92
63 models selected
> select add #2.66
64 models selected
> select add #2.127
65 models selected
> select add #2.90
66 models selected
> select add #2.98
67 models selected
> select add #2.49
68 models selected
> select add #2.56
69 models selected
> select add #2.84
70 models selected
> select subtract #2.84
69 models selected
> select add #2.84
70 models selected
> select add #2.82
71 models selected
> select add #2.129
72 models selected
> select add #2.118
73 models selected
> select add #2.143
74 models selected
> select add #2.142
75 models selected
> select add #2.141
76 models selected
> select add #2.144
77 models selected
> select add #2.146
78 models selected
> select add #2.32
79 models selected
> select add #2.122
80 models selected
> select add #2.137
81 models selected
> select add #2.136
82 models selected
> select add #2.132
83 models selected
> select add #2.128
84 models selected
> select add #2.139
85 models selected
> select add #2.123
86 models selected
> select add #2.133
87 models selected
> select add #2.125
88 models selected
> select add #2.138
89 models selected
> select add #2.134
90 models selected
> select add #2.140
91 models selected
Grouped 91 regions
Opened Hp-C1-4_imasked as #4, grid size 220,220,220, pixel 4.3, shown at step
1, values float32
Segmenting Hp-C1-4_imasked, density threshold 0.005152
Showing 55 region surfaces
953 watershed regions, grouped to 55 regions
Showing Hp-C1-4_imasked.seg - 55 regions, 55 surfaces
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Chimera-Dec11_2024/All_periplasm.mrc
> models #4
> select #2.16
1 model selected
> select add #2.2
2 models selected
> select add #2.7
3 models selected
> select add #2.10
4 models selected
> select add #2.13
5 models selected
> select add #2.8
6 models selected
> select add #2.14
7 models selected
> select add #2.6
8 models selected
> select add #2.9
9 models selected
> select add #2.18
10 models selected
> select add #2.1
11 models selected
> select add #2.17
12 models selected
> select add #2.4
13 models selected
> select add #2.3
14 models selected
> select add #2.15
15 models selected
> select add #2.11
16 models selected
> select add #2.12
17 models selected
> select add #2.5
18 models selected
Ungrouped to 44 regions
Ungrouped to 140 regions
> select clear
> select #2.105
1 model selected
> select add #2.104
2 models selected
> select add #2.216
3 models selected
> select add #2.217
4 models selected
> select add #2.130
5 models selected
> select add #2.134
6 models selected
> select add #2.133
7 models selected
> select add #2.131
8 models selected
> select add #2.10
9 models selected
> select add #2.8
10 models selected
> select add #2.9
11 models selected
> select add #2.203
12 models selected
> select add #2.204
13 models selected
> select add #2.4
14 models selected
> select add #2.3
15 models selected
> select add #2.1
16 models selected
> select add #2.116
17 models selected
> select add #2.115
18 models selected
> select add #2.177
19 models selected
> select add #2.190
20 models selected
> select add #2.189
21 models selected
> select add #2.181
22 models selected
> select add #2.159
23 models selected
> select add #2.113
24 models selected
> select add #2.114
25 models selected
> select add #2.201
26 models selected
> select subtract #2.201
25 models selected
> select add #2.200
26 models selected
> select add #2.201
27 models selected
> select add #2.135
28 models selected
> select add #2.124
29 models selected
> select add #2.198
30 models selected
> select add #2.199
31 models selected
> select add #2.103
32 models selected
> select add #2.102
33 models selected
> select add #2.156
34 models selected
> select add #2.206
35 models selected
> hide #!4 models
> select add #2.125
36 models selected
> select add #2.182
37 models selected
> select add #2.19
38 models selected
> select subtract #2.19
37 models selected
> select add #2.137
38 models selected
> select add #2.140
39 models selected
> select subtract #2.140
38 models selected
> select subtract #2.137
37 models selected
Grouped 37 regions
> select clear
> select #2.120
1 model selected
> select add #2.112
2 models selected
> select add #2.197
3 models selected
> select add #2.195
4 models selected
> select subtract #2.195
3 models selected
> select add #2.191
4 models selected
> select add #2.59
5 models selected
> select add #2.19
6 models selected
> select subtract #2.19
5 models selected
> select add #2.183
6 models selected
> select add #2.220
7 models selected
> select add #2.218
8 models selected
> select subtract #2.218
7 models selected
> select add #2.188
8 models selected
> select add #2.207
9 models selected
> select subtract #2.207
8 models selected
> select add #2.211
9 models selected
> select add #2.163
10 models selected
> select add #2.5
11 models selected
> select add #2.137
12 models selected
> select add #2.146
13 models selected
> select add #2.16
14 models selected
> select add #2.169
15 models selected
> select add #2.63
16 models selected
> select add #2.128
17 models selected
> select add #2.100
18 models selected
Grouped 18 regions
> select #2.179
1 model selected
Ungrouped to 6 regions
> select clear
> select #2.8
1 model selected
> select add #2.5
2 models selected
> select add #2.150
3 models selected
> select clear
> select #2.150
1 model selected
Ungrouped to 4 regions
> select #2.58
1 model selected
> select add #2.3
2 models selected
> select add #2.5
3 models selected
> select add #2.8
4 models selected
Grouped 4 regions
> select #2.140
1 model selected
Ungrouped to 4 regions
> select #2.63
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.132
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.126
1 model selected
Ungrouped to 6 regions
Ungrouped to 7 regions
> select #2.75
1 model selected
> select add #2.3
2 models selected
> select subtract #2.3
1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #2.75
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
Ungrouped to 2 regions
Grouped 2 regions
> select clear
> select #2.111
1 model selected
Ungrouped to 2 regions
Ungrouped to 8 regions
> select #2.78
1 model selected
> select add #2.82
2 models selected
> select add #2.3
3 models selected
> select clear
> select #2.78
1 model selected
> select #2.82
1 model selected
Ungrouped to 0 regions
Ungrouped to 6 regions
> select #2.78
1 model selected
> select add #2.3
2 models selected
> select #2.78
1 model selected
> select #2.3
1 model selected
> select #2.195
1 model selected
Ungrouped to 5 regions
> select #2.38
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.187
1 model selected
Ungrouped to 5 regions
Ungrouped to 6 regions
> select #2.98
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.144
1 model selected
> select add #2.3
2 models selected
> select add #2.7
3 models selected
> select subtract #2.7
2 models selected
Grouped 2 regions
> select clear
> select #2.7
1 model selected
Ungrouped to 5 regions
Ungrouped to 3 regions
> select #2.104
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.14
1 model selected
Ungrouped to 4 regions
> select #2.105
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.218
1 model selected
Ungrouped to 6 regions
Ungrouped to 2 regions
> select #2.115
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
> select #2.3
1 model selected
Ungrouped to 2 regions
Ungrouped to 4 regions
Ungrouped to 20 regions
> select clear
> select #2.169
1 model selected
Ungrouped to 4 regions
> select #2.197
1 model selected
Ungrouped to 2 regions
> select #2.198
1 model selected
> select add #2.195
2 models selected
Grouped 2 regions
> select add #2.163
2 models selected
> select add #2.131
3 models selected
> select add #2.112
4 models selected
> select add #2.183
5 models selected
> select add #2.181
6 models selected
> select add #2.177
7 models selected
> select add #2.187
8 models selected
> select add #2.115
9 models selected
> select add #2.188
10 models selected
> select add #2.128
11 models selected
> select add #2.146
12 models selected
> select add #2.140
13 models selected
> select add #2.126
14 models selected
> select add #2.159
15 models selected
> select add #2.125
16 models selected
> select add #2.179
17 models selected
> select add #2.132
18 models selected
> select add #2.137
19 models selected
> select add #2.190
20 models selected
> select add #2.124
21 models selected
> select add #2.130
22 models selected
> select add #2.133
23 models selected
> select add #2.3
24 models selected
> select add #2.182
25 models selected
> select add #2.189
26 models selected
> select add #2.156
27 models selected
> select add #2.144
28 models selected
> select add #2.150
29 models selected
Grouped 29 regions
Showing 180 region surfaces
> select clear
> select #2.1
1 model selected
Opened All_periplasm_imasked as #5, grid size 220,220,220, pixel 4.3, shown at
step 1, values float32
> select #2.1
1 model selected
> select add #2.3
2 models selected
Grouped 2 regions
Opened All_periplasm_imasked as #6, grid size 220,220,220, pixel 4.3, shown at
step 1, values float32
Segmenting All_periplasm_imasked, density threshold 0.005152
Showing 56 region surfaces
848 watershed regions, grouped to 56 regions
Showing All_periplasm_imasked.seg - 56 regions, 56 surfaces
> hide #!5 models
> hide #!6 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/shoichitachiyama/Desktop/Chimera-Dec11_2024/Cage-spoke.mrc
> models #6
> save /Users/shoichitachiyama/Desktop/Chimera-Dec11_2024/SegmentationC1.cxs
> includeMaps true
> close session
> open /Users/shoichitachiyama/Desktop/For-Fig4FG-3_Dec112024.cxs
Opened 0838-bottom.mrc as #16, grid size 240,240,240, pixel 4.3, shown at
level 0.0144, step 1, values float32
Opened Hpwt-L0.08-Global-Rod-no-MS.mrc as #113, grid size 240,240,240, pixel
4.3, shown at level 0.0151, step 1, values float32
Opened Single-MotA-truncated.mrc copy as #281, grid size 110,110,140, pixel
4.3,4.3,4.3, shown at level 0.00853, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #282, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #283, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #284, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #285, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #286, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #287, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #288, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #289, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #290, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #291, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #292, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #293, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #294, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #295, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #296, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #297, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Single-MotA-truncated.mrc copy gaussian as #298, grid size 110,110,140,
pixel 4.3,4.3,4.3, shown at level 0.00654, step 1, values float32
Opened Disk.mrc gaussian as #312, grid size 250,250,250, pixel 4.3, shown at
level 0.0186, step 1, values float32
Opened IM-old-maps.mrc gaussian as #313, grid size 120,120,120, pixel 8.8,
shown at level 0.0702, step 1, values float32
Opened OM.mrc copy gaussian as #316, grid size 240,240,240, pixel 4.3, shown
at level 0.0323, step 1, values float32
Opened Cage-bottom.mrc as #356, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #357, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #358, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #359, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #360, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #361, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #362, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #363, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #364, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #365, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #366, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #367, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #368, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #369, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #370, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #371, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #372, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened Cage-bottom.mrc copy as #373, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00933, step 1, values float32
Opened PilM-region.mrc gaussian as #377, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #378, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #379, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #380, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #381, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #382, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #383, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #384, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #385, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #386, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #387, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #388, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #389, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #390, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #391, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #415, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #416, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #417, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PilM-region.mrc gaussian copy as #418, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.0038, step 1, values float32
Opened PflA.mrc as #424, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00712, step 1, values float32
Opened PflA.mrc copy as #425, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #426, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #427, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #428, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #429, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #430, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #431, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #432, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #433, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #434, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #435, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #436, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #437, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #438, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #439, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #440, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened PflA.mrc copy as #441, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc as #442, grid size 160,160,200, pixel 4.3,4.3,4.3, shown
at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #443, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #444, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #445, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #446, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #447, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #448, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #449, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #450, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #451, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #452, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #453, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #454, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #455, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #456, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #457, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #458, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened Cage_top.mrc copy as #459, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00712, step 1, values float32
Opened MotB_PG.mrc as #460, grid size 160,160,200, pixel 4.3,4.3,4.3, shown at
level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #461, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #462, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #463, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #464, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #465, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #466, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #467, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #468, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #469, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #470, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #471, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #472, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #473, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #474, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #475, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #476, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened MotB_PG.mrc copy as #477, grid size 160,160,200, pixel 4.3,4.3,4.3,
shown at level 0.00707, step 1, values float32
Opened New_FliF.mrc gaussian as #479, grid size 256,256,256, pixel 2.1, shown
at level 0.0115, step 1, values float32
Opened New_FlhA.mrc gaussian as #481, grid size 256,256,256, pixel 2.1, shown
at level 0.00316, step 1, values float32
Opened PflBC13.mrc as #482, grid size 256,256,256, pixel 2.1, shown at level
0.00615, step 1, values float32
Opened New_IM_Bottom2.mrc as #483, grid size 256,256,256, pixel 2.1, shown at
level 0.0072, step 1, values float32
Opened New_IM_Bottom2.mrc gaussian as #484, grid size 256,256,256, pixel 2.1,
shown at level 0.0072, step 1, values float32
Opened PflB_C13.mrc as #507, grid size 256,256,256, pixel 2.1, shown at level
0.0015, step 1, values float32
Opened PflB_monomer.mrc as #508, grid size 256,256,256, pixel 2.1, shown at
level 0.00116, step 1, values float32
Opened Unknown-ring.mrc as #509, grid size 256,256,256, pixel 2.1, shown at
level 0.000608, step 1, values float32
Opened PflB_C13.mrc gaussian as #510, grid size 256,256,256, pixel 2.1, shown
at level 0.00108, step 1, values float32
Opened PflB_monomer.mrc gaussian as #511, grid size 256,256,256, pixel 2.1,
shown at level 0.000387, step 1, values float32
Opened Unknown-ring.mrc gaussian as #512, grid size 256,256,256, pixel 2.1,
shown at level 0.00109, step 1, values float32
Opened 0838-disk.mrc gaussian as #513, grid size 240,240,240, pixel 4.3, shown
at level 0.0153, step 1, values float32
Opened 0838-top.mrc gaussian as #514, grid size 240,240,240, pixel 4.3, shown
at level 0.00979, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.1, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.2, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.3, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
Opened HP_C-ring_monomer.mrc copy gaussian as #177.4, grid size 160,160,160,
pixel 4.2, shown at level 0.04, step 1, values float32
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Opened MotB_new.mrc copy as #125, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #126, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #127, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #128, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #129, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #130, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #131, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #132, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #133, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #134, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #135, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #136, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #137, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #138, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #139, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #140, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened MotB_new.mrc copy as #141, grid size 240,240,240, pixel 2.1, shown at
level 0.0995, step 1, values float32
Opened volume sum as #144, grid size 642,583,278, pixel 2.1, shown at level
0.162, step 1, values float32
Opened FlgY-with-joints.mrc copy as #143, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened FlgY-with-joints.mrc copy as #145, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened PilM-region.mrc gaussian copy as #146, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #147, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #148, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #149, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #150, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #151, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #152, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #153, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #154, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #155, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #156, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #157, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #158, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #159, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #160, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #161, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #162, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #163, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened PilM-region.mrc gaussian copy as #164, grid size 160,160,200, pixel
4.3,4.3,4.3, shown at level 0.00437, step 1, values float32
Opened 1x_Cage-units.mrc as #89, grid size 240,240,240, pixel 2.1, shown at
level 0.143, step 1, values float32
Opened PilNO_PL-ring.mrc as #95, grid size 120,120,120, pixel 8.59, shown at
level 6.53e-05, step 1, values float32
Opened New_PL-ring.mrc as #96, grid size 240,240,240, pixel 4.3, shown at
level 0.0141, step 1, values float32
Opened Outer-ring-near-PL.mrc as #97, grid size 240,240,240, pixel 4.3, shown
at level 0.0141, step 1, values float32
Opened Hpwt-L0.08-Global-PL.mrc as #115, grid size 240,240,240, pixel 4.3,
shown at level 0.0148, step 1, values float32
Opened Hpwt-L0.08-rev.mrc as #142, grid size 240,240,240, pixel 4.3, shown at
level 0.0425, step 1, values float32
Opened New_PL-ring.mrc gaussian as #165, grid size 240,240,240, pixel 4.3,
shown at level 0.0105, step 1, values float32
Opened FlgY-with-joints.mrc copy as #173, grid size 220,220,220, pixel 4.3,
shown at level 2.81, step 1, values float32
Opened Hp-C1-4.296A-msk.mrc as #174, grid size 220,220,220, pixel 4.3, shown
at level 0.0868, step 1, values float32
opened ChimeraX session
> open /Users/shoichitachiyama/Desktop/Chimera-Dec11_2024/Cage-spoke.mrc
Opened Cage-spoke.mrc as #193, grid size 220,220,220, pixel 4.3, shown at
level 0.0952, step 1, values float32
> volume #193 level 0.02963
> volume #193 color #5e5e5e
> volume #193 color #5e5e5e28
> select add #193
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #193,1,0,0,83.336,0,1,0,-2.4889,0,0,1,34.567
> view matrix models #193,1,0,0,57.418,0,1,0,44.02,0,0,1,34.824
> view matrix models #193,1,0,0,57.008,0,1,0,29.274,0,0,1,35.08
> view matrix models #193,1,0,0,59.035,0,1,0,36.724,0,0,1,34.879
> view matrix models #193,1,0,0,59.557,0,1,0,42.484,0,0,1,34.765
> open /Users/shoichitachiyama/Desktop/Chimera-Dec11_2024/Hp-C1-4.296A-msk.mrc
Opened Hp-C1-4.296A-msk.mrc as #194, grid size 220,220,220, pixel 4.3, shown
at level 0.151, step 1, values float32
> volume #194 level 0.0372
> ui tool show "Fit in Map"
> show #!113 models
> color #194 #e5bf995e models
> color #194 #797979ff models
> color #194 #79797981 models
> select subtract #193
Nothing selected
> select add #194
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #194,0.99975,0.0015176,-0.022318,9.8812,-0.0014704,1,0.0021354,-0.31061,0.022321,-0.0021021,0.99975,-9.373
> ui mousemode right "translate selected models"
> view matrix models
> #194,0.99975,0.0015176,-0.022318,8.3028,-0.0014704,1,0.0021354,27.013,0.022321,-0.0021021,0.99975,-9.2503
> view matrix models
> #194,0.99975,0.0015176,-0.022318,7.4135,-0.0014704,1,0.0021354,43.585,0.022321,-0.0021021,0.99975,-8.1276
> view matrix models
> #194,0.99975,0.0015176,-0.022318,6.541,-0.0014704,1,0.0021354,60.337,0.022321,-0.0021021,0.99975,-6.584
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #194 inMap #113
Fit map Hp-C1-4.296A-msk.mrc in map Hpwt-L0.08-Global-Rod-no-MS.mrc using
2080788 points
correlation = -0.3348, correlation about mean = -0.03006, overlap = -1927
steps = 252, shift = 22.1, angle = 2.4 degrees
Position of Hp-C1-4.296A-msk.mrc (#194) relative to Hpwt-L0.08-Global-Rod-no-
MS.mrc (#113) coordinates:
Matrix rotation and translation
0.99773391 0.06698400 0.00633813 -56.24624814
-0.06697889 0.99775386 -0.00101567 95.00363878
-0.00639193 0.00058884 0.99997938 -26.30547751
Axis 0.01192270 0.09459386 -0.99544455
Axis point 1339.79992650 891.16347695 0.00000000
Rotation angle (degrees) 3.85823228
Shift along axis 34.50179800
> fitmap #194 inMap #113
Fit map Hp-C1-4.296A-msk.mrc in map Hpwt-L0.08-Global-Rod-no-MS.mrc using
2080788 points
correlation = -0.3348, correlation about mean = -0.02999, overlap = -1927
steps = 40, shift = 1.1, angle = 0.00763 degrees
Position of Hp-C1-4.296A-msk.mrc (#194) relative to Hpwt-L0.08-Global-Rod-no-
MS.mrc (#113) coordinates:
Matrix rotation and translation
0.99773618 0.06694947 0.00634562 -55.93143295
-0.06694353 0.99775610 -0.00114382 96.11417939
-0.00640796 0.00071643 0.99997919 -26.34052321
Axis 0.01382959 0.09481373 -0.99539896
Axis point 1357.02354461 888.45236230 0.00000000
Rotation angle (degrees) 3.85639283
Shift along axis 34.55876498
> view matrix models
> #194,0.99947,0.031817,0.0063641,7.9257,-0.031812,0.99949,-0.00093959,93.69,-0.0063908,0.00073664,0.99998,-3.3709
> close session
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-
> version_model/Flo_PflA_Local/Fig4_After_review2.cxs
Opened PflA-2.1A-230911.mrc as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened Disk.mrc as #3, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #4, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened PflA-2_imasked as #5, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits.mrc as #6, grid size 240,240,240, pixel 2.1, shown at level
0.0379, step 1, values float32
Opened PflA-2_imasked_imasked as #7, grid size 240,240,240, pixel 2.1, shown
at level 0.185, step 1, values float32
Opened 3XfliL.mrc as #8, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened PflA-2_imasked_imasked_imasked as #9, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened IM.mrc as #10, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened 1Xunit-no-topcage.mrc as #17, grid size 240,240,240, pixel 2.1, shown
at step 1, values float32
Opened 1xPflAB-New.mrc as #19, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 1xPflAB-New-no-cyt-cage.mrc as #20, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 2xFliL.mrc as #21, grid size 240,240,240, pixel 2.1, shown at level
0.185, step 1, values float32
Opened 3Xunits_imasked as #24, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 3xOnly-PflAB.mrc as #25, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 3xOnly-PflAB.mrc as #26, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened 1xOnly-PflAB.mrc as #27, grid size 240,240,240, pixel 2.1, shown at
level 0.0379, step 1, values float32
Opened Rod.mrc as #31, grid size 240,240,240, pixel 2.1, shown at level 0.185,
step 1, values float32
Opened PflA-2.1A-230911_imasked as #30, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened PflA-2.1A-230911_imasked as #29, grid size 240,240,240, pixel 2.1,
shown at level 0.185, step 1, values float32
Opened 3xOnly-PflAB.mrc as #34, grid size 240,240,240, pixel 2.1, shown at
level 0.185, step 1, values float32
Opened 2xMotB.mrc as #37, grid size 240,240,240, pixel 2.1, shown at level
0.000313, step 1, values float32
opened ChimeraX session
Showing PflA-2.seg - 27 regions, 27 surfaces
> hide #!11 models
> hide #!32 models
> hide #!33 models
> hide #!34 models
> show #!26 models
> hide #!26 models
> show #!27 models
> show #!37 models
> show #!36 models
> select add #36.4
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> select add #36.1
5540 atoms, 5658 bonds, 672 residues, 4 models selected
> select add #36
11080 atoms, 11316 bonds, 1344 residues, 9 models selected
> select subtract #36
8 models selected
> hide #!36 models
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/Fixed_2xCage_Dec112024.pdb
Chain information for Fixed_2xCage_Dec112024.pdb
---
Chain | Description
38.1/A 38.2/A | No description available
38.1/B 38.2/B | No description available
> select add #38
5540 atoms, 5658 bonds, 672 residues, 3 models selected
> view matrix models #38,1,0,0,-442.26,0,1,0,-137.27,0,0,1,0
> view matrix models #38,1,0,0,-418.42,0,1,0,-279.9,0,0,1,-333.76
> show #!35 models
> hide #!35 models
> show #!23 models
> hide #!23 models
> show #!33 models
> hide #!33 models
> show #!18 models
> hide #!18 models
> show #!36 models
> show #!26 models
> hide #!26 models
> show #!25 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!20 models
> hide #!27 models
> view matrix models #38,1,0,0,-386.02,0,1,0,-261.29,0,0,1,-488.85
> view matrix models #38,1,0,0,-417.28,0,1,0,-263.97,0,0,1,-562.64
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.39632,-0.87424,0.28041,-16.682,0.88657,0.28506,-0.36432,-544.05,0.23857,0.39299,0.88806,-728.28
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.39632,-0.87424,0.28041,-28.61,0.88657,0.28506,-0.36432,-482.24,0.23857,0.39299,0.88806,-753.18
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.39116,-0.87373,0.28913,-29.257,0.88891,0.27729,-0.36463,-482.27,0.23842,0.39964,0.88512,-752.91
> view matrix models
> #38,0.32466,-0.89681,0.30056,11.443,0.94354,0.28497,-0.16888,-603.37,0.065802,0.33842,0.93869,-657.48
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.32466,-0.89681,0.30056,-35.623,0.94354,0.28497,-0.16888,-609,0.065802,0.33842,0.93869,-617.07
> view matrix models
> #38,0.32466,-0.89681,0.30056,-75.708,0.94354,0.28497,-0.16888,-603.31,0.065802,0.33842,0.93869,-592.25
> view matrix models
> #38,0.32466,-0.89681,0.30056,-82.461,0.94354,0.28497,-0.16888,-617.09,0.065802,0.33842,0.93869,-612.43
> hide #!36 models
> view matrix models
> #38,0.32466,-0.89681,0.30056,-92.253,0.94354,0.28497,-0.16888,-543.3,0.065802,0.33842,0.93869,-618.27
> view matrix models
> #38,0.32466,-0.89681,0.30056,-88.132,0.94354,0.28497,-0.16888,-543.43,0.065802,0.33842,0.93869,-622.31
> view matrix models
> #38,0.32466,-0.89681,0.30056,-83.466,0.94354,0.28497,-0.16888,-541.5,0.065802,0.33842,0.93869,-614.06
> view matrix models
> #38,0.32466,-0.89681,0.30056,-81.683,0.94354,0.28497,-0.16888,-548.85,0.065802,0.33842,0.93869,-611.73
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.30195,-0.91367,0.27211,-52.139,0.95,0.3122,-0.0058814,-628.72,-0.079579,0.26028,0.96225,-517.5
> view matrix models
> #38,0.3023,-0.92239,0.24046,-37.07,0.95066,0.31019,-0.0052681,-629.07,-0.069729,0.23019,0.97065,-522.33
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.3023,-0.92239,0.24046,-34.048,0.95066,0.31019,-0.0052681,-632,-0.069729,0.23019,0.97065,-522.93
> view matrix models
> #38,0.3023,-0.92239,0.24046,-34.116,0.95066,0.31019,-0.0052681,-631.77,-0.069729,0.23019,0.97065,-522.97
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.25997,-0.93285,0.24941,-9.6491,0.96286,0.26994,0.0060097,-637.64,-0.072933,0.23858,0.96838,-521.37
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.25997,-0.93285,0.24941,-10.748,0.96286,0.26994,0.0060097,-637.49,-0.072933,0.23858,0.96838,-521.06
> view matrix models
> #38,0.25997,-0.93285,0.24941,-9.5424,0.96286,0.26994,0.0060097,-635.14,-0.072933,0.23858,0.96838,-519.02
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.29846,-0.92223,0.24579,-33.949,0.95064,0.31016,0.0094364,-635.67,-0.084938,0.23084,0.96928,-510.56
> view matrix models
> #38,0.29335,-0.93332,0.20702,-11.937,0.95205,0.30488,0.025485,-642.69,-0.086902,0.18962,0.97801,-506.25
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.29335,-0.93332,0.20702,-7.5644,0.95205,0.30488,0.025485,-645.07,-0.086902,0.18962,0.97801,-507.51
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.28501,-0.94206,0.1769,12.302,0.95249,0.29902,0.057806,-658.49,-0.10735,0.15202,0.98253,-490.33
> view matrix models
> #38,0.24497,-0.9522,0.18247,36.758,0.96433,0.25876,0.055691,-658.28,-0.10025,0.16232,0.98163,-496.14
> view matrix models
> #38,0.23657,-0.96276,0.13085,66.371,0.96594,0.24758,0.075304,-665.98,-0.10489,0.10857,0.98854,-487.23
> view matrix models
> #38,0.21019,-0.96843,0.13405,82.519,0.97253,0.22114,0.072627,-664.55,-0.099978,0.11511,0.98831,-491.32
> view matrix models
> #38,0.2172,-0.96693,0.13366,78.031,0.9721,0.22669,0.060271,-659.8,-0.088577,0.11684,0.98919,-499.17
> view matrix models
> #38,0.19635,-0.97082,0.13766,90.057,0.97717,0.20536,0.054463,-656.9,-0.081143,0.12382,0.98898,-504.93
> view matrix models
> #38,0.19603,-0.97175,0.13144,93.136,0.97745,0.20437,0.053222,-656.36,-0.078581,0.11804,0.98989,-505.98
> show #!19 models
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.19603,-0.97175,0.13144,96.442,0.97745,0.20437,0.053222,-656.36,-0.078581,0.11804,0.98989,-507.82
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.19455,-0.97367,0.1188,103.22,0.97789,0.202,0.054116,-656.63,-0.076688,0.10564,0.99144,-507.62
> view matrix models
> #38,0.14768,-0.98113,0.12482,131.35,0.98765,0.15296,0.033799,-645.77,-0.052253,0.11829,0.9916,-525.19
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.14768,-0.98113,0.12482,133.33,0.98765,0.15296,0.033799,-646.35,-0.052253,0.11829,0.9916,-525.63
> ui mousemode right "rotate selected models"
> view matrix models
> #38,0.13839,-0.98559,0.097291,151.96,0.98855,0.14342,0.046822,-651.03,-0.060101,0.089698,0.99415,-517.08
> view matrix models
> #38,0.1195,-0.98764,0.10139,162.41,0.99131,0.12436,0.043006,-647.96,-0.055083,0.095373,0.99392,-521.08
> view matrix models
> #38,0.09882,-0.99507,0.0087033,217.18,0.99389,0.099127,0.048567,-647.87,-0.04919,0.0038507,0.99878,-511.87
> select clear
> open /Volumes/Backup-95/Chimera-2023/PflB-PflA-project/Start-
> from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-reviewer-
> response/Fixed_2xCage_Dec112024.pdb
Summary of feedback from opening /Volumes/Backup-95/Chimera-2023/PflB-PflA-
project/Start-from_June2024/July_2024/Final-version_model/Flo_PflA_Local/For-
reviewer-response/Fixed_2xCage_Dec112024.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 2 LEU A 78 1 77
Start residue of secondary structure not found: HELIX 2 2 LEU A 79 ILE A 81 1
3
Start residue of secondary structure not found: HELIX 3 3 LYS A 107 LEU A 118
1 12
Start residue of secondary structure not found: HELIX 4 4 ASN A 119 MET A 121
1 3
Start residue of secondary structure not found: HELIX 5 5 GLU A 154 ILE A 156
1 3
33 messages similar to the above omitted
Chain information for Fixed_2xCage_Dec112024.pdb
---
Chain | Description
39.1/A 39.2/A | No description available
39.1/B 39.2/B | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select add #39.2
2770 atoms, 2829 bonds, 336 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #39.2,1,0,0,39.707,0,1,0,88.254,0,0,1,-202.5
> undo
> select add #39
5540 atoms, 5658 bonds, 672 residues, 3 models selected
> view matrix models #39,1,0,0,-370.51,0,1,0,-174.95,0,0,1,-681.81
> view matrix models #39,1,0,0,-458.53,0,1,0,-149.1,0,0,1,-645.65
> view matrix models #39,1,0,0,-449.95,0,1,0,-115.62,0,0,1,-576.36
> ui mousemode right "rotate selected models"
> view matrix models
> #39,0.26396,-0.93016,0.25521,54.145,0.96421,0.26129,-0.044956,-580.08,-0.024868,0.25794,0.96584,-588.23
Cell requested for row 44 is out of bounds for table with 47 rows! Resizing
table model.
> close #39
> combine #38 modelId #39 name Fixed_2xCage_Dec112024
Remapping chain ID 'A' in Fixed_2xCage_Dec112024.pdb #38.2 to 'C'
Remapping chain ID 'B' in Fixed_2xCage_Dec112024.pdb #38.2 to 'D'
> split #39
Split Fixed_2xCage_Dec112024 (#39) into 4 models
Chain information for Fixed_2xCage_Dec112024 A #39.1
---
Chain | Description
A | No description available
Chain information for Fixed_2xCage_Dec112024 B #39.2
---
Chain | Description
B | No description available
Chain information for Fixed_2xCage_Dec112024 C #39.3
---
Chain | Description
C | No description available
Chain information for Fixed_2xCage_Dec112024 D #39.4
---
Chain | Description
D | No description available
> hide #!38 models
> select add #39.1
1487 atoms, 1518 bonds, 179 residues, 1 model selected
> select add #39.2
2770 atoms, 2829 bonds, 336 residues, 2 models selected
> ui mousemode right "translate selected models"
> view orient
> turn x 90
> turn y 90
> view matrix models
> #39.1,0.09882,-0.99507,0.0087033,217.18,0.99389,0.099127,0.048567,-522.4,-0.04919,0.0038507,0.99878,-513.22,#39.2,0.09882,-0.99507,0.0087033,217.18,0.99389,0.099127,0.048567,-522.4,-0.04919,0.0038507,0.99878,-513.22
> view orient
> view matrix models
> #39.1,0.09882,-0.99507,0.0087033,197.64,0.99389,0.099127,0.048567,-515.73,-0.04919,0.0038507,0.99878,-513.22,#39.2,0.09882,-0.99507,0.0087033,197.64,0.99389,0.099127,0.048567,-515.73,-0.04919,0.0038507,0.99878,-513.22
> turn x 90
> view matrix models
> #39.1,0.09882,-0.99507,0.0087033,197.2,0.99389,0.099127,0.048567,-518.58,-0.04919,0.0038507,0.99878,-512.67,#39.2,0.09882,-0.99507,0.0087033,197.2,0.99389,0.099127,0.048567,-518.58,-0.04919,0.0038507,0.99878,-512.67
> ui mousemode right "rotate selected models"
> view matrix models
> #39.1,0.08762,-0.99607,0.013075,202.17,0.99522,0.088098,0.042168,-514.78,-0.043154,0.0093178,0.99902,-517.3,#39.2,0.08762,-0.99607,0.013075,202.17,0.99522,0.088098,0.042168,-514.78,-0.043154,0.0093178,0.99902,-517.3
> view matrix models
> #39.1,0.063523,-0.99772,0.022745,212.67,0.99753,0.064161,0.02853,-506.28,-0.029924,0.020876,0.99933,-527.26,#39.2,0.063523,-0.99772,0.022745,212.67,0.99753,0.064161,0.02853,-506.28,-0.029924,0.020876,0.99933,-527.26
> undo
> view matrix models
> #39.1,0.077273,-0.99681,-0.020071,223.14,0.99566,0.076106,0.053528,-518.12,-0.05183,-0.02412,0.99836,-506.38,#39.2,0.077273,-0.99681,-0.020071,223.14,0.99566,0.076106,0.053528,-518.12,-0.05183,-0.02412,0.99836,-506.38
> view matrix models
> #39.1,0.069716,-0.99648,-0.046629,239.35,0.99591,0.066832,0.060802,-519.98,-0.057471,-0.050678,0.99706,-498.13,#39.2,0.069716,-0.99648,-0.046629,239.35,0.99591,0.066832,0.060802,-519.98,-0.057471,-0.050678,0.99706,-498.13
> ui mousemode right "translate selected models"
> view matrix models
> #39.1,0.069716,-0.99648,-0.046629,240.58,0.99591,0.066832,0.060802,-521.25,-0.057471,-0.050678,0.99706,-498.15,#39.2,0.069716,-0.99648,-0.046629,240.58,0.99591,0.066832,0.060802,-521.25,-0.057471,-0.050678,0.99706,-498.15
> select add #39.3
4257 atoms, 4347 bonds, 515 residues, 3 models selected
> select add #39.4
5540 atoms, 5658 bonds, 672 residues, 4 models selected
> select subtract #39.1
4053 atoms, 4140 bonds, 493 residues, 3 models selected
> select subtract #39.2
2770 atoms, 2829 bonds, 336 residues, 2 models selected
> save /Users/shoichitachiyama/Desktop/For-Fig4CDEH-1_Dec112024.cxs
> includeMaps true
> view orient
> turn x 90
> turn y 90
> select clear
> select add #39.3
1487 atoms, 1518 bonds, 179 residues, 1 model selected
> select add #39.4
2770 atoms, 2829 bonds, 336 residues, 2 models selected
> view matrix models
> #39.3,0.09882,-0.99507,0.0087033,217.18,0.99389,0.099127,0.048567,-785.08,-0.04919,0.0038507,0.99878,-510.5,#39.4,0.09882,-0.99507,0.0087033,217.18,0.99389,0.099127,0.048567,-785.08,-0.04919,0.0038507,0.99878,-510.5
> turn x 90
> view matrix models
> #39.3,0.09882,-0.99507,0.0087033,223.83,0.99389,0.099127,0.048567,-783.29,-0.04919,0.0038507,0.99878,-510.5,#39.4,0.09882,-0.99507,0.0087033,223.83,0.99389,0.099127,0.048567,-783.29,-0.04919,0.0038507,0.99878,-510.5
> ui mousemode right "rotate selected models"
> view matrix models
> #39.3,0.18012,-0.98356,0.012663,166.65,0.98241,0.18053,0.047688,-789.15,-0.04919,0.0038507,0.99878,-510.5,#39.4,0.18012,-0.98356,0.012663,166.65,0.98241,0.18053,0.047688,-789.15,-0.04919,0.0038507,0.99878,-510.5
> view matrix models
> #39.3,0.16707,-0.98562,-0.025165,191.97,0.98539,0.16607,0.037725,-784.35,-0.033003,-0.0311,0.99897,-515.32,#39.4,0.16707,-0.98562,-0.025165,191.97,0.98539,0.16607,0.037725,-784.35,-0.033003,-0.0311,0.99897,-515.32
> ui mousemode right "translate selected models"
> view matrix models
> #39.3,0.16707,-0.98562,-0.025165,190.09,0.98539,0.16607,0.037725,-783.33,-0.033003,-0.0311,0.99897,-515.67,#39.4,0.16707,-0.98562,-0.025165,190.09,0.98539,0.16607,0.037725,-783.33,-0.033003,-0.0311,0.99897,-515.67
> view matrix models
> #39.3,0.16707,-0.98562,-0.025165,191.46,0.98539,0.16607,0.037725,-783.01,-0.033003,-0.0311,0.99897,-511.42,#39.4,0.16707,-0.98562,-0.025165,191.46,0.98539,0.16607,0.037725,-783.01,-0.033003,-0.0311,0.99897,-511.42
> ui mousemode right "rotate selected models"
> view matrix models
> #39.3,0.019214,-0.99981,0.0025058,279.22,0.99979,0.019195,-0.0074049,-748.09,0.0073554,0.0026475,0.99997,-544.14,#39.4,0.019214,-0.99981,0.0025058,279.22,0.99979,0.019195,-0.0074049,-748.09,0.0073554,0.0026475,0.99997,-544.14
> view matrix models
> #39.3,0.2776,-0.9598,-0.041496,121.41,0.95882,0.2741,0.074353,-799.64,-0.05999,-0.060428,0.99637,-487.58,#39.4,0.2776,-0.9598,-0.041496,121.41,0.95882,0.2741,0.074353,-799.64,-0.05999,-0.060428,0.99637,-487.58
> view matrix models
> #39.3,0.23507,-0.97123,-0.038229,149.91,0.97081,0.23269,0.058098,-793.5,-0.047531,-0.050771,0.99758,-497.93,#39.4,0.23507,-0.97123,-0.038229,149.91,0.97081,0.23269,0.058098,-793.5,-0.047531,-0.050771,0.99758,-497.93
> show #!38 models
> view matrix models
> #39.3,0.35613,-0.93249,-0.060241,73.228,0.93221,0.35009,0.091769,-802.48,-0.064484,-0.088839,0.99396,-478.78,#39.4,0.35613,-0.93249,-0.060241,73.228,0.93221,0.35009,0.091769,-802.48,-0.064484,-0.088839,0.99396,-478.78
> ui mousemode right "translate selected models"
> view matrix models
> #39.3,0.35613,-0.93249,-0.060241,71.971,0.93221,0.35009,0.091769,-803,-0.064484,-0.088839,0.99396,-478.37,#39.4,0.35613,-0.93249,-0.060241,71.971,0.93221,0.35009,0.091769,-803,-0.064484,-0.088839,0.99396,-478.37
> ui mousemode right "rotate selected models"
> view matrix models
> #39.3,0.36126,-0.9324,-0.011037,47.293,0.93124,0.36016,0.055573,-788.4,-0.047842,-0.030354,0.99839,-501.12,#39.4,0.36126,-0.9324,-0.011037,47.293,0.93124,0.36016,0.055573,-788.4,-0.047842,-0.030354,0.99839,-501.12
> ui mousemode right "translate selected models"
> view matrix models
> #39.3,0.36126,-0.9324,-0.011037,42.864,0.93124,0.36016,0.055573,-785.11,-0.047842,-0.030354,0.99839,-501.34,#39.4,0.36126,-0.9324,-0.011037,42.864,0.93124,0.36016,0.055573,-785.11,-0.047842,-0.030354,0.99839,-501.34
> ui mousemode right "rotate selected models"
> view matrix models
> #39.3,0.36594,-0.93057,0.011208,29.849,0.92904,0.36599,0.05426,-784.08,-0.054594,-0.0094432,0.99846,-500.46,#39.4,0.36594,-0.93057,0.011208,29.849,0.92904,0.36599,0.05426,-784.08,-0.054594,-0.0094432,0.99846,-500.46
> select clear
> color #39.1 #23a0d0ff
> color #39.2 #23a0d0ff
> color #39.3 #23a0d0ff
> color #39.4 #23a0d0ff
> color #38 #23a0d0ff models
> select clear
> hide #!19 models
> hide #!20 models
> show #!19 models
> show #!33 models
> hide #!33.2 models
> show #!33.2 models
> hide #!33.2 models
> hide #!33.4 models
> show #!33.4 models
> hide #!33.1 models
> hide #!33 models
> select add #38
5540 atoms, 5658 bonds, 672 residues, 3 models selected
> select add #39
11080 atoms, 11316 bonds, 1344 residues, 8 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> hide #!19 models
> show #!19 models
> view orient
> show #!33 models
> show #!2 models
> show #!22 models
> select add #22.1
9605 atoms, 9765 bonds, 1250 residues, 1 model selected
> select subtract #22.1
1 model selected
> select add #22.22
4099 atoms, 4171 bonds, 518 residues, 1 model selected
> select subtract #22.22
2 models selected
> color #22.22 #dfba68ff
> color #2.22 #dfba68ff
> color #2.1 #e5ea15ff
> color #22.1 #e5ea15ff
> select add #2.2
799 atoms, 807 bonds, 98 residues, 1 model selected
> select subtract #2.2
1 model selected
> color #2.2 #dfba68ff
> color #2.2 #d5720eff
> color #2.3 #d5720eff
> color #2.4 #d5720eff
> select add #2.5
799 atoms, 807 bonds, 98 residues, 1 model selected
> select add #2.6
1598 atoms, 1614 bonds, 196 residues, 3 models selected
> select add #2.7
2397 atoms, 2421 bonds, 294 residues, 5 models selected
> select add #2.8
3196 atoms, 3228 bonds, 392 residues, 7 models selected
> select add #2.9
3995 atoms, 4035 bonds, 490 residues, 9 models selected
> select add #2.10
4794 atoms, 4842 bonds, 588 residues, 11 models selected
> select add #2.11
5593 atoms, 5649 bonds, 686 residues, 13 models selected
> select add #22.2
6392 atoms, 6456 bonds, 784 residues, 15 models selected
> select add #22.3
7191 atoms, 7263 bonds, 882 residues, 17 models selected
> select add #22.4
7990 atoms, 8070 bonds, 980 residues, 19 models selected
> select add #22.5
8789 atoms, 8877 bonds, 1078 residues, 21 models selected
> select add #22.6
9588 atoms, 9684 bonds, 1176 residues, 23 models selected
> select add #22.7
10387 atoms, 10491 bonds, 1274 residues, 25 models selected
> select add #22.8
11186 atoms, 11298 bonds, 1372 residues, 27 models selected
> select add #22.9
11985 atoms, 12105 bonds, 1470 residues, 29 models selected
> select add #22.10
12784 atoms, 12912 bonds, 1568 residues, 31 models selected
> select add #22.11
13583 atoms, 13719 bonds, 1666 residues, 33 models selected
> color sel #d5720eff
> select clear
> save /Users/shoichitachiyama/Desktop/For-Fig4CDEH-1_Dec112024.cxs
> includeMaps true
> save /Users/shoichitachiyama/Desktop/Fig4E_12122024.png supersample 2
> transparentBackground true
> turn x 90
> save /Users/shoichitachiyama/Desktop/Fig4H_12122024.png supersample 2
> transparentBackground true
> select add #28.4
6829 atoms, 6972 bonds, 843 residues, 1 model selected
Alignment identifier is 28.4/Ch
> select #28.4/Ch:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28.4/Ch:1-141
1093 atoms, 1100 bonds, 140 residues, 1 model selected
> select
> #28.4/Ch:2-14,27-29,34-57,59-83,114-117,119-121,143-155,159-171,174-187,191-203,208-221,225-242,248-258,264-270,278-291,295-304,308-310,312-320,324-337,342-355,358-368,372-380,390-392,395-403,405-409,412-422,431-434,447-457,462-480,484-497,502-514,518-531,536-549,554-566,572-585,594-596,604-616,620-633,638-648,654-664,671-676,679-692,695-708,716-728,732-744,751-763,767-780,785-797,801-810,827-841
4725 atoms, 4774 bonds, 580 residues, 1 model selected
> select #28.4/Ch:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28.4/Ch:1-142
1102 atoms, 1109 bonds, 141 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> select add #28.6
7931 atoms, 8081 bonds, 984 residues, 3 models selected
> select add #28.4
13658 atoms, 13944 bonds, 1686 residues, 4 models selected
> select subtract #28.4
6829 atoms, 6972 bonds, 843 residues, 3 models selected
Alignment identifier is 28.6/Cj
> select #28.6/Cj:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28.6/Cj:1-142
1102 atoms, 1109 bonds, 141 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> save /Users/shoichitachiyama/Desktop/Fig4H_12122024.png supersample 2
> transparentBackground true
> turn x -90
> turn x 90
> save /Users/shoichitachiyama/Desktop/Fig4E_12122024.png supersample 2
> transparentBackground true
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!22 models
> hide #!2 models
> select add #28
38799 atoms, 39588 bonds, 4776 residues, 11 models selected
> select subtract #28
4 models selected
> hide #!37 models
> hide #!38 models
> hide #!39 models
> show #!27 models
> save /Users/shoichitachiyama/Desktop/FigD_12122024.png supersample 2
> transparentBackground true
> show #!26 models
> hide #!26 models
> show #!25 models
> hide #!25 models
> hide #!27 models
> show #!34 models
> hide #!34 models
> show #!34 models
> show #!32 models
> hide #!32 models
> show #!32 models
> select add #32.3
6829 atoms, 6972 bonds, 843 residues, 1 model selected
> select subtract #32.3
1 model selected
> select add #32.4
1109 atoms, 1136 bonds, 137 residues, 1 model selected
> select subtract #32.4
1 model selected
> select add #32.4
1109 atoms, 1136 bonds, 137 residues, 1 model selected
> select subtract #32.4
1 model selected
> select add #33
19762 atoms, 20168 bonds, 2435 residues, 5 models selected
> select subtract #33
3 models selected
> select add #32.4
1109 atoms, 1136 bonds, 137 residues, 1 model selected
> select subtract #32.4
1 model selected
> hide #!32.4 models
> show #!32.4 models
> select add #32.3
6829 atoms, 6972 bonds, 843 residues, 1 model selected
> hide #!32.3 models
> show #!32.3 models
Alignment identifier is 32.3/Cj
> select #32.3/Cj:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32.3/Cj:1-3
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #32.3/Cj:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32.3/Cj:1-18
142 atoms, 141 bonds, 18 residues, 1 model selected
> select add #28.6
6971 atoms, 7113 bonds, 861 residues, 3 models selected
Alignment identifier is 1
> select #28.6/Cj:1-2 #32.3/Cj:1-2
32 atoms, 30 bonds, 4 residues, 2 models selected
> select #28.6/Cj:1-13 #32.3/Cj:1-13
208 atoms, 206 bonds, 26 residues, 2 models selected
1 [ID: 1] region 2 chains [1-13] RMSD: 130.896
> select add #28
38903 atoms, 39691 bonds, 4789 residues, 13 models selected
> select subtract #28
104 atoms, 103 bonds, 13 residues, 6 models selected
> select add #32
19762 atoms, 20168 bonds, 2435 residues, 6 models selected
> select subtract #32
3 models selected
> select add #28.4
6829 atoms, 6972 bonds, 843 residues, 1 model selected
Alignment identifier is 28.4/Ch
> select #28.4/Ch:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #28.4/Ch:1-142
1102 atoms, 1109 bonds, 141 residues, 1 model selected
> select add #28.4
6829 atoms, 6972 bonds, 843 residues, 2 models selected
> select subtract #28.4
1 model selected
> select add #32.3
6829 atoms, 6972 bonds, 843 residues, 1 model selected
Alignment identifier is 32.3/Cj
> select #32.3/Cj:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #32.3/Cj:1-142
1102 atoms, 1109 bonds, 141 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> select add #32
19762 atoms, 20168 bonds, 2435 residues, 6 models selected
> select subtract #32
3 models selected
> select add #33
19762 atoms, 20168 bonds, 2435 residues, 5 models selected
> select subtract #33
3 models selected
> show #!33.1 models
> show #!33.2 models
> select add #33.2
6829 atoms, 6972 bonds, 843 residues, 1 model selected
Alignment identifier is 33.2/Ch
> select #33.2/Ch:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #33.2/Ch:1-142
1102 atoms, 1109 bonds, 141 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> save /Users/shoichitachiyama/Desktop/FigC_12122024.png supersample 2
> transparentBackground true
> save /Users/shoichitachiyama/Desktop/For-Fig4CDEH-1_Dec112024.cxs
> includeMaps true
> hide #!32 models
> hide #!33 models
> show #!33 models
> show #!32 models
> select add #33
19762 atoms, 20168 bonds, 2435 residues, 6 models selected
> select subtract #33
3 models selected
> hide #!32 models
> hide #!33 models
> hide #!34 models
> show #!27 models
> select add #28.2
4995 atoms, 5088 bonds, 612 residues, 1 model selected
> select add #28.4
11824 atoms, 12060 bonds, 1455 residues, 3 models selected
> select add #28.6
18653 atoms, 19032 bonds, 2298 residues, 5 models selected
> select add #28.7
19762 atoms, 20168 bonds, 2435 residues, 7 models selected
> hide sel surfaces
> select clear
> save /Users/shoichitachiyama/Desktop/FigS6B_12122024.png supersample 2
> transparentBackground true
> select add #28.2
4995 atoms, 5088 bonds, 612 residues, 1 model selected
> select add #28.4
11824 atoms, 12060 bonds, 1455 residues, 3 models selected
> select add #28.6
18653 atoms, 19032 bonds, 2298 residues, 5 models selected
> select add #28.7
19762 atoms, 20168 bonds, 2435 residues, 7 models selected
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> save /Users/shoichitachiyama/Desktop/FigS6B_12122024.png supersample 2
> transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: 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: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 38 days, 23 hours, 17 minutes
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
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