![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16460 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-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
[deleted to fit within ticket limits]
> 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
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0.0891, step 1, values float32
Opened Cage.mrc copy as #197, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #198, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #199, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #200, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #201, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #202, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #203, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #204, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #205, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #206, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #207, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #208, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #209, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #210, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #211, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened Cage.mrc copy as #212, grid size 240,240,240, pixel 2.1, shown at level
0.0891, step 1, values float32
Opened PflA_new.mrc as #68, grid size 240,240,240, pixel 2.1, shown at level
0.162, step 1, values float32
Opened Unknown_near_PflA.mrc as #69, grid size 240,240,240, pixel 2.1, shown
at level 0.127, step 1, values float32
Opened PflB_new.mrc as #70, grid size 240,240,240, pixel 2.1, shown at level
0.0467, step 1, values float32
Opened Top-cage.mrc as #71, grid size 240,240,240, pixel 2.1, shown at level
0.143, step 1, values float32
Opened PflA_new.mrc copy as #1, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #2, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #3, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #4, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #5, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #6, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #7, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #8, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #9, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #10, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #11, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #12, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #13, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
Opened PflA_new.mrc copy as #14, grid size 240,240,240, pixel 2.1, shown at
level 0.162, step 1, values float32
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
> 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
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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