![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17487 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202501142332 (2025-01-14 23:32:44 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020bec0c80 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1050 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1213 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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, chimerax.graphics._graphics (total: 50)
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{
"uptime" : 55000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,13",
"coalitionID" : 1086,
"osVersion" : {
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"build" : "24E263",
"releaseType" : "User"
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"captureTime" : "2025-04-25 18:53:38.2558 -0400",
"codeSigningMonitor" : 1,
"incident" : "E7191929-98A9-471E-AEB1-6F8CADE3F0B2",
"pid" : 1288,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-24 11:47:49.4663 -0400",
"procStartAbsTime" : 2457261697,
"procExitAbsTime" : 1332113912054,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FA4AF413-754C-5291-B86B-2CD1672D06D3","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2C7F30CA-7D51-4774-E901-C35538930052",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "3F30C7CF-E900-4AD7-85B0-D95B95DEB839",
"wakeTime" : 8,
"sleepWakeUUID" : "62045FEB-A83D-49B6-97E5-50951745C461",
"sip" : "enabled",
"vmRegionInfo" : "0x303354320d70 is not in any region. Bytes after previous region: 52515977694577 Bytes before following region: 52556102234768\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000b03354320d70","rawCodes":[1,193734502387056],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000b03354320d70 -> 0x0000303354320d70 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1288},
"vmregioninfo" : "0x303354320d70 is not in any region. Bytes after previous region: 52515977694577 Bytes before following region: 52556102234768\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/maryamfeghhi/Desktop/maps/one-tail-ec.mrc
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> close #1
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> format mrc
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> select clear
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> open /Users/maryamfeghhi/Desktop/maps/Newly-emerged/Single-tail-emerged.mrc
> format mrc
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> volume #2 color #0433ff
> volume #2 color #011993
> volume #2 color #005493
> volume #2 level 0.5
> volume #2 level 0.507
> volume #2 level 0.509
> volume #2 level 0.508
> transparency #2.1 30
> select clear
> volume #1 level 0.507
> volume #1 level 0.508
> volume #1 level 0.507
> volume #2 color #0096ff
> volume #2 color #011993
> volume #2 level 0.507
> volume #1 level 0.508
> volume #1 level 0.506
> volume #2 level 0.5166
> volume #2 level 0.518
> volume #2 level 0.519
> volume #2 level 0.52
> volume #2 level 0.521
> volume #2 level 0.522
> volume #2 level 0.524
> volume #2 level 0.526
> volume #2 level 0.527
> volume #2 level 0.528
> volume #2 level 0.529
> volume #2 level 0.53
> volume #2 level 0.54
> volume #2 level 0.55
> volume #2 level 0.56
> volume #2 level 0.57
> volume #2 level 0.58
> volume #1 color #73fdff
> volume #1 color #76d6ff
> volume #2 level 0.59
> volume #2 level 0.6
> volume #2 level 0.62
> transparency #1.1 60
> transparency #1.1 40
> transparency #1.1 30
> select clear
> volume #1 level 0.51
> volume #1 level 0.53
> volume #1 level 0.51
> volume #1 level 0.45
> open /Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/Eclosed-single-
> tail.mrc
Opened Eclosed-single-tail.mrc as #3, grid size 93,46,662, pixel
0.927,0.927,0.927, shown at level 0.807, step 1, values float32
> close #1
> volume #3 level 0.332
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,20.36,0,1,0,13.519,0,0,1,13.705
> ui tool show "Fit in Map"
> fitmap #2 inMap #3
Fit map Single-tail-emerged.mrc in map Eclosed-single-tail.mrc using 202398
points
correlation = 0.7795, correlation about mean = 0.4346, overlap = 1.029e+05
steps = 108, shift = 5.23, angle = 0.923 degrees
Position of Single-tail-emerged.mrc (#2) relative to Eclosed-single-tail.mrc
(#3) coordinates:
Matrix rotation and translation
0.99987080 0.01589603 -0.00238570 -23.98839297
-0.01589331 0.99987302 0.00115627 -11.91084337
0.00240378 -0.00111821 0.99999649 -12.73444275
Axis -0.07057360 -0.14861018 -0.98637436
Axis point -611.04162232 1432.97268636 0.00000000
Rotation angle (degrees) 0.92331779
Shift along axis 16.02394769
> select clear
> open /Users/maryamfeghhi/Desktop/maps/foragers-single-tail.mrc format mrc
Opened foragers-single-tail.mrc as #1, grid size 93,62,670, pixel
0.927,0.927,0.927, shown at level 1.69, step 1, values float32
> volume #1 color silver
> volume #1 level 0.6668
> view matrix models #1,1,0,0,38.654,0,1,0,13.364,0,0,1,14.3
> volume #1 color #73fdff
> volume #1 color #73fcd6
> volume #1 color #00fdff
> volume #1 color #74f9fe
> volume #1 color #76d6ff
> volume #3 color darkgrey
> ui mousemode right "move picked models"
> view matrix models #3,1,0,0,34.684,0,1,0,16.564,0,0,1,14.682
> view matrix models #3,1,0,0,35.449,0,1,0,16.896,0,0,1,15.543
> view matrix models #3,1,0,0,36.056,0,1,0,14.22,0,0,1,16.268
> fitmap #1 inMap #3
Fit map foragers-single-tail.mrc in map Eclosed-single-tail.mrc using 175989
points
correlation = 0.9445, correlation about mean = 0.7333, overlap = 1.371e+05
steps = 132, shift = 2.55, angle = 1.74 degrees
Position of foragers-single-tail.mrc (#1) relative to Eclosed-single-tail.mrc
(#3) coordinates:
Matrix rotation and translation
0.99953824 0.03037297 0.00089218 -10.81372580
-0.03037233 0.99953839 -0.00072497 11.51848171
-0.00091379 0.00069753 0.99999934 0.57887202
Axis 0.02340068 0.02970885 -0.99928464
Axis point 374.22942740 361.34368166 0.00000000
Rotation angle (degrees) 1.74173866
Shift along axis -0.48930564
> select clear
> volume #1 color #00fdff
> volume #1 color #73fdff
> transparency #1.1 30
> select clear
> volume #1 level 0.665
> volume #1 level 0.66
> volume #3 level 0.2751
> volume #1 level 0.66
> volume #1 level 0.67
> volume #1 level 0.68
> volume #1 level 0.65
> save /Users/maryamfeghhi/Desktop/image5.png supersample 3
> save /Users/maryamfeghhi/Desktop/image6.png supersample 3
> view matrix models
> #2,0.99987,0.015896,-0.0023857,0.81209,-0.015893,0.99987,0.0011563,-5.5199,0.0024038,-0.0011182,1,3.2727
> view matrix models
> #2,0.99987,0.015896,-0.0023857,12.38,-0.015893,0.99987,0.0011563,-2.3235,0.0024038,-0.0011182,1,-3.6686
> view matrix models
> #2,0.99987,0.015896,-0.0023857,12.673,-0.015893,0.99987,0.0011563,0.83348,0.0024038,-0.0011182,1,-4.7511
> fitmap #1 inMap #2
Fit map foragers-single-tail.mrc in map Single-tail-emerged.mrc using 179147
points
correlation = 0.9198, correlation about mean = 0.6617, overlap = 3.072e+05
steps = 116, shift = 2.52, angle = 1.48 degrees
Position of foragers-single-tail.mrc (#1) relative to Single-tail-emerged.mrc
(#2) coordinates:
Matrix rotation and translation
0.99917863 0.04036765 0.00353895 2.45877765
-0.04036079 0.99918319 -0.00198865 34.08819178
-0.00361634 0.00184418 0.99999176 23.63619420
Axis 0.04723992 0.08818941 -0.99498292
Axis point 890.49996730 -66.65769625 0.00000000
Rotation angle (degrees) 2.32499896
Shift along axis -20.39523975
> volume #1 level 0.655
> fitmap #1 inMap #2
Fit map foragers-single-tail.mrc in map Single-tail-emerged.mrc using 178215
points
correlation = 0.9203, correlation about mean = 0.662, overlap = 3.069e+05
steps = 40, shift = 0.0168, angle = 0.204 degrees
Position of foragers-single-tail.mrc (#1) relative to Single-tail-emerged.mrc
(#2) coordinates:
Matrix rotation and translation
0.99902848 0.04393024 0.00349807 1.04430028
-0.04392324 0.99903280 -0.00205445 35.53031911
-0.00358494 0.00189880 0.99999177 23.59942053
Axis 0.04480762 0.08028155 -0.99576461
Axis point 847.14453078 -26.04874286 0.00000000
Rotation angle (degrees) 2.52834250
Shift along axis -20.60024593
> fitmap #1 inMap #2
Fit map foragers-single-tail.mrc in map Single-tail-emerged.mrc using 178215
points
correlation = 0.9206, correlation about mean = 0.6626, overlap = 3.067e+05
steps = 28, shift = 0.00938, angle = 0.0493 degrees
Position of foragers-single-tail.mrc (#1) relative to Single-tail-emerged.mrc
(#2) coordinates:
Matrix rotation and translation
0.99899060 0.04478767 0.00344103 0.72093480
-0.04478072 0.99899469 -0.00207298 35.87880388
-0.00353041 0.00191680 0.99999193 23.56247861
Axis 0.04436640 0.07752266 -0.99600294
Axis point 837.36502301 -17.68530907 0.00000000
Rotation angle (degrees) 2.57711161
Shift along axis -20.65489233
> save /Users/maryamfeghhi/Desktop/image7.png supersample 3
> fitmap #3 inMap #1
Fit map Eclosed-single-tail.mrc in map foragers-single-tail.mrc using 195767
points
correlation = 0.9406, correlation about mean = 0.7713, overlap = 1.393e+05
steps = 96, shift = 2.49, angle = 1.19 degrees
Position of Eclosed-single-tail.mrc (#3) relative to foragers-single-tail.mrc
(#1) coordinates:
Matrix rotation and translation
0.99919931 -0.04000241 -0.00074496 15.23826773
0.04000308 0.99919914 0.00090910 -14.81086828
0.00070799 -0.00093817 0.99999931 -0.41452856
Axis -0.02307938 -0.01815282 0.99956882
Axis point 377.93789013 373.08206192 0.00000000
Rotation angle (degrees) 2.29358952
Shift along axis -0.49718057
> volume #3 level 0.28
> volume #3 level 0.29
> volume #3 level 0.2666
> save /Users/maryamfeghhi/Desktop/image8.png supersample 3
> transparency #2.1 40
> select clear
> transparency #1.1 40
> select clear
> transparency #3.1 40
> select clear
> save /Users/maryamfeghhi/Desktop/image9.png supersample 3
> save /Users/maryamfeghhi/Desktop/image10.png supersample 3
> save /Users/maryamfeghhi/Desktop/image11.png supersample 3
> open /Users/maryamfeghhi/Desktop/maps/fo-flit.mrc
Opened fo-flit.mrc as #4, grid size 48,53,91, pixel 0.927,0.927,0.927, shown
at level 1.72, step 1, values float32
> close #4
> open /Users/maryamfeghhi/Desktop/maps/flit-ne.mrc
Opened flit-ne.mrc as #4, grid size 59,120,83, pixel 0.927,0.927,0.927, shown
at level 0.000139, step 1, values float32
> volume #4 color #ff7e79
> open /Users/maryamfeghhi/Desktop/maps/fo-fli-.mrc
Opened fo-fli-.mrc as #5, grid size 65,144,87, pixel 0.927,0.927,0.927, shown
at level 0.81, step 1, values float32
> volume #5 color #941100
> open /Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/fl-ec.mrc
Opened fl-ec.mrc as #6, grid size 74,133,86, pixel 0.927,0.927,0.927, shown at
level 0.275, step 1, values float32
> close #6
> open /Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/FLI-EC-SINGLE.mrc
Opened FLI-EC-SINGLE.mrc as #6, grid size 67,135,87, pixel 0.927,0.927,0.927,
shown at level 7.23e-05, step 1, values float32
> close #6
> open /Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/fl-ec.mrc
Opened fl-ec.mrc as #6, grid size 74,133,86, pixel 0.927,0.927,0.927, shown at
level 0.275, step 1, values float32
> close #5
> close #6
> open /Users/maryamfeghhi/Desktop/maps/fo-fli-.mrc format mrc
Opened fo-fli-.mrc as #5, grid size 65,144,87, pixel 0.927,0.927,0.927, shown
at level 0.81, step 1, values float32
> open /Users/maryamfeghhi/Desktop/maps/my-ec.mrc format mrc
Opened my-ec.mrc as #6, grid size 63,133,86, pixel 0.927,0.927,0.927, shown at
level 6.73e-05, step 1, values float32
> view matrix models #4,1,0,0,-13.898,0,1,0,-26.574,0,0,1,-17.213
> view matrix models #4,1,0,0,-18.477,0,1,0,-15.707,0,0,1,-19.228
> volume #5 color #941100
> volume #5 level 0.4945
> volume #6 color #ff7e79
> volume #5 level 0.03506
> volume #4 color #ff2600
> volume #4 color #ff2f92
> volume #4 color #ff9300
> volume #4 color #945200
> volume #4 color #ff2600
> view matrix models #5,1,0,0,-11.736,0,1,0,15.462,0,0,1,34.661
> save /Users/maryamfeghhi/Desktop/image12.png supersample 3
> save /Users/maryamfeghhi/Desktop/image13.png supersample 3
> view matrix models #6,1,0,0,2.3552,0,1,0,8.9148,0,0,1,37.069
> view matrix models #5,1,0,0,-14.913,0,1,0,3.9097,0,0,1,36.429
> view matrix models #6,1,0,0,-0.41036,0,1,0,-1.5381,0,0,1,36.338
> view matrix models #6,1,0,0,-15.268,0,1,0,1.3605,0,0,1,37
> fitmap #5 inMap #6
Fit map fo-fli-.mrc in map my-ec.mrc using 10009 points
correlation = 0.8282, correlation about mean = 0.6086, overlap = 5912
steps = 36, shift = 1.67, angle = 1.61 degrees
Position of fo-fli-.mrc (#5) relative to my-ec.mrc (#6) coordinates:
Matrix rotation and translation
0.99960325 0.02812157 0.00159000 -10.62805894
-0.02812068 0.99960437 -0.00057831 10.45347473
-0.00160563 0.00053337 0.99999857 0.73454948
Axis 0.01973028 0.05671656 -0.99819535
Axis point 367.05561041 382.86567687 0.00000000
Rotation angle (degrees) 1.61434831
Shift along axis -0.35003326
> fitmap #5 inMap #6
Fit map fo-fli-.mrc in map my-ec.mrc using 10009 points
correlation = 0.8283, correlation about mean = 0.609, overlap = 5909
steps = 40, shift = 0.0122, angle = 0.105 degrees
Position of fo-fli-.mrc (#5) relative to my-ec.mrc (#6) coordinates:
Matrix rotation and translation
0.99958328 0.02886634 0.00000321 -10.43487954
-0.02886634 0.99958328 -0.00007209 10.54678672
-0.00000529 0.00007197 1.00000000 0.41814226
Axis 0.00249519 0.00014712 -0.99999688
Axis point 360.07544345 366.64934965 0.00000000
Rotation angle (degrees) 1.65415452
Shift along axis -0.44262626
> transparency #6.1 50
> select clear
> transparency #6.1 10
> select clear
> save /Users/maryamfeghhi/Desktop/image14.png supersample 3
> transparency #5.1 70
> select clear
> transparency #6.1 0
> select clear
> transparency #5.1 100
> transparency #5.1 70
> select clear
> transparency #5.1 0
> transparency #5.1 80
> select clear
> save /Users/maryamfeghhi/Desktop/image15.png supersample 3
> save /Users/maryamfeghhi/Desktop/image12.png supersample 3
> save /Users/maryamfeghhi/Desktop/image13.png supersample 3
> view matrix models #4,1,0,0,-16.654,0,1,0,-21.299,0,0,1,12.613
> fitmap #4 inMap #5
Fit map flit-ne.mrc in map fo-fli-.mrc using 3926 points
correlation = 0.9157, correlation about mean = 0.5935, overlap = 7940
steps = 196, shift = 16.8, angle = 0.317 degrees
Position of flit-ne.mrc (#4) relative to fo-fli-.mrc (#5) coordinates:
Matrix rotation and translation
0.99954175 -0.02979268 -0.00535528 -3.98757337
0.02979933 0.99955522 0.00116739 -29.52640000
0.00531812 -0.00132644 0.99998498 -23.94560113
Axis -0.04115806 -0.17615295 0.98350198
Axis point 1095.71530979 -175.82008100 0.00000000
Rotation angle (degrees) 1.73608867
Shift along axis -18.18526283
> save /Users/maryamfeghhi/Desktop/image14.png supersample 3
> open /Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/or-ec.mrc
Opened or-ec.mrc as #7, grid size 29,23,38, pixel 0.927,0.927,0.927, shown at
level 0.932, step 1, values float32
> open /Users/maryamfeghhi/Desktop/maps/my-ec.mrc
Opened my-ec.mrc as #8, grid size 63,133,86, pixel 0.927,0.927,0.927, shown at
level 6.73e-05, step 1, values float32
> close #8
> open /Users/maryamfeghhi/Desktop/maps/or-ne.mrc
Opened or-ne.mrc as #8, grid size 30,24,38, pixel 0.927,0.927,0.927, shown at
level 2.25, step 1, values float32
> open /Users/maryamfeghhi/Desktop/maps/oran-f0.mrc
Opened oran-f0.mrc as #9, grid size 32,22,39, pixel 0.927,0.927,0.927, shown
at level 2.32, step 1, values float32
> open /Users/maryamfeghhi/Desktop/maps/myofil-ec.mrc
Opened myofil-ec.mrc as #10, grid size 46,49,81, pixel 0.927,0.927,0.927,
shown at level 0.769, step 1, values float32
> open /Users/maryamfeghhi/Desktop/maps/myo-ne.mrc
Opened myo-ne.mrc as #11, grid size 48,49,79, pixel 0.927,0.927,0.927, shown
at level 1.72, step 1, values float32
> open /Users/maryamfeghhi/Desktop/maps/fo-myofilin.mrc
Opened fo-myofilin.mrc as #12, grid size 48,53,91, pixel 0.927,0.927,0.927,
shown at level 1.72, step 1, values float32
> volume #7 level 0.2584
> volume #8 level 0.4298
> volume #9 level 0.5463
> volume #10 level 0.2516
> volume #11 level 0.5011
> volume #12 level 0.5379
> volume #10 color #d4fb79
> volume #10 color #fffc79
> volume #11 color #ffd479
> volume #12 color #fffb00
> transparency #12.1 50
> select clear
> transparency #12.1 70
> select clear
> view matrix models #12,1,0,0,54.292,0,1,0,-30.788,0,0,1,79.077
> view matrix models #9,1,0,0,73.086,0,1,0,-59.283,0,0,1,55.654
> view matrix models #9,1,0,0,77.497,0,1,0,-39.794,0,0,1,84.535
> view matrix models #10,1,0,0,61.393,0,1,0,-15.689,0,0,1,73.622
> view matrix models #10,1,0,0,49.134,0,1,0,-26.941,0,0,1,80.243
> view matrix models #12,1,0,0,47.243,0,1,0,-30.177,0,0,1,81.514
> fitmap #12 inMap #10
Fit map fo-myofilin.mrc in map myofil-ec.mrc using 7431 points
correlation = 0.8793, correlation about mean = 0.612, overlap = 6139
steps = 68, shift = 5.44, angle = 1.41 degrees
Position of fo-myofilin.mrc (#12) relative to myofil-ec.mrc (#10) coordinates:
Matrix rotation and translation
0.99971688 0.02373584 0.00166610 -9.01613317
-0.02372462 0.99969765 -0.00646135 10.70713230
-0.00181896 0.00641999 0.99997774 -1.51175686
Axis 0.26128042 0.07068962 -0.96267103
Axis point 446.84795244 383.60317453 0.00000000
Rotation angle (degrees) 1.41250715
Shift along axis -0.14353143
> view matrix models #7,1,0,0,78.558,0,1,0,-15.459,0,0,1,92.303
> view matrix models #7,1,0,0,76.542,0,1,0,-41.814,0,0,1,86.531
> view matrix models #7,1,0,0,78.53,0,1,0,-41.75,0,0,1,85.378
> view matrix models #9,1,0,0,77.678,0,1,0,-39.858,0,0,1,84.749
> view matrix models #9,1,0,0,69.076,0,1,0,-32.954,0,0,1,89.569
> view matrix models #7,1,0,0,70.2,0,1,0,-34.929,0,0,1,90.57
> fitmap #7 inMap #9
Fit map or-ec.mrc in map oran-f0.mrc using 2580 points
correlation = 0.9176, correlation about mean = 0.7007, overlap = 2038
steps = 84, shift = 1.55, angle = 1.09 degrees
Position of or-ec.mrc (#7) relative to oran-f0.mrc (#9) coordinates:
Matrix rotation and translation
0.99995970 -0.00895142 0.00068893 3.36149291
0.00893857 0.99981858 0.01681961 -10.08730232
-0.00083937 -0.01681277 0.99985830 6.02364574
Axis -0.88215803 0.04008634 0.46924438
Axis point 0.00000000 368.36072932 602.41328975
Rotation angle (degrees) 1.09227031
Shift along axis -0.54316909
> select clear
> select #9
2 models selected
> volume #7 color #945200
> volume #7 color #ff9300
> volume #9 color #ff7e79
> volume #9 color #ffd479
> volume #9 color #ff7e79
> select clear
> volume #10 color #fec22c
> volume #9 color #f2bb7d
> select clear
> volume #8 color #fb7721
> view matrix models #8,1,0,0,49.561,0,1,0,-57.432,0,0,1,63.014
> view matrix models #8,1,0,0,54.313,0,1,0,-55.294,0,0,1,64.627
> view matrix models #8,1,0,0,52.582,0,1,0,-55.548,0,0,1,65.492
> fitmap #8 inMap #9
Fit map or-ne.mrc in map oran-f0.mrc using 2468 points
correlation = 0.9322, correlation about mean = 0.7321, overlap = 4748
steps = 52, shift = 2.92, angle = 1.29 degrees
Position of or-ne.mrc (#8) relative to oran-f0.mrc (#9) coordinates:
Matrix rotation and translation
0.99978697 -0.01378089 0.01536579 -16.05478588
0.01364104 0.99986492 0.00916878 -27.31900818
-0.01549007 -0.00895723 0.99983990 -14.53214978
Axis -0.40204663 0.68440284 0.60823619
Axis point -126.85412293 0.00000000 1594.67730810
Rotation angle (degrees) 1.29168077
Shift along axis -21.08141345
> select clear
> view matrix models #11,1,0,0,29.426,0,1,0,-18.447,0,0,1,63.835
> view matrix models #11,1,0,0,24.483,0,1,0,-43.389,0,0,1,62.018
> view matrix models #11,1,0,0,32.482,0,1,0,-41.29,0,0,1,59.311
> view matrix models #11,1,0,0,33.636,0,1,0,-43.588,0,0,1,57.911
> fitmap #12 inMap #11
Fit map fo-myofilin.mrc in map myo-ne.mrc using 7431 points
correlation = 0.8853, correlation about mean = 0.6895, overlap = 1.458e+04
steps = 56, shift = 2.2, angle = 0.965 degrees
Position of fo-myofilin.mrc (#12) relative to myo-ne.mrc (#11) coordinates:
Matrix rotation and translation
0.99979751 0.01521682 0.01316744 8.40202039
-0.01501525 0.99977060 -0.01527359 28.32258203
-0.01339684 0.01507279 0.99979665 20.71959827
Axis 0.60206545 0.52702944 -0.59979761
Axis point 0.00000000 -1653.55384432 1618.39467212
Rotation angle (degrees) 1.44411505
Shift along axis 7.55783507
> save /Users/maryamfeghhi/Desktop/image15.png supersample 3
> save /Users/maryamfeghhi/Desktop/image16.png supersample 3
> fitmap #10 inMap #12
Fit map myofil-ec.mrc in map fo-myofilin.mrc using 7357 points
correlation = 0.9096, correlation about mean = 0.7372, overlap = 6143
steps = 68, shift = 2.18, angle = 0.951 degrees
Position of myofil-ec.mrc (#10) relative to fo-myofilin.mrc (#12) coordinates:
Matrix rotation and translation
0.99971143 -0.02392654 -0.00214063 9.43450032
0.02394037 0.99969105 0.00668315 -10.61420640
0.00198006 -0.00673247 0.99997538 1.60240193
Axis -0.26894785 -0.08260891 0.95960555
Axis point 448.78516209 387.51701362 0.00000000
Rotation angle (degrees) 1.42915827
Shift along axis -0.12288678
> save /Users/maryamfeghhi/Desktop/image17.png supersample 3
> open /Users/maryamfeghhi/Desktop/maps/Newly-emerged/Heads-
> Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc
Opened Heads-Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc
as #13, grid size 421,421,688, pixel 0.927,0.927,0.927, shown at level 0.0717,
step 2, values float32
> volume #13 step 1
> volume #13 level 0.04336
> ui tool show "Map Filter"
> volume gaussian #13 sDev 1.1
Opened Heads-Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc
gaussian as #14, grid size 421,421,688, pixel 0.927,0.927,0.927, shown at step
1, values float32
> volume #13 level 0.03583
> volume #14 level 0.02603
> surface dust #14 size 9.27
> volume #14 level 0.02261
> surface dust #14 size 9.27
> select clear
> volume #14 level 0.0213
> surface dust #14 size 9.27
> volume #14 level 0.01762
> volume gaussian #13 sDev 1.5 modelId #14
Opened Heads-Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc
gaussian as #14, grid size 421,421,688, pixel 0.927,0.927,0.927, shown at step
1, values float32
> volume #14 level 0.02485
> surface dust #14 size 9.27
> open /Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/Heads-N-
> Eclosed_122017.mrc
Opened Heads-N-Eclosed_122017.mrc as #15, grid size 407,410,669, pixel
0.927,0.927,0.927, shown at level 0.138, step 2, values float32
> volume #15 step 1
> volume #15 level 0.08707
> surface dust #14 size 9.27
> surface dust #15 size 9.27
> select clear
> surface dust #14 size 9.27
> surface dust #15 size 9.27
Drag select of 14 Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian ,
15 Heads-N-Eclosed_122017.mrc
> view matrix models #15,1,0,0,14.275,0,1,0,12.554,0,0,1,19.054
> fitmap #14 inMap #12
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map fo-myofilin.mrc using 4658813 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to fo-myofilin.mrc (#12) coordinates:
Matrix rotation and translation
0.99979751 -0.01501525 -0.01339684 -41.20488563
0.01521682 0.99977060 0.01507279 13.43716187
0.01316744 -0.01527359 0.99979665 -79.40115237
Axis -0.60206545 -0.52702944 0.59979761
Axis point 0.00000000 -4025.70844363 92.66184011
Rotation angle (degrees) 1.44411505
Shift along axis -29.89836342
> fitmap #14 inMap #12
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map fo-myofilin.mrc using 4658813 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to fo-myofilin.mrc (#12) coordinates:
Matrix rotation and translation
0.99979751 -0.01501525 -0.01339684 -41.20488563
0.01521682 0.99977060 0.01507279 13.43716187
0.01316744 -0.01527359 0.99979665 -79.40115237
Axis -0.60206545 -0.52702944 0.59979761
Axis point 0.00000000 -4025.70844363 92.66184011
Rotation angle (degrees) 1.44411505
Shift along axis -29.89836342
> volume #15 level 0.07012
> fitmap #14 inMap #12
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map fo-myofilin.mrc using 4658813 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to fo-myofilin.mrc (#12) coordinates:
Matrix rotation and translation
0.99979751 -0.01501525 -0.01339684 -41.20488563
0.01521682 0.99977060 0.01507279 13.43716187
0.01316744 -0.01527359 0.99979665 -79.40115237
Axis -0.60206545 -0.52702944 0.59979761
Axis point 0.00000000 -4025.70844363 92.66184011
Rotation angle (degrees) 1.44411505
Shift along axis -29.89836342
> transparency #14.1#15.1 70
> select clear
> transparency #14.1 10
> select clear
> surface dust #14 size 9.27
> surface dust #15 size 9.27
> ui tool show "Map Filter"
> volume gaussian #15 sDev 1.5
Opened Heads-N-Eclosed_122017.mrc gaussian as #16, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> select clear
> transparency #16.1 60
> select clear
> volume #16 color #aefaf066
> volume #16 level 0.02401
> ui tool show "Color Actions"
> volume #14 color #a786bfe6
> volume #14 color #005493
> volume #15 level 0.04188
> transparency #14.1#16.1 50
> select clear
> volume #14 level 0.03016
> volume #16 level 0.01779
> fitmap #14 inMap #16
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads-N-Eclosed_122017.mrc gaussian using 4092104 points
correlation = 0.8053, correlation about mean = 0.5349, overlap = 2.212e+04
steps = 120, shift = 6.12, angle = 5.56 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads-N-Eclosed_122017.mrc gaussian (#16) coordinates:
Matrix rotation and translation
0.99528964 -0.09694541 0.00034636 20.53383218
0.09694563 0.99528945 -0.00067521 -52.06410043
-0.00027927 0.00070561 0.99999971 -19.36705936
Axis 0.00712141 0.00322660 0.99996944
Axis point 545.47214401 186.72914303 0.00000000
Rotation angle (degrees) 5.56347738
Shift along axis -19.38822782
> volume #14 level 0.03309
> volume #16 level -1.903e-16
> volume #16 level 0.003953
> volume #14 level 0.03505
> transparency #16.1 30
> select clear
> transparency #16.1 70
> select clear
> transparency #16.1 70
> select clear
> fitmap #16 inMap #14
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 6563146 points
correlation = 0.7491, correlation about mean = 0.4955, overlap = 2.335e+04
steps = 56, shift = 0.342, angle = 0.804 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99655210 0.08296910 -0.00018757 -10.89898185
-0.08296894 0.99655187 0.00072943 48.34918759
0.00024745 -0.00071136 0.99999972 19.03389638
Axis -0.00868235 -0.00262149 -0.99995887
Axis point 575.59968264 157.27688481 0.00000000
Rotation angle (degrees) 4.75944192
Shift along axis -19.06523154
> select clear
> volume #15 level 0.03229
> volume #14 level 0.03818
> volume #14 level 0.03994
> select clear
> transparency #16.1 90
> select clear
> volume #14 level 0.04366
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> volume erase #16 center 372.07,370.12,611.71 radius 206.82
> volume erase #16 center 371.61,380.04,622.88 radius 206.82
> volume erase #16 center 367.95,367.07,147.41 radius 206.82
> volume erase #14 center 367.95,367.07,147.41 radius 206.64
> volume erase #14 center 362.7,371.16,626.25 radius 206.64
> volume erase #14 center 410.84,362.38,621.41 radius 206.64
> volume erase #16 center 352.23,285.82,632.84 radius 206.51
> volume erase #16 center 292.01,354.79,645.35 radius 206.51
> transparency #16.1 90
> select clear
> transparency #14.1 10
> select clear
> lighting shadows true
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting simple
> select clear
> transparency #16.1 100
> select clear
> transparency #16.1 60
> select clear
> transparency #16.1 50
> select clear
> volume gaussian #15 sDev 2 modelId #16
Opened Heads-N-Eclosed_122017.mrc gaussian as #16, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> volume #16 level 0.02942
> surface dust #14 size 9.27
> surface dust #16 size 9.27
> volume #16 level 0.0233
> volume erase #16 center 364.58,368.2,128.93 radius 206.2
> volume erase #16 center 431.86,340.3,114.5 radius 206.2
> volume erase #16 center 373.56,371.25,604.46 radius 206.2
> select clear
> open /Users/maryamfeghhi/Desktop/maps/foragers2024/Heads.mrc
Opened Heads.mrc as #18, grid size 361,361,661, pixel 0.927,0.927,0.927, shown
at level 0.151, step 2, values float32
> volume #18 step 1
> volume #18 level 0.0782
> volume erase #18 center 339.74,341.79,99.157 radius 206.19
Opened Heads.mrc copy as #19, grid size 361,361,661, pixel 0.927,0.927,0.927,
shown at step 1, values float32
> volume erase #19 center 387.46,311.67,99.873 radius 206.19
> volume erase #19 center 357.3,414.7,80.595 radius 206.19
> volume erase #19 center 383.14,415.7,611 radius 206.19
> volume erase #19 center 395.03,286.45,614.68 radius 206.19
> volume erase #19 center 282.07,278.63,616.44 radius 206.19
> volume #18 level 0.06415
> volume #19 level 0.06277
> volume #19 color #00fdff
> volume #19 color #bcdffd
> volume #16 color #d4f88d80
> volume #16 color #d6d6d6
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using
1290513 points
correlation = 0.9529, correlation about mean = 0.9369, overlap = 1.535e+04
steps = 176, shift = 27, angle = 0.0873 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999884 -0.00102947 -0.00112106 0.70707786
0.00102940 0.99999947 -0.00006315 -0.44463380
0.00112112 0.00006200 0.99999937 -0.35501119
Axis 0.04107700 -0.73595389 0.67578439
Axis point 387.14962612 0.00000000 626.05938366
Rotation angle (degrees) 0.08727969
Shift along axis 0.11636360
> transparency #16.1 70
> select clear
> save /Users/maryamfeghhi/Desktop/image18.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/maryamfeghhi/Desktop/movie1.mp4
Movie saved to /Users/maryamfeghhi/Desktop/movie1.mp4
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> volume #!16,19 style surface
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> volume #!16,19 style surface
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> transparency #16.1 70
> transparency sel 0
> transparency sel 50
> select clear
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> volume #!16,19 style surface
> volume #!16,19 showOutlineBox true
> volume #!16,19 style image
> volume #!16,19 style mesh
> volume #!16,19 showOutlineBox false
> volume #!16,19 style mesh
> volume #!16,19 style surface
> lighting flat
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting full
> volume #!16,19 step 1
> volume #!16,19 step 2
> volume #!16,19 step 1
> volume #!16,19 step 2
> volume #!16,19 showOutlineBox true
> volume #!16,19 showOutlineBox false
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> transparency #16.1#19.1 0
> transparency #16.1 80
> select clear
> save /Users/maryamfeghhi/Desktop/image19.png supersample 3
> volume #16 change image level -9.714e-17,0 level 0.03517,0.8 level 0.3168,1
> fitmap #19 inMap #14
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 97906 points
correlation = 0.8163, correlation about mean = 0.423, overlap = 801.7
steps = 184, shift = 26.9, angle = 0.937 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99357251 0.11319751 -0.00000512 -20.39213785
-0.11319751 0.99357251 -0.00004216 60.21391513
0.00000032 0.00004246 1.00000000 19.16735025
Axis 0.00037377 -0.00002403 -0.99999993
Axis point 520.03070828 209.61119525 0.00000000
Rotation angle (degrees) 6.49967134
Shift along axis -19.17641755
> transparency #19.1 70
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> transparency sel 0
> select clear
> transparency #19.1 80
> select clear
> transparency #19.1 50
> select clear
> surface dust #14 size 9.27
> surface dust #19 size 9.27
> select clear
> transparency #19.1 90
> transparency #19.1 70
> select clear
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
Unsupported scale factor (0.000000) detected on Display0
> transparency #19.1 60
> select clear
> transparency sel 0
> select clear
> transparency #19.1 60
> select clear
> volume #19 change image level 0,0 level 0.03765,0.8 level 0.3765,1
> select clear
> volume #19 step 1
> select clear
> transparency #19.1 70
> select clear
> fitmap #19 inMap #14
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 783640 points
correlation = 0.8166, correlation about mean = 0.423, overlap = 6417
steps = 48, shift = 0.0107, angle = 0.0182 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99360846 0.11288149 -0.00000461 -20.29260542
-0.11288149 0.99360846 -0.00004266 60.08835991
-0.00000024 0.00004291 1.00000000 19.15670396
Axis 0.00037906 -0.00001934 -0.99999993
Axis point 520.46654607 209.17444718 0.00000000
Rotation angle (degrees) 6.48144842
Shift along axis -19.16555687
> fitmap #19 inMap #14
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 783640 points
correlation = 0.8166, correlation about mean = 0.4231, overlap = 6417
steps = 48, shift = 0.0256, angle = 0.00525 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99361387 0.11283389 0.00000358 -20.27936586
-0.11283389 0.99361386 0.00003496 60.03081686
0.00000039 -0.00003514 1.00000000 19.16112822
Axis -0.00031060 0.00001416 -0.99999995
Axis point 520.18917257 209.22182869 0.00000000
Rotation angle (degrees) 6.47870330
Shift along axis -19.15397870
> select clear
> select #19
3 models selected
> transparency #19.1 80
> select clear
> surface style #19 mesh
> select clear
> transparency #19.1 80
> select clear
> lighting simple
> lighting soft
> lighting full
> select clear
> surface style #19 solid
> select clear
> transparency #19.1 70
> select clear
> volume #19 level 0
> volume #19 level 0.001804
> select clear
> select #19
3 models selected
> select clear
> volume #14 level 0.05007
> select clear
> graphics silhouettes false
> graphics silhouettes true
> select clear
> volume #14 level 0.05235
> select clear
> select #14
2 models selected
> transparency #14.1 50
> select clear
> transparency #19.1 20
> select clear
> transparency #14.1 20
> select clear
> save /Users/maryamfeghhi/Desktop/image20.png supersample 3
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> transparency #14.1#19.1 0
> transparency #14.1#19.1 50
> transparency #14.1#19.1 0
> select clear
> transparency sel 50
> select clear
> save /Users/maryamfeghhi/Desktop/image21.png supersample 3
> graphics silhouettes false
> graphics silhouettes true
> select clear
> transparency #9.1 80
> transparency #9.1 50
> transparency #9.1 40
> select clear
> save /Users/maryamfeghhi/Desktop/image1.png supersample 3
> volume #11 color #fffc79
> volume #11 color #fffb00
> volume #11 color #929000
> volume #11 color #d4fb79
> volume #11 color #d8fa92
> volume #11 color #b3fa78
> volume #11 color #fae209
> volume #11 color #faf709
> volume #11 color #faf808
> volume #11 color #fa9410
> volume #11 color #c9fa15
> volume #12 color #feee814c
> volume #12 color #fee97d4c
> volume #12 color #fef0824c
> volume #12 color #fef0824d
> select #12
2 models selected
> transparency #12.1 80
> select clear
> volume #12 level 0.06206
> select #12
2 models selected
> transparency #12.1 70
> select clear
> volume #11 level 0.5633
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> select clear
> graphics silhouettes false
> graphics silhouettes true
> select clear
> volume #11 level 0.9136
> save /Users/maryamfeghhi/Desktop/image2.png supersample 3
> volume #7 color #f4b44e
> volume #7 color #f48553
> volume #7 color #f47c50
> volume #7 color #f46549
> volume #7 color #d3f4ac
> volume #7 color #f34d1c
> volume #7 color #f37c00
> volume #7 color #cce9bf
> volume #7 color #e9aa00
> volume #10 color #f7e8a4
> volume #10 color #f7e3b0
> volume #10 color #f4f750
> save /Users/maryamfeghhi/Desktop/image3.png supersample 3
> fitmap #12 inMap #6
Fit map fo-myofilin.mrc in map my-ec.mrc using 7727 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of fo-myofilin.mrc (#12) relative to my-ec.mrc (#6) coordinates:
Matrix rotation and translation
0.99979751 0.01521682 0.01316744 57.30561921
-0.01501525 0.99977060 -0.01527359 -16.62602972
-0.01339684 0.01507279 0.99979665 41.63015539
Axis 0.60206545 0.52702944 -0.59979761
Axis point 0.00000000 -2807.04434589 -1072.94577748
Rotation angle (degrees) 1.44411505
Shift along axis 0.76965841
> ui mousemode right "move picked models"
> view matrix models
> #12,0.9998,0.015217,0.013167,41.441,-0.015015,0.99977,-0.015274,-16.376,-0.013397,0.015073,0.9998,79.919
> view matrix models
> #12,0.9998,0.015217,0.013167,41.59,-0.015015,0.99977,-0.015274,-16.938,-0.013397,0.015073,0.9998,80.416
> fitmap #12 inMap #6
Fit map fo-myofilin.mrc in map my-ec.mrc using 7727 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of fo-myofilin.mrc (#12) relative to my-ec.mrc (#6) coordinates:
Matrix rotation and translation
0.99979751 0.01521682 0.01316744 56.85850243
-0.01501525 0.99977060 -0.01527359 -18.29847315
-0.01339684 0.01507279 0.99979665 43.41599737
Axis 0.60206545 0.52702944 -0.59979761
Axis point 0.00000000 -2837.55078236 -1105.32258902
Rotation angle (degrees) 1.44411505
Shift along axis -1.45210583
> fitmap #12 inMap #10
Fit map fo-myofilin.mrc in map myofil-ec.mrc using 7727 points
correlation = 0.8776, correlation about mean = 0.615, overlap = 6176
steps = 60, shift = 2.5, angle = 0.0175 degrees
Position of fo-myofilin.mrc (#12) relative to myofil-ec.mrc (#10) coordinates:
Matrix rotation and translation
0.99971418 0.02384624 0.00170670 -9.07190766
-0.02383443 0.99969392 -0.00663198 10.78774747
-0.00186432 0.00658941 0.99997655 -1.58040725
Axis 0.26651468 0.07198394 -0.96113903
Axis point 448.04423172 384.43726979 0.00000000
Rotation angle (degrees) 1.42132479
Shift along axis -0.12226093
> save /Users/maryamfeghhi/Desktop/image4.png supersample 3
> save /Users/maryamfeghhi/Desktop/image5.png supersample 3
> volume #11 color #f6d648
> volume #11 color #f6d549
> save /Users/maryamfeghhi/Desktop/image6.png supersample 3
> volume #11 level 0.4841
> save /Users/maryamfeghhi/Desktop/image7.png supersample 3
> volume #3 color #65b4b899
> volume #3 color #8af6fb99
> volume #2 color #3c649e99
> volume #2 color #38529e99
> volume #1 color #4922fd99
> volume #1 color #3815fd99
> volume #1 color #1d34fd99
> volume #1 color #111d9099
> volume #2 color #4273a999
> volume #2 color #4387a999
> volume #1 color #233cc699
> volume #1 color #223abf99
> volume #1 color #1a38bf99
> volume #1 color #1835b299
> save /Users/maryamfeghhi/Desktop/image8.png supersample 3
> save /Users/maryamfeghhi/Desktop/image9.png supersample 3
> save /Users/maryamfeghhi/Desktop/image10.png supersample 3
> volume #19 color #4681fb80
> volume #19 color #3c50fb80
> volume #19 color #3a4bfb80
> volume #19 color #3a4cfb80
> volume #19 color #1835b2
> volume #16 color white
> volume #16 color #8af6fb
> volume #14 color #4387a9
> select clear
> transparency sel 50
> select clear
> save /Users/maryamfeghhi/Desktop/image11.png supersample 3
> graphics silhouettes false
> graphics silhouettes true
> transparency sel 50
> select clear
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using 161385
points
correlation = 0.9529, correlation about mean = 0.9369, overlap = 1919
steps = 156, shift = 26.9, angle = 0.916 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999882 -0.00104077 -0.00113045 0.71181211
0.00104072 0.99999946 -0.00005291 -0.45005198
0.00113050 0.00005174 0.99999936 -0.36460772
Axis 0.03403270 -0.73527488 0.67691405
Axis point 387.73770799 0.00000000 626.00724885
Rotation angle (degrees) 0.08809140
Shift along axis 0.10832871
> transparency sel 0
> transparency sel 50
> select clear
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency #16.1 90
> select clear
> volume #!16,19 style surface
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> select clear
> transparency sel 0
> transparency sel 50
> transparency #16.1 80
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> volume #!16,19 style image
> volume #!16,19 style mesh
> volume #!16,19 style surface
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> volume #!16,19 style image
> volume #!16,19 style surface
> lighting simple
> select clear
> transparency #19.1 30
> select clear
> transparency sel 0
> transparency sel 50
> transparency #16.1 80
> select clear
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> transparency #16.1#19.1 0
> transparency #16.1#19.1 50
> transparency #16.1#19.1 0
> transparency #16.1#19.1#!16,19 80
> select clear
> transparency #19.1 20
> select clear
> transparency sel 0
> transparency sel 50
> select #16
3 models selected
> select clear
> transparency sel 0
> volume sel style surface
> transparency sel 50
> transparency sel 0
> transparency sel 50
> volume sel showOutlineBox true
> volume sel showOutlineBox false
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> volume #16 step 1
> select clear
> volume sel style mesh
> volume sel style surface
> transparency sel 0
> transparency sel 50
> select clear
> volume #16 level 0.04227
> select clear
> transparency sel 0
> transparency sel 50
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> transparency sel 0
> transparency sel 50
> surface style #16 solid
> transparency #16.1 80
> select clear
> view matrix models
> #16,0.99989,0.014935,-0.00078461,-18.053,-0.014936,0.99989,-0.00067492,-90.157,0.00077444,0.00068656,1,47.049
> transparency sel 0
> transparency sel 50
> transparency #16.1#19.1#!16,19 100
> transparency #16.1#19.1#!16,19 10
> select clear
> transparency #16.1 50
> transparency #16.1 70
> select clear
> view matrix models
> #16,0.99989,0.014935,-0.00078461,1.4643,-0.014936,0.99989,-0.00067492,-11.872,0.00077444,0.00068656,1,-20.961
> view matrix models
> #19,0.99987,0.015976,0.00034653,-21.487,-0.015976,0.99987,-0.00064007,-13.585,-0.00035672,0.00063446,1,-12.725
> view matrix models
> #19,0.99987,0.015976,0.00034653,-11.758,-0.015976,0.99987,-0.00064007,-1.338,-0.00035672,0.00063446,1,-2.9222
> view matrix models
> #19,0.99987,0.015976,0.00034653,3.9877,-0.015976,0.99987,-0.00064007,-3.8929,-0.00035672,0.00063446,1,-21.801
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using
1031772 points
correlation = 0.9628, correlation about mean = 0.9223, overlap = 1.533e+04
steps = 76, shift = 8.27, angle = 0.00665 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999899 -0.00095888 -0.00105159 0.65994450
0.00095880 0.99999954 -0.00007588 -0.42048550
0.00105166 0.00007487 0.99999944 -0.34754653
Axis 0.05289007 -0.73791948 0.67281311
Axis point 402.04281795 0.00000000 621.58059958
Rotation angle (degrees) 0.08165355
Shift along axis 0.11135510
> select clear
> volume sel step 1
> volume sel step 2
> volume sel step 1
> transparency sel 0
> transparency sel 50
> volume sel style image
> volume sel style mesh
> volume sel style surface
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using
1031772 points
correlation = 0.9628, correlation about mean = 0.9223, overlap = 1.533e+04
steps = 28, shift = 0.0168, angle = 0.006 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999908 -0.00086047 -0.00105024 0.62406083
0.00086043 0.99999963 -0.00003977 -0.39890153
0.00105027 0.00003886 0.99999945 -0.31745232
Axis 0.02894456 -0.77321806 0.63347932
Axis point 378.20373623 0.00000000 590.41953757
Rotation angle (degrees) 0.07782454
Shift along axis 0.12540155
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using
1031772 points
correlation = 0.9628, correlation about mean = 0.9223, overlap = 1.533e+04
steps = 28, shift = 0.0144, angle = 0.00382 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999902 -0.00092420 -0.00104898 0.64676460
0.00092414 0.99999957 -0.00005915 -0.41461386
0.00104903 0.00005818 0.99999945 -0.33823919
Axis 0.04192294 -0.74968325 0.66046763
Axis point 394.86995555 0.00000000 611.62023928
Rotation angle (degrees) 0.08017202
Shift along axis 0.11454730
> select clear
> transparency #16.1 60
> select clear
> transparency #16.1#19.1 0
> surface dust #16 size 9.27
> volume #16 level 0.01496
> volume #19 level 0.08928
> select clear
> transparency sel 50
> select clear
> view matrix models #17,1,0,0,263.43,0,1,0,509.93,0,0,1,545.8
> view matrix models #17,1,0,0,284.98,0,1,0,520.21,0,0,1,188.2
> volume erase #16 center 284.98,520.21,188.2 radius 40.621
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using
1461186 points
correlation = 0.9498, correlation about mean = 0.9378, overlap = 1.536e+04
steps = 44, shift = 0.0104, angle = 0.00975 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999879 -0.00107710 -0.00112294 0.72484675
0.00107702 0.99999942 -0.00006856 -0.45540305
0.00112301 0.00006735 0.99999937 -0.36834927
Axis 0.04363124 -0.72102047 0.69153872
Axis point 393.17553672 0.00000000 640.97649552
Rotation angle (degrees) 0.08923724
Shift along axis 0.10525310
> save /Users/maryamfeghhi/Desktop/image12.png supersample 3
> save /Users/maryamfeghhi/Desktop/image13.png supersample 3
> save /Users/maryamfeghhi/Desktop/image14.png supersample 3
> volume #2 level 0.5879
> volume #14 level 0.03291
> surface dust #14 size 9.27
> surface dust #19 size 9.27
> view matrix models #17,1,0,0,223.2,0,1,0,573.18,0,0,1,484.39
> view matrix models #17,1,0,0,336.06,0,1,0,543.97,0,0,1,507.71
> view matrix models #17,1,0,0,326.2,0,1,0,531.06,0,0,1,500.34
> volume erase #14 center 326.2,531.06,500.34 radius 40.18
> view matrix models #17,1,0,0,177.96,0,1,0,379.97,0,0,1,461.27
> view matrix models #17,1,0,0,218.94,0,1,0,348.44,0,0,1,503.22
> volume erase #14 center 218.94,348.44,503.22 radius 40.18
> volume #14 level 0.0352
> volume #14 level 0.03543
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 821108 points
correlation = 0.8145, correlation about mean = 0.5313, overlap = 6087
steps = 288, shift = 47, angle = 1.46 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.99040730 -0.13817876 0.00002663 37.57915950
0.13817876 0.99040730 0.00001402 -65.65764649
-0.00002831 -0.00001020 1.00000000 -19.65629613
Axis -0.00008765 0.00019879 0.99999998
Axis point 491.64601879 237.81674809 0.00000000
Rotation angle (degrees) 7.94247308
Shift along axis -19.67264138
> select clear
> transparency sel 50
> select clear
> volume #19 level 0.006313
> volume #14 level 0.04778
> select clear
> transparency #19.1 50
> select clear
> volume #19 level 0.003607
> select clear
> view matrix models
> #14,0.99249,-0.12234,0.00037338,35.502,0.12234,0.99249,-0.00062648,-71.373,-0.00029394,0.00066746,1,-41.093
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 587996 points
correlation = 0.8503, correlation about mean = 0.4801, overlap = 5729
steps = 72, shift = 5.24, angle = 1.56 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98627834 -0.16509101 -0.00003389 49.20275048
0.16509101 0.98627834 0.00000838 -74.16479007
0.00003204 -0.00001386 1.00000000 -20.13817087
Axis -0.00006738 -0.00019965 0.99999998
Axis point 470.77851572 258.89676644 0.00000000
Rotation angle (degrees) 9.50252192
Shift along axis -20.12667865
> volume #19 level 0.003156
> select clear
> transparency #19.1 40
> select clear
> transparency #14.1 60
> select clear
> transparency #14.1 30
> select clear
> vop gaussian #14 sdev 2.78
Opened Heads-Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc
gaussian as #20, grid size 421,421,688, pixel 0.927,0.927,0.927, shown at step
1, values float32
> select clear
> volume #20 level 0.02176
> select clear
> volume #20 color #b3b3b3
> volume #20 color #4387a9
> volume #14 level 0.05487
> volume #14 level 0.05785
> volume #20 level 0.0593
> select clear
> transparency #19.1 70
> select clear
> save /Users/maryamfeghhi/Desktop/image15.png supersample 3
> select clear
> transparency #19.1 40
> select clear
> volume #20 level 0.04553
> volume #20 level 0.04908
> volume #19 level 0.002706
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 534514 points
correlation = 0.8587, correlation about mean = 0.4463, overlap = 5335
steps = 56, shift = 0.161, angle = 0.566 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98459793 -0.17483396 -0.00004597 53.47595127
0.17483396 0.98459793 0.00000961 -77.17719397
0.00004358 -0.00001749 1.00000000 -20.30227263
Axis -0.00007750 -0.00025611 0.99999996
Axis point 464.79856734 264.91145818 0.00000000
Rotation angle (degrees) 10.06899610
Shift along axis -20.28665016
> save /Users/maryamfeghhi/Desktop/image16.png supersample 3
> save /Users/maryamfeghhi/Desktop/image17.png supersample 3
> save /Users/maryamfeghhi/Desktop/image18.png supersample 3
> save /Users/maryamfeghhi/Desktop/image19.png supersample 3
> select clear
> transparency sel 0
> select clear
> transparency #16.1 50
> select clear
> transparency sel 0
> transparency sel 50
> select clear
Drag select of 16 Heads-N-Eclosed_122017.mrc gaussian
> transparency sel 0
> transparency sel 50
> transparency #16.1 70
> select clear
> transparency #16.1 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> select clear
> volume #16 level 0.05356
> select clear
> view matrix models #17,1,0,0,514.68,0,1,0,250.05,0,0,1,481.45
> view matrix models #17,1,0,0,510.86,0,1,0,233.72,0,0,1,314.38
> view matrix models #17,1,0,0,512.7,0,1,0,236.76,0,0,1,314.66
> volume erase #16 center 512.7,236.76,314.66 radius 39.69
> view matrix models #17,1,0,0,262.14,0,1,0,193.73,0,0,1,350.12
> volume erase #16 center 262.14,193.73,350.12 radius 39.69
> view matrix models #17,1,0,0,218.97,0,1,0,416.19,0,0,1,431.61
> view matrix models #17,1,0,0,220.72,0,1,0,403.36,0,0,1,422.64
> view matrix models
> #16,0.99989,0.014899,-0.00077736,-3.3153,-0.0149,0.99989,-0.00069068,17.181,0.00076698,0.00070219,1,-6.6848
> view matrix models
> #16,0.99989,0.014899,-0.00077736,136.68,-0.0149,0.99989,-0.00069068,-105.65,0.00076698,0.00070219,1,-102.8
> view matrix models #17,1,0,0,348.19,0,1,0,285.59,0,0,1,331.05
> view matrix models #17,1,0,0,350.64,0,1,0,354.17,0,0,1,245.52
> volume erase #16 center 350.64,354.17,245.52 radius 39.69
> view matrix models #17,1,0,0,237.02,0,1,0,234.62,0,0,1,275.6
> view matrix models #17,1,0,0,598.58,0,1,0,403.64,0,0,1,283.02
> view matrix models #17,1,0,0,601.45,0,1,0,406.14,0,0,1,269.66
> view matrix models #17,1,0,0,605.36,0,1,0,396.24,0,0,1,267.71
> volume erase #16 center 605.36,396.24,267.71 radius 39.69
> view matrix models
> #19,0.99987,0.015976,0.00034653,135.42,-0.015976,0.99987,-0.00064007,-113.37,-0.00035672,0.00063446,1,-39.797
> view matrix models
> #19,0.99987,0.015976,0.00034653,144.71,-0.015976,0.99987,-0.00064007,-91.408,-0.00035672,0.00063446,1,-50.561
> view matrix models
> #19,0.99987,0.015976,0.00034653,135.94,-0.015976,0.99987,-0.00064007,-105.37,-0.00035672,0.00063446,1,-104.28
> view matrix models
> #16,0.99989,0.014899,-0.00077736,137.2,-0.0149,0.99989,-0.00069068,-105.38,0.00076698,0.00070219,1,-101.15
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using 915761
points
correlation = 0.9716, correlation about mean = 0.9064, overlap = 1.531e+04
steps = 64, shift = 3.56, angle = 0.0199 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999925 -0.00082208 -0.00090371 0.56205772
0.00082194 0.99999965 -0.00015239 -0.33733550
0.00090384 0.00015165 0.99999958 -0.31008315
Axis 0.12348465 -0.73411749 0.66769982
Axis point 424.62220910 0.00000000 606.56085801
Rotation angle (degrees) 0.07053709
Shift along axis 0.11000693
> select clear
> transparency sel 0
> transparency sel 50
> select clear
> transparency #16.1 80
> select clear
> transparency sel 0
> transparency sel 50
> select clear
> transparency sel 0
> transparency sel 50
> select clear
> transparency sel 0
> transparency sel 50
> select clear
> transparency #16.1 80
> select clear
> save /Users/maryamfeghhi/Desktop/image20.png supersample 3
> graphics silhouettes false
> graphics silhouettes true
> transparency sel 0
> transparency sel 50
> select clear
> transparency #16.1 90
> select clear
> volume #16 color #8af6fb
> select clear
> transparency sel 50
> select clear
> save /Users/maryamfeghhi/Desktop/image21.png supersample 3
> transparency #16.1 60
> select clear
> transparency #16.1 70
> select clear
> transparency #16.1 80
> select clear
> save /Users/maryamfeghhi/Desktop/image22.png supersample 3
> save /Users/maryamfeghhi/Desktop/image23.png supersample 3
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 443870 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98627834 -0.16509101 -0.00003389 -84.38016735
0.16509101 0.98627834 0.00000838 25.24530298
0.00003204 -0.00001386 1.00000000 62.23443017
Axis -0.00006738 -0.00019965 0.99999998
Axis point -194.13107948 -494.95227195 0.00000000
Rotation angle (degrees) 9.50252192
Shift along axis 62.23507411
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 443870 points
correlation = 0, correlation about mean = 0, overlap = 0
steps = 24, shift = 0, angle = 0 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98627834 -0.16509101 -0.00003389 -84.38016735
0.16509101 0.98627834 0.00000838 25.24530298
0.00003204 -0.00001386 1.00000000 62.23443017
Axis -0.00006738 -0.00019965 0.99999998
Axis point -194.13107948 -494.95227195 0.00000000
Rotation angle (degrees) 9.50252192
Shift along axis 62.23507411
> view matrix models
> #14,0.98879,-0.14931,0.00031279,179.72,0.14931,0.98879,-0.00063115,-170.43,-0.00021504,0.00067078,1,-24.17
> view matrix models
> #14,0.98879,-0.14931,0.00031279,201.51,0.14931,0.98879,-0.00063115,-172.48,-0.00021504,0.00067078,1,-113.44
> view matrix models
> #14,0.98879,-0.14931,0.00031279,186.66,0.14931,0.98879,-0.00063115,-179.5,-0.00021504,0.00067078,1,-112
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 443870 points
correlation = 0.8744, correlation about mean = 0.3954, overlap = 5313
steps = 104, shift = 13.1, angle = 0.746 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98404544 -0.17791733 0.00003252 54.80018037
0.17791733 0.98404544 0.00000633 -78.12233697
-0.00003313 -0.00000044 1.00000000 -20.44726238
Axis -0.00001902 0.00018449 0.99999998
Axis point 462.96955140 266.49071228 0.00000000
Rotation angle (degrees) 10.24847351
Shift along axis -20.46271724
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 443870 points
correlation = 0.8745, correlation about mean = 0.3954, overlap = 5312
steps = 44, shift = 0.0136, angle = 0.00359 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98404652 -0.17791137 -0.00002839 54.82282998
0.17791137 0.98404652 -0.00000683 -78.11424430
0.00002915 0.00000167 1.00000000 -20.48462034
Axis 0.00002387 -0.00016172 0.99999999
Axis point 462.99052741 266.63280533 0.00000000
Rotation angle (degrees) 10.24812647
Shift along axis -20.47067877
> select clear
> save /Users/maryamfeghhi/Desktop/image24.png supersample 3
> save /Users/maryamfeghhi/Desktop/image25.png supersample 3
> save /Users/maryamfeghhi/Desktop/image26.png supersample 3
> select clear
> transparency #16.1 80
> select clear
> transparency #16.1 10
> select clear
> transparency #16.1 0
> select #16
3 models selected
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> select clear
> volume #14 color #f0f0f0
> volume #14 color #4387a9
> save /Users/maryamfeghhi/Desktop/image27.png supersample 3
> save /Users/maryamfeghhi/Desktop/image28.png supersample 3
> volume #19 level 0.112
> volume #19 level 0.004505
> transparency #19.1 80
> select clear
> volume #14 level 0.072
> volume #19 style mesh
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 305744 points
correlation = 0.8998, correlation about mean = 0.2894, overlap = 4541
steps = 52, shift = 0.153, angle = 0.447 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98262858 -0.18558306 0.00004144 58.18746411
0.18558306 0.98262858 0.00000959 -80.45915596
-0.00004250 -0.00000173 1.00000000 -20.60993120
Axis -0.00003049 0.00022614 0.99999997
Axis point 458.85077202 270.58474136 0.00000000
Rotation angle (degrees) 10.69512844
Shift along axis -20.62989986
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 305744 points
correlation = 0.8997, correlation about mean = 0.2897, overlap = 4541
steps = 60, shift = 0.0209, angle = 0.0049 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98263647 -0.18554130 -0.00002951 58.20264641
0.18554130 0.98263647 -0.00001244 -80.43408519
0.00003130 0.00000675 1.00000000 -20.62145750
Axis 0.00005173 -0.00016387 0.99999999
Axis point 458.86667076 270.75462609 0.00000000
Rotation angle (degrees) 10.69269318
Shift along axis -20.60526534
> volume #19 style surface
> transparency #19.1 80
> select clear
> transparency #19.1 0
> select clear
> ui tool show "Color Actions"
> color royal blue
> color medium blue
> color blue
> color cornflower blue
> color dodger blue
> color deep sky blue
> color dodger blue
> color royal blue
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using 915761
points
correlation = 0.9716, correlation about mean = 0.9064, overlap = 1.531e+04
steps = 40, shift = 0.0176, angle = 0.00527 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999923 -0.00088456 -0.00087045 0.57342279
0.00088448 0.99999960 -0.00009364 -0.38145536
0.00087053 0.00009287 0.99999962 -0.29489687
Axis 0.07492941 -0.69945923 0.71073368
Axis point 352.33405676 639.46323654 0.00000000
Rotation angle (degrees) 0.07130566
Shift along axis 0.10018557
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads.mrc copy using 915761
points
correlation = 0.9716, correlation about mean = 0.9064, overlap = 1.531e+04
steps = 40, shift = 0.0146, angle = 0.00454 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads.mrc
copy (#19) coordinates:
Matrix rotation and translation
0.99999928 -0.00080692 -0.00088537 0.55096498
0.00080684 0.99999967 -0.00009996 -0.35270533
0.00088545 0.00009925 0.99999960 -0.28787649
Axis 0.08286408 -0.73658059 0.67125448
Axis point 410.46259557 0.00000000 611.46717017
Rotation angle (degrees) 0.06887235
Shift along axis 0.11221272
> select clear
> volume #16 level 0.05659
> select clear
> volume #16 level 0.05772
> select clear
> volume #16 level 0.05659
> volume #16 level 0.05545
> select clear
> select #16
3 models selected
> volume #16 level 0.05015
> select clear
> save /Users/maryamfeghhi/Desktop/image29.png supersample 3
> view matrix models
> #2,0.99987,0.015896,-0.0023857,12.857,-0.015893,0.99987,0.0011563,-0.028325,0.0024038,-0.0011182,1,23.104
> view matrix models
> #2,0.99987,0.015896,-0.0023857,12.762,-0.015893,0.99987,0.0011563,-0.15417,0.0024038,-0.0011182,1,26.309
> volume #3 color #e7feff
> volume #3 color #b2d5ff
> volume #3 color #a9d9ff
> save /Users/maryamfeghhi/Desktop/image30.png supersample 3
> volume #2 color #97cbec
> volume #2 color #81aecb
> save /Users/maryamfeghhi/Desktop/image31.png supersample 3
> open "/Users/maryamfeghhi/Desktop/maps/foragers2024/Green protein-
> Foragers.mrc" /Users/maryamfeghhi/Desktop/maps/foragers2024/Flighthin-
> Foragers.mrc
Opened Green protein-Foragers.mrc as #21.1, grid size 173,173,506, pixel
0.927,0.927,0.927, shown at level 0.000204, step 1, values float32
Opened Flighthin-Foragers.mrc as #21.2, grid size 220,221,556, pixel
0.927,0.927,0.927, shown at level 0.000237, step 2, values float32
> volume #21.1 color #dde78f
> volume #21.1 color #d6e786
> volume #21.1 color #ff9300
> volume #21.2 color #ff2600
> open /Users/maryamfeghhi/Desktop/maps/foragers2024/myofilin-foragers.mrc
Opened myofilin-foragers.mrc as #22, grid size 171,171,549, pixel
0.927,0.927,0.927, shown at level 0.000237, step 1, values float32
> volume #22 color #fffb00
> open /Users/maryamfeghhi/Desktop/maps/fo-paro-core_48130.mrc
Opened fo-paro-core_48130.mrc as #23, grid size 113,122,677, pixel
0.927,0.927,0.927, shown at level 0.39, step 1, values float32
> volume #23 color #ff2f92
> volume #23 color #ff8ad8
> volume #23 level 0.05106
> volume #23 level 0.2579
> volume #23 level 0.3003
> volume #23 level 0.2791
> volume #23 level 0.2685
> open /Users/maryamfeghhi/Desktop/maps/Newly-emerged/fli-newlyemerged.mrc
> "/Users/maryamfeghhi/Desktop/maps/Newly-emerged/Myofilin-Newly emerged.mrc"
> "/Users/maryamfeghhi/Desktop/maps/Newly-emerged/Blue protein-Newly
> emerged.mrc"
Opened fli-newlyemerged.mrc as #24.1, grid size 180,176,539, pixel
0.927,0.927,0.927, shown at level 0.000139, step 2, values float32
Opened Myofilin-Newly emerged.mrc as #24.2, grid size 171,171,526, pixel
0.927,0.927,0.927, shown at level 0.000254, step 1, values float32
Opened Blue protein-Newly emerged.mrc as #24.3, grid size 171,173,512, pixel
0.927,0.927,0.927, shown at level 0.000208, step 1, values float32
> volume #24.2 color #fffb00
> volume #24.3 color #ff9300
> volume #24.1 color #ff2600
> open /Users/maryamfeghhi/Desktop/maps/Newly-emerged/NE-Para-ap18.mrc
Opened NE-Para-ap18.mrc as #25, grid size 77,79,445, pixel 1.46,1.46,1.46,
shown at level 0.467, step 1, values float32
> volume #25 color #ff8ad8
> volume #25 level 0.309
> open "/Users/maryamfeghhi/Desktop/maps/segmentation-Eclosed/green
> protein.mrc" /Users/maryamfeghhi/Desktop/maps/segmentation-
> Eclosed/myofilin.mrc /Users/maryamfeghhi/Desktop/maps/segmentation-
> Eclosed/FLIGHTIN-eclosed.mrc
Opened green protein.mrc as #26.1, grid size 169,169,511, pixel
0.927,0.927,0.927, shown at level 7.76e-05, step 1, values float32
Opened myofilin.mrc as #26.2, grid size 163,163,552, pixel 0.927,0.927,0.927,
shown at level 9.65e-05, step 1, values float32
Opened FLIGHTIN-eclosed.mrc as #26.3, grid size 197,197,555, pixel
0.927,0.927,0.927, shown at level 6.86e-05, step 2, values float32
> volume #26.3 color #ff2600
> volume #26.3 step 1
> volume #26.2 color #fffb00
> volume #26.1 color #ff9300
> ui tool show "Side View"
> view orient
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> volume #26.1 color #fffb00
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> volume #25 level 0.305
> surface dust #24.1 size 9.27
> surface dust #24.2 size 9.27
> surface dust #24.3 size 9.27
> surface dust #25 size 14.6
> surface dust #24.1 size 9.27
> surface dust #24.2 size 9.27
> surface dust #24.3 size 9.27
> surface dust #25 size 14.6
> save /Users/maryamfeghhi/Desktop/image34.png supersample 3
> volume #24.3 color #fffb00
> save /Users/maryamfeghhi/Desktop/image35.png supersample 3
> view orient
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> volume #21.1 color #fffb00
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> volume #21.1 color #ff9300
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> volume #26.1 color #ff9300
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> volume #24.3 color #ff9300
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> volume #24.3 color #fffc79
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> volume #24.3 color #ff9300
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> volume #24.3 color #fffc79
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> ui tool show "Side View"
> view matrix models
> #16,0.99988,0.015169,-0.00054031,5.6132,-0.01517,0.99988,-0.00072588,-3.7893,0.00052924,0.00073399,1,-114.66
> view matrix models
> #16,0.99988,0.015169,-0.00054031,9.7293,-0.01517,0.99988,-0.00072588,-24.122,0.00052924,0.00073399,1,-31.1
> view matrix models
> #16,0.99988,0.015169,-0.00054031,-15.709,-0.01517,0.99988,-0.00072588,-20.156,0.00052924,0.00073399,1,-33.377
> view matrix models
> #16,0.99988,0.015169,-0.00054031,-1.4899,-0.01517,0.99988,-0.00072588,-8.2108,0.00052924,0.00073399,1,-32.166
> volume #16 level 0.02919
> surface dust #16 size 9.27
> surface dust #20 size 9.27
> fitmap #16 inMap #20
Fit map Heads-N-Eclosed_122017.mrc gaussian in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 1151436 points
correlation = 0.8242, correlation about mean = 0.536, overlap = 6264
steps = 120, shift = 10.9, angle = 3.93 degrees
Position of Heads-N-Eclosed_122017.mrc gaussian (#16) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
0.99430954 0.10639839 -0.00528353 -17.82560249
-0.10637680 0.99431697 0.00421301 56.93578358
0.00570176 -0.00362699 0.99997717 18.36870871
Axis -0.03677250 -0.05152511 -0.99799446
Axis point 514.44388046 202.17321203 0.00000000
Rotation angle (degrees) 6.11943729
Shift along axis -20.61000026
> volume #16 level 0.003239
> ui mousemode right "map eraser"
> volume erase #16 center 188.72,251.75,229.64 radius 54.946
> transparency #16.1 70
> select clear
> volume #16 level 0.02688
> close #16
> volume erase #15 center 418.36,312.24,127.35 radius 215.82
Opened Heads-N-Eclosed_122017.mrc copy as #16, grid size 407,410,669, pixel
0.927,0.927,0.927, shown at step 1, values float32
> volume erase #16 center 221.59,379.31,126.13 radius 215.82
> volume erase #16 center 426.74,378.76,127.3 radius 215.82
> volume erase #16 center 306.3,394.69,114.27 radius 215.82
> volume erase #16 center 393.2,396.29,643.1 radius 215.82
> volume erase #16 center 339.61,320.18,634.49 radius 215.82
> volume erase #16 center 591.74,341.19,610.77 radius 215.82
> surface dust #16 size 9.27
> volume #16 level 0.02883
> volume #16 level 0.008421
> ui mousemode right "move picked models"
> view matrix models
> #20,0.98727,-0.15908,0.00030072,53.104,0.15908,0.98727,-0.00062974,-54.842,-0.00019671,0.00066956,1,2.8478
> view matrix models
> #20,0.98727,-0.15908,0.00030072,66.834,0.15908,0.98727,-0.00062974,-59.929,-0.00019671,0.00066956,1,-2.8608
> view matrix models
> #20,0.98727,-0.15908,0.00030072,64.322,0.15908,0.98727,-0.00062974,-55.264,-0.00019671,0.00066956,1,3.8421
> fitmap #16 inMap #20
Fit map Heads-N-Eclosed_122017.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 1049597 points
correlation = 0.8119, correlation about mean = 0.5015, overlap = 6537
steps = 104, shift = 6.52, angle = 3.6 degrees
Position of Heads-N-Eclosed_122017.mrc copy (#16) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
0.99526387 0.09709811 -0.00466773 -14.96598582
-0.09708029 0.99526889 0.00390586 53.38595797
0.00502489 -0.00343421 0.99998148 18.39958845
Axis -0.03772678 -0.04981849 -0.99804549
Axis point 530.25748040 187.94590011 0.00000000
Rotation angle (degrees) 5.58252378
Shift along axis -20.45861545
> fitmap #16 inMap #20
Fit map Heads-N-Eclosed_122017.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 1049597 points
correlation = 0.8118, correlation about mean = 0.5015, overlap = 6537
steps = 48, shift = 0.0197, angle = 0.00528 degrees
Position of Heads-N-Eclosed_122017.mrc copy (#16) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
0.99526395 0.09709634 -0.00468795 -14.95649900
-0.09707799 0.99526876 0.00399576 53.34803889
0.00505374 -0.00352174 0.99998103 18.43964469
Axis -0.03863768 -0.05006936 -0.99799809
Axis point 529.80266203 188.03580495 0.00000000
Rotation angle (degrees) 5.58267236
Shift along axis -20.49594761
> volume #16 level 0.005341
> view matrix models
> #19,0.99987,0.015976,0.00034653,56.861,-0.015976,0.99987,-0.00064007,22.104,-0.00035672,0.00063446,1,50.537
> view matrix models
> #19,0.99987,0.015976,0.00034653,4.3626,-0.015976,0.99987,-0.00064007,25.644,-0.00035672,0.00063446,1,46.01
> view matrix models
> #19,0.99987,0.015976,0.00034653,5.6772,-0.015976,0.99987,-0.00064007,26.862,-0.00035672,0.00063446,1,20.689
> view matrix models
> #16,0.99803,-0.06247,-0.0049632,45.003,0.062483,0.99804,0.0025694,-0.49902,0.004793,-0.0028744,0.99998,23.44
> view matrix models
> #19,0.99987,0.015976,0.00034653,12.88,-0.015976,0.99987,-0.00064007,23.952,-0.00035672,0.00063446,1,20.77
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc copy in map Heads.mrc copy using 1049597
points
correlation = 0.9368, correlation about mean = 0.896, overlap = 1.635e+04
steps = 112, shift = 5.28, angle = 4.51 degrees
Position of Heads-N-Eclosed_122017.mrc copy (#16) relative to Heads.mrc copy
(#19) coordinates:
Matrix rotation and translation
0.99999980 0.00003362 -0.00063838 0.19765502
-0.00003367 1.00000000 -0.00007586 -0.01758953
0.00063838 0.00007588 0.99999979 -0.23100167
Axis 0.11785131 -0.99165498 -0.05226343
Axis point 357.63009158 0.00000000 299.75523026
Rotation angle (degrees) 0.03688431
Shift along axis 0.05280959
> volume #16 level 0.0577
> volume #16 level 0.07541
> volume #16 level 0.02459
> volume #16 level 0.006111
> ui tool show "Map Filter"
> volume gaussian #16 sDev 1.2
Opened Heads-N-Eclosed_122017.mrc copy gaussian as #17, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> surface dust #19 size 9.27
> surface dust #17 size 9.27
> volume gaussian #16 sDev 1.5 modelId #17
Opened Heads-N-Eclosed_122017.mrc copy gaussian as #17, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> volume gaussian #16 sDev 2 modelId #17
Opened Heads-N-Eclosed_122017.mrc copy gaussian as #17, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> volume #17 level 0.07482
> volume #19 level 0.00258
> volume #19 orthoplanes xyz positionPlanes 180,180,330 style image region all
> mousemode rightMode "move planes"
> volume #17 orthoplanes xyz positionPlanes 203,205,334 style image region all
> mousemode rightMode "move planes"
> volume #!17,19 region all imageMode "full region"
> volume unzone #!17,19
> mousemode rightMode "crop volume"
> volume #!17,19 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
> volume #!17,19 style surface
> volume #!17,19 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #19 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 359.2 tiltedSlabSpacing 0.927 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #17 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 360.1 tiltedSlabSpacing 0.927 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #19 orthoplanes xyz positionPlanes 180,180,330 style image region all
> mousemode rightMode "move planes"
> volume #17 orthoplanes xyz positionPlanes 203,205,334 style image region all
> mousemode rightMode "move planes"
> volume #!17,19 region all imageMode "full region"
> volume unzone #!17,19
> mousemode rightMode "crop volume"
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
> volume #17 style surface
> volume #!17,19 showOutlineBox false
> volume #19 style surface
> volume #17 change image level -9.516e-17,0 level 0.03517,0.8 level 0.3168,1
> select clear
> ui tool show "Color Actions"
> color sel deep sky blue
> select clear
> transparency sel 50
> select clear
> select #19
3 models selected
> select clear
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> view
> ui tool show "Side View"
> save /Users/maryamfeghhi/Desktop/image32.png supersample 3
> select clear
> transparency #19.1 70
> select clear
> save /Users/maryamfeghhi/Desktop/image33.png supersample 3
> volume #17 color #97f0fa
> volume #17 color #96c9f9
> volume #17 color #a9d9ff
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> transparency #17.1 40
> select clear
> transparency #19.1 30
> select clear
> transparency #19.1 50
> select clear
> select #19
3 models selected
> transparency #19.1 30
> select clear
> save /Users/maryamfeghhi/Desktop/image34.png supersample 3
> transparency #17.1 30
> select clear
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting simple
> volume sel style mesh
> select clear
> volume sel style surface
> select clear
> save /Users/maryamfeghhi/Desktop/image35.png supersample 3
> save /Users/maryamfeghhi/Desktop/image36.png supersample 3
> volume #19 color #78e0deb3
> volume #20 color #aa8de0
> volume #20 color #37a0e0
> volume #20 color #4ad4e0
> volume #20 color #49d5e0
> volume #20 color #81aecb
> volume #19 color #2239e3b3
> volume #20 level 0.05715
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 426820 points
correlation = 0.8778, correlation about mean = 0.3807, overlap = 4971
steps = 80, shift = 3.94, angle = 0.495 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98305128 -0.18333079 0.00001985 57.20017727
0.18333079 0.98305128 0.00003201 -79.78230368
-0.00002538 -0.00002783 1.00000000 -20.49440953
Axis -0.00016319 0.00012336 0.99999998
Axis point 460.07907474 269.45325477 0.00000000
Rotation angle (degrees) 10.56382965
Shift along axis -20.51358608
> ui mousemode right "move picked models"
> view matrix models
> #20,0.98585,-0.1676,0.00036689,69.161,0.1676,0.98585,-0.00060839,-49.955,-0.00025974,0.00066127,1,-0.63613
> view matrix models
> #20,0.98585,-0.1676,0.00036689,147.99,0.1676,0.98585,-0.00060839,-29.977,-0.00025974,0.00066127,1,-42.197
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.97635,-0.21613,0.0060509,167.54,0.21621,0.97594,-0.028051,-34.138,0.00015733,0.028696,0.99959,-52.672
> view matrix models
> #20,-0.78636,-0.6168,-0.034532,990.96,-0.59757,0.77365,-0.21066,413.97,0.15665,-0.14502,-0.97695,695.4
> view matrix models
> #20,-0.77844,-0.60241,-0.17645,1035.9,-0.57797,0.79751,-0.17297,383.59,0.24492,-0.03266,-0.96899,617.46
> view matrix models
> #20,-0.80172,-0.59373,-0.068784,1000.9,-0.58063,0.80096,-0.14605,373.19,0.14181,-0.077151,-0.98688,679.32
> ui mousemode right "move picked models"
> view matrix models
> #20,-0.80172,-0.59373,-0.068784,985.86,-0.58063,0.80096,-0.14605,357.39,0.14181,-0.077151,-0.98688,735.97
> view matrix models
> #20,-0.80172,-0.59373,-0.068784,928,-0.58063,0.80096,-0.14605,344.52,0.14181,-0.077151,-0.98688,733.3
> view matrix models
> #20,-0.80172,-0.59373,-0.068784,921.78,-0.58063,0.80096,-0.14605,346.63,0.14181,-0.077151,-0.98688,723.68
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 426820 points
correlation = 0.7774, correlation about mean = 0.3464, overlap = 3461
steps = 396, shift = 3.52, angle = 21.7 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.54778639 -0.83661823 -0.00001576 873.15926290
-0.83661823 0.54778639 0.00002053 463.86375333
-0.00000855 0.00002443 -1.00000000 728.37138540
Axis 0.47543236 -0.87975227 0.00005739
Axis point 561.91852221 0.00000000 364.20183550
Rotation angle (degrees) 179.99976521
Shift along axis 7.08478180
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 426820 points
correlation = 0.7774, correlation about mean = 0.346, overlap = 3461
steps = 40, shift = 0.0154, angle = 0.00382 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.54773579 -0.83665136 0.00000461 873.15270462
-0.83665136 0.54773579 0.00000109 463.90218046
-0.00000344 -0.00000326 -1.00000000 728.36642207
Axis -0.47560023 0.87966153 0.00006223
Axis point 561.98461651 0.00000000 364.16567176
Rotation angle (degrees) 179.99973784
Shift along axis -7.14940292
> view matrix models
> #20,-0.56103,-0.82779,-0.00034191,924.61,-0.82779,0.56103,0.00064109,482.32,-0.00033887,0.0006427,-1,753.73
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.05752,-0.98272,0.17594,685.26,0.98363,0.025635,-0.17839,72.804,0.1708,0.18332,0.9681,-116.92
> view matrix models
> #20,0.079531,-0.9817,0.17304,677.75,0.98795,0.0545,-0.14488,47.831,0.1328,0.18248,0.9742,-104.7
> ui mousemode right "move picked models"
> view matrix models
> #20,0.079531,-0.9817,0.17304,634.35,0.98795,0.0545,-0.14488,37.382,0.1328,0.18248,0.9742,-110.57
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.075186,-0.97511,0.20858,676.36,0.97236,-0.11806,-0.20144,128.9,0.22106,0.18767,0.95703,-139.04
> ui mousemode right "move picked models"
> view matrix models
> #20,-0.075186,-0.97511,0.20858,700.14,0.97236,-0.11806,-0.20144,124.97,0.22106,0.18767,0.95703,-139.77
> view matrix models
> #20,-0.075186,-0.97511,0.20858,688.36,0.97236,-0.11806,-0.20144,131.76,0.22106,0.18767,0.95703,-153.91
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.11234,-0.93471,0.33718,638.9,0.99326,-0.095881,0.065119,15.643,-0.028539,0.34222,0.93919,-111.71
> view matrix models
> #20,0.089467,-0.97835,0.18663,636.3,0.99172,0.10484,0.074174,-62.164,-0.092134,0.17845,0.97963,-41.942
> ui mousemode right "move picked models"
> view matrix models
> #20,0.089467,-0.97835,0.18663,617.09,0.99172,0.10484,0.074174,-57.985,-0.092134,0.17845,0.97963,-16.375
> view matrix models
> #20,0.089467,-0.97835,0.18663,642.07,0.99172,0.10484,0.074174,-75.604,-0.092134,0.17845,0.97963,-12.143
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 426820 points
correlation = 0.8778, correlation about mean = 0.3807, overlap = 4971
steps = 292, shift = 18, angle = 19.2 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18334094 -0.98304939 0.00003576 791.69298790
0.98304939 -0.18334094 0.00003318 57.19508418
-0.00002606 0.00004124 1.00000000 -20.53451544
Axis 0.00000410 0.00003145 1.00000000
Axis point 372.08912800 357.44366267 0.00000000
Rotation angle (degrees) 100.56442092
Shift along axis -20.52947002
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 426820 points
correlation = 0.8777, correlation about mean = 0.3807, overlap = 4972
steps = 48, shift = 0.0264, angle = 0.00567 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18330712 -0.98305570 -0.00003682 791.71721181
0.98305570 -0.18330712 -0.00002451 57.21120489
0.00001735 -0.00004069 1.00000000 -20.49660112
Axis -0.00000823 -0.00002755 1.00000000
Axis point 372.09408866 357.47258292 0.00000000
Rotation angle (degrees) 100.56244987
Shift along axis -20.50469168
> volume #20 level 0.08545
> volume #19 level 0.08189
> volume #20 level 0.06231
> select clear
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8884, correlation about mean = 0.3395, overlap = 4702
steps = 48, shift = 0.0659, angle = 0.229 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18723960 -0.98231428 0.00003417 792.87570588
0.98231428 -0.18723960 0.00002424 58.93112635
-0.00001742 0.00003810 1.00000000 -20.57812639
Axis 0.00000705 0.00002626 1.00000000
Axis point 372.05808786 357.47597961 0.00000000
Rotation angle (degrees) 100.79173378
Shift along axis -20.57098557
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8885, correlation about mean = 0.3395, overlap = 4702
steps = 40, shift = 0.00642, angle = 0.00246 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18728150 -0.98230629 0.00003035 792.89216410
0.98230629 -0.18728150 0.00002117 58.95364690
-0.00001512 0.00003378 1.00000000 -20.58268101
Axis 0.00000642 0.00002314 1.00000000
Axis point 372.05807937 357.47976565 0.00000000
Rotation angle (degrees) 100.79417812
Shift along axis -20.57623007
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8884, correlation about mean = 0.3395, overlap = 4702
steps = 60, shift = 0.00439, angle = 0.00447 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18724810 -0.98231266 -0.00002749 792.90617031
0.98231266 -0.18724810 -0.00001858 58.95636388
0.00001310 -0.00003048 1.00000000 -20.56672082
Axis -0.00000606 -0.00002066 1.00000000
Axis point 372.06335864 357.49771770 0.00000000
Rotation angle (degrees) 100.79222955
Shift along axis -20.57274326
Correlation = 0.8884, Correlation about mean = 0.3395, Overlap = 4702
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8884, correlation about mean = 0.3395, overlap = 4702
steps = 60, shift = 0.00661, angle = 0.0038 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18724858 -0.98231256 0.00002735 792.88133182
0.98231256 -0.18724858 0.00001885 58.93763792
-0.00001340 0.00003039 1.00000000 -20.57951334
Axis 0.00000588 0.00002074 1.00000000
Axis point 372.05846877 357.47844288 0.00000000
Rotation angle (degrees) 100.79225765
Shift along axis -20.57363257
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8884, correlation about mean = 0.3395, overlap = 4702
steps = 60, shift = 0.00663, angle = 0.00381 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18724816 -0.98231264 -0.00002736 792.90613543
0.98231264 -0.18724816 -0.00001903 58.95658845
0.00001357 -0.00003044 1.00000000 -20.56685085
Axis -0.00000581 -0.00002083 1.00000000
Axis point 372.06325381 357.49779576 0.00000000
Rotation angle (degrees) 100.79223301
Shift along axis -20.57268493
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8884, correlation about mean = 0.3395, overlap = 4702
steps = 60, shift = 0.00666, angle = 0.00385 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18724718 -0.98231283 0.00002752 792.88087025
0.98231283 -0.18724719 0.00001960 58.93667497
-0.00001410 0.00003070 1.00000000 -20.57935427
Axis 0.00000565 0.00002118 1.00000000
Axis point 372.05859506 357.47824674 0.00000000
Rotation angle (degrees) 100.79217639
Shift along axis -20.57362335
> fitmap #20 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 370550 points
correlation = 0.8884, correlation about mean = 0.3395, overlap = 4702
steps = 60, shift = 0.00673, angle = 0.00387 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
-0.18724668 -0.98231293 -0.00002752 792.90575051
0.98231293 -0.18724668 -0.00001951 58.95620695
0.00001401 -0.00003069 1.00000000 -20.56691964
Axis -0.00000569 -0.00002114 1.00000000
Axis point 372.06318571 357.49794521 0.00000000
Rotation angle (degrees) 100.79214695
Shift along axis -20.57267881
> volume #19 level 0
> volume #19 level 0.00231
> view matrix models
> #14,0.98548,-0.16982,0.00031683,112.49,0.16982,0.98548,-0.00065204,-99.228,-0.0002015,0.00069638,1,37.445
> view matrix models
> #14,0.98548,-0.16982,0.00031683,111.85,0.16982,0.98548,-0.00065204,-97.926,-0.0002015,0.00069638,1,37.33
> view matrix models
> #14,0.98548,-0.16982,0.00031683,78.314,0.16982,0.98548,-0.00065204,-45.071,-0.0002015,0.00069638,1,32.018
> view matrix models
> #14,0.98548,-0.16982,0.00031683,74.896,0.16982,0.98548,-0.00065204,-41.099,-0.0002015,0.00069638,1,7.2038
> view matrix models
> #14,0.98548,-0.16982,0.00031683,69.536,0.16982,0.98548,-0.00065204,-54.457,-0.0002015,0.00069638,1,10.4
> view matrix models
> #19,0.99987,0.015976,0.00034653,13.969,-0.015976,0.99987,-0.00064007,27.415,-0.00035672,0.00063446,1,31.325
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 305744 points
correlation = 0.8997, correlation about mean = 0.2897, overlap = 4541
steps = 64, shift = 1.45, angle = 0.00415 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98263104 -0.18557006 0.00003422 58.18589917
0.18557006 0.98263104 0.00000570 -80.45292715
-0.00003468 0.00000075 1.00000000 -20.59750194
Axis -0.00001332 0.00018564 0.99999998
Axis point 458.85202278 270.60313880 0.00000000
Rotation angle (degrees) 10.69437002
Shift along axis -20.61321231
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 305744 points
correlation = 0.8997, correlation about mean = 0.2897, overlap = 4541
steps = 60, shift = 0.00612, angle = 0.00374 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98263414 -0.18555361 -0.00002744 58.20711541
0.18555361 0.98263414 -0.00000728 -80.44052310
0.00002831 0.00000206 1.00000000 -20.62004360
Axis 0.00002517 -0.00015023 0.99999999
Axis point 458.87250001 270.75149724 0.00000000
Rotation angle (degrees) 10.69341117
Shift along axis -20.60649357
> volume #13 level 0.03684
> volume #18 level 0.05294
> volume #14 color #4dafe0
> volume #14 color #99b9f3
> volume #14 color #81aecb
> volume #17 level 0.08356
> volume #14 level 0.07493
> volume #14 level 0.07102
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 313640 points
correlation = 0.8984, correlation about mean = 0.2962, overlap = 4600
steps = 60, shift = 0.00721, angle = 0.0123 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98267258 -0.18534996 0.00002818 58.08961452
0.18534996 0.98267258 0.00000823 -80.38742082
-0.00002922 -0.00000286 1.00000000 -20.59427696
Axis -0.00002991 0.00015483 0.99999999
Axis point 458.97608571 270.49438343 0.00000000
Rotation angle (degrees) 10.68153690
Shift along axis -20.60846043
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 313640 points
correlation = 0.8984, correlation about mean = 0.2962, overlap = 4600
steps = 60, shift = 0.00193, angle = 0.00094 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98267516 -0.18533626 0.00003009 58.08285264
0.18533626 0.98267516 0.00001666 -80.38760391
-0.00003265 -0.00001079 1.00000000 -20.58848984
Axis -0.00007406 0.00016926 0.99999998
Axis point 459.00398596 270.47678045 0.00000000
Rotation angle (degrees) 10.68073803
Shift along axis -20.60639777
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 313640 points
correlation = 0.8984, correlation about mean = 0.2963, overlap = 4600
steps = 60, shift = 0.00112, angle = 0.000585 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98267547 -0.18533462 0.00002707 58.08383949
0.18533462 0.98267547 0.00002627 -80.39167112
-0.00003147 -0.00002080 1.00000000 -20.58515142
Axis -0.00012699 0.00015791 0.99999998
Axis point 459.03081327 270.47687275 0.00000000
Rotation angle (degrees) 10.68064245
Shift along axis -20.60522206
> fitmap #14 inMap #19 metric cam
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 313640 points
correlation = 0.8892, correlation about mean = 0.3151, overlap = 4519
steps = 72, shift = 2.01, angle = 0.765 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98506064 -0.17220774 -0.00018454 52.29136732
0.17220779 0.98506061 0.00028493 -76.36435912
0.00013272 -0.00031246 0.99999994 -18.53141721
Axis -0.00173450 -0.00092114 0.99999807
Axis point 466.35890508 263.00841896 0.00000000
Rotation angle (degrees) 9.91622718
Shift along axis -18.55173844
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 313640 points
correlation = 0.8984, correlation about mean = 0.2962, overlap = 4600
steps = 60, shift = 2.01, angle = 0.767 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98266877 -0.18537016 0.00002515 58.09573209
0.18537016 0.98266877 0.00000305 -80.39128051
-0.00002528 0.00000166 1.00000000 -20.59693953
Axis -0.00000376 0.00013601 0.99999999
Axis point 458.95445519 270.49340690 0.00000000
Rotation angle (degrees) 10.68271459
Shift along axis -20.60809170
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 313640 points
correlation = 0.8985, correlation about mean = 0.2959, overlap = 4599
steps = 48, shift = 0.0231, angle = 0.00315 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98265914 -0.18542117 0.00004351 58.10933961
0.18542117 0.98265914 0.00000269 -80.40782067
-0.00004326 0.00000542 1.00000000 -20.61464165
Axis 0.00000737 0.00023397 0.99999997
Axis point 458.91863626 270.47315628 0.00000000
Rotation angle (degrees) 10.68568870
Shift along axis -20.63302585
Correlation = 0.8985, Correlation about mean = 0.2959, Overlap = 4599
> transparency #19.1 80
> transparency #19.1 70
> transparency #19.1 40
> select clear
> transparency #19.1 30
> transparency #19.1 60
> select #19
3 models selected
> select clear
> volume #14 level 0.07883
> volume #19 level 0.00229
> volume #19 level 0.00225
> volume #19 level 0.00223
> volume #19 level 0.00221
> volume #19 level 0.00219
> volume #19 level 0.00215
> volume #19 level 0.00216
> volume #19 level 0.00212
> volume #19 level 0.002
> view matrix models
> #19,0.99987,0.015976,0.00034653,11.756,-0.015976,0.99987,-0.00064007,20.312,-0.00035672,0.00063446,1,30.918
> view matrix models
> #19,0.99987,0.015976,0.00034653,17.682,-0.015976,0.99987,-0.00064007,17.224,-0.00035672,0.00063446,1,25.722
> view matrix models
> #19,0.99987,0.015976,0.00034653,26.458,-0.015976,0.99987,-0.00064007,10.444,-0.00035672,0.00063446,1,23.429
> view matrix models
> #14,0.9855,-0.1697,0.00039008,81.688,0.1697,0.9855,-0.00063808,-69.326,-0.00027614,0.00069502,1,10.199
> view matrix models
> #19,0.99987,0.015976,0.00034653,25.734,-0.015976,0.99987,-0.00064007,15.354,-0.00035672,0.00063446,1,33.369
> view matrix models
> #19,0.99987,0.015976,0.00034653,23.487,-0.015976,0.99987,-0.00064007,15.142,-0.00035672,0.00063446,1,33.387
> view matrix models
> #14,0.9855,-0.1697,0.00039008,82.27,0.1697,0.9855,-0.00063808,-42.287,-0.00027614,0.00069502,1,100.99
Drag select of 14 Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian ,
19 Heads.mrc copy
> view matrix models
> #14,0.9855,-0.1697,0.00039008,79.581,0.1697,0.9855,-0.00063808,-76.689,-0.00027614,0.00069502,1,95.621
> view matrix models
> #14,0.9855,-0.1697,0.00039008,72.53,0.1697,0.9855,-0.00063808,-78.602,-0.00027614,0.00069502,1,15.509
> view matrix models
> #14,0.9855,-0.1697,0.00039008,81.338,0.1697,0.9855,-0.00063808,-71.216,-0.00027614,0.00069502,1,22.809
> fitmap #14 inMap #19
Fit map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian in
map Heads.mrc copy using 254582 points
correlation = 0.9076, correlation about mean = 0.2482, overlap = 4114
steps = 120, shift = 11.3, angle = 0.0985 degrees
Position of Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) relative to Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.98233904 -0.18710962 0.00001565 58.87870721
0.18710962 0.98233904 0.00002967 -80.93007112
-0.00002093 -0.00002622 1.00000000 -20.59462567
Axis -0.00014934 0.00009776 0.99999998
Axis point 458.13528698 271.41586256 0.00000000
Rotation angle (degrees) 10.78415315
Shift along axis -20.61133000
> volume #19 level 0.0019
> volume #19 level 0.0017
> volume #19 level 0.0015
> volume #19 level 0.001
> volume #19 level 0.0009
> volume #19 level 0.0008
> volume #19 level 0.000415
> transparency #19.1 40
> select clear
> transparency #19.1 60
> select clear
> transparency #14.1 50
> select clear
> select #14
2 models selected
> transparency #14.1 30
> select clear
> transparency #19.1 70
> select clear
> volume #14 level 0.09
> select #19
3 models selected
> select clear
> transparency sel 0
> transparency sel 50
> select clear
> transparency #14.1 60
> select clear
> surface style #14 dot
> select clear
> select #14
2 models selected
> select clear
> volume sel style mesh
> select clear
> select #14
2 models selected
> surface style #14 solid
> select clear
> volume #19 level 3.001e-05
> volume #20 level 0.06391
> volume #14 level 0.09527
> volume #14 level 0.09625
> surface dust #14 size 9.27
> surface dust #19 size 9.27
> volume #14 level 0.1011
> volume #16 level 0.07375
> volume #16 level 0.08006
> fitmap #16 inMap #19
Fit map Heads-N-Eclosed_122017.mrc copy in map Heads.mrc copy using 939468
points
correlation = 0.9515, correlation about mean = 0.8836, overlap = 1.629e+04
steps = 132, shift = 18.7, angle = 0.00577 degrees
Position of Heads-N-Eclosed_122017.mrc copy (#16) relative to Heads.mrc copy
(#19) coordinates:
Matrix rotation and translation
0.99999985 0.00001687 -0.00053948 0.17146965
-0.00001691 1.00000000 -0.00006613 -0.01847170
0.00053948 0.00006614 0.99999985 -0.20717714
Axis 0.12161938 -0.99209086 -0.03105554
Axis point 381.48710106 0.00000000 307.45377656
Rotation angle (degrees) 0.03115658
Shift along axis 0.04561364
> select #16
2 models selected
> transparency sel 0
> select clear
> transparency sel 50
> select clear
> fitmap #17 inMap #19
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads.mrc copy using
688329 points
correlation = 0.9934, correlation about mean = 0.9213, overlap = 1.481e+04
steps = 136, shift = 18.7, angle = 0.0428 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to
Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.99999972 -0.00065629 -0.00036692 0.35336057
0.00065629 0.99999978 0.00001616 -0.26907609
0.00036691 -0.00001640 0.99999993 -0.10739553
Axis -0.02164276 -0.48787539 0.87264494
Axis point 387.93604954 539.24233252 0.00000000
Rotation angle (degrees) 0.04309050
Shift along axis 0.02990974
> select clear
> volume #17 level 0.09988
> volume #17 level 0.1029
> save /Users/maryamfeghhi/Desktop/image37.png supersample 3
> save /Users/maryamfeghhi/Desktop/image38.png supersample 3
> volume #17 level 0.09039
> volume #17 level 0.09077
> save /Users/maryamfeghhi/Desktop/image39.png supersample 3
> surface style #19 solid
> select #19
3 models selected
> save /Users/maryamfeghhi/Desktop/image40.png supersample 3
No visible atoms, bonds, or surfaces selected
> select #19
3 models selected
> graphics silhouettes false
> graphics silhouettes true
> select clear
> transparency #19.1 70
> select clear
> save /Users/maryamfeghhi/Desktop/image41.png supersample 3
> volume #14 level 0.09648
> fitmap #17 inMap #14
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 632541 points
correlation = 0.8533, correlation about mean = 0.4901, overlap = 5686
steps = 108, shift = 2.21, angle = 4.55 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99410972 0.10821322 -0.00598013 -18.25911079
-0.10818715 0.99412025 0.00452436 57.54491146
0.00643456 -0.00385074 0.99997188 18.44778601
Axis -0.03860952 -0.05723220 -0.99761404
Axis point 509.71120126 203.96723191 0.00000000
Rotation angle (degrees) 6.22648941
Shift along axis -20.99221696
> fitmap #17 inMap #14
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 632541 points
correlation = 0.8533, correlation about mean = 0.49, overlap = 5686
steps = 48, shift = 0.0239, angle = 0.0052 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99410729 0.10823301 -0.00602658 -18.24272483
-0.10820627 0.99411782 0.00459991 57.52010362
0.00648899 -0.00392069 0.99997126 18.47627315
Axis -0.03927121 -0.05768391 -0.99756220
Axis point 509.28119412 203.90967151 0.00000000
Rotation angle (degrees) 6.22793787
Shift along axis -21.03280207
> fitmap #17 inMap #14
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 632541 points
correlation = 0.8533, correlation about mean = 0.4901, overlap = 5686
steps = 48, shift = 0.0223, angle = 0.00573 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#14) coordinates:
Matrix rotation and translation
0.99411048 0.10820592 -0.00598589 -18.25307203
-0.10817990 0.99412109 0.00451255 57.54606088
0.00643898 -0.00383842 0.99997190 18.44310413
Axis -0.03850092 -0.05728307 -0.99761532
Axis point 509.75090004 203.90290066 0.00000000
Rotation angle (degrees) 6.22606102
Shift along axis -20.99277845
> save /Users/maryamfeghhi/Desktop/image42.png supersample 3
> save /Users/maryamfeghhi/Desktop/image43.png supersample 3
> fitmap #17 inMap #19
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads.mrc copy using
632541 points
correlation = 0.994, correlation about mean = 0.922, overlap = 1.433e+04
steps = 100, shift = 2.2, angle = 4.53 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to
Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.99999932 -0.00107239 -0.00046653 0.53478415
0.00107243 0.99999942 0.00010178 -0.44573181
0.00046642 -0.00010228 0.99999989 -0.12890228
Axis -0.08691605 -0.39736393 0.91353572
Axis point 411.12417677 499.46755859 0.00000000
Rotation angle (degrees) 0.06726023
Shift along axis 0.01287959
> save /Users/maryamfeghhi/Desktop/image44.png supersample 3
> volume #17 level 0.08229
> volume #17 level 0.07851
> volume #17 level 0.07726
> volume #16 color #a9d9ff
> volume #16 level 0.07633
> ui tool show "Map Filter"
> volume gaussian #16 sDev 0.46
Opened Heads-N-Eclosed_122017.mrc copy gaussian as #27, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> volume gaussian #16 sDev 1.2 modelId #27
Opened Heads-N-Eclosed_122017.mrc copy gaussian as #27, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> surface dust #27 size 9.27
> volume #27 level 0.04875
> volume gaussian #16 sDev 0.8 modelId #27
Opened Heads-N-Eclosed_122017.mrc copy gaussian as #27, grid size 407,410,669,
pixel 0.927,0.927,0.927, shown at step 1, values float32
> volume #27 level 0.04005
> volume #27 level 0.01136
> view matrix models
> #27,0.99987,0.015993,-0.00019394,26.924,-0.015993,0.99987,-0.00069758,16.243,0.00018276,0.00070059,1,33.573
> transparency #17.1 50
> volume #17 level 0.07474
> select #17
3 models selected
> select clear
> save /Users/maryamfeghhi/Desktop/image45.png supersample 3
> volume #20 level 0.05527
> transparency #20.1 40
> select clear
> select #20
2 models selected
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> volume #20 color #7f94d299
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> volume #20 level 0.03558
> select clear
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> volume sel style mesh
> select clear
> volume #!20 style surface
> volume #!20 style mesh
> graphics silhouettes true
> save /Users/maryamfeghhi/Desktop/image46.png supersample 3
> volume #20 color #9fb0d6
> save /Users/maryamfeghhi/Desktop/image47.png supersample 3
> volume #20 level 0.04199
> save /Users/maryamfeghhi/Desktop/image48.png supersample 3
> ui tool show "Fit in Map"
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4203, overlap = 6194
steps = 164, shift = 19.7, angle = 3.85 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12085871 0.99266972 0.00003721 63.22790230
-0.99266972 -0.12085871 0.00000947 769.95656726
0.00001390 -0.00003580 1.00000000 19.12960557
Axis -0.00002280 0.00001174 -1.00000000
Axis point 372.56339369 356.98022331 0.00000000
Rotation angle (degrees) 96.94166370
Shift along axis -19.12200571
> volume #20 level 0.04609
> save /Users/maryamfeghhi/Desktop/image49.png supersample 3
> select clear
> transparency #19.1 70
> select clear
> transparency #19.1 90
> select clear
> save /Users/maryamfeghhi/Desktop/image50.png supersample 3
> surface style #19 solid
> select clear
> transparency #19.1 20
> select #19
3 models selected
> transparency #19.1 50
> select clear
> save /Users/maryamfeghhi/Desktop/image51.png supersample 3
> save /Users/maryamfeghhi/Desktop/image52.png supersample 3
> surface style #20 solid
> select clear
> lighting full
> lighting soft
> select clear
> save /Users/maryamfeghhi/Desktop/image53.png supersample 3
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4203, overlap = 6194
steps = 48, shift = 0.00732, angle = 0.00234 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12082801 0.99267345 0.00006123 63.20772065
-0.99267345 -0.12082801 0.00002132 769.94271320
0.00002857 -0.00005821 1.00000000 19.12507033
Axis -0.00004006 0.00001645 -1.00000000
Axis point 372.55766468 356.98155211 0.00000000
Rotation angle (degrees) 96.93989185
Shift along axis -19.11493378
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4203, overlap = 6194
steps = 48, shift = 0.023, angle = 0.00161 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12085258 0.99267046 0.00004897 63.22203361
-0.99267046 -0.12085258 0.00001645 769.95228870
0.00002225 -0.00004662 1.00000000 19.14620836
Axis -0.00003177 0.00001346 -1.00000000
Axis point 372.56061429 356.98060129 0.00000000
Rotation angle (degrees) 96.94130990
Shift along axis -19.13785434
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4203, overlap = 6194
steps = 48, shift = 0.0198, angle = 0.00158 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12087989 0.99266714 0.00005031 63.23113011
-0.99266714 -0.12087989 0.00001568 769.96045569
0.00002164 -0.00004804 1.00000000 19.12717224
Axis -0.00003210 0.00001444 -1.00000000
Axis point 372.55933368 356.98144453 0.00000000
Rotation angle (degrees) 96.94288643
Shift along axis -19.11808585
> volume #19 level 0.001155
> volume #20 level 0.04644
> surface style #19 solid
> select clear
> surface style #19 solid
> select clear
> select #20
2 models selected
> surface style #20 solid
> select clear
> volume #20 level 0.04769
> surface style #19 solid
> select clear
> surface style #19 solid
> select clear
> surface style #20 solid
> select clear
> select #19
3 models selected
> volume #20 level 0.05214
> surface style #20 solid
> select clear
> save /Users/maryamfeghhi/Desktop/image54.png supersample 3
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4202, overlap = 6194
steps = 48, shift = 0.0287, angle = 0.00184 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12091022 0.99266344 0.00004048 63.24264226
-0.99266344 -0.12091022 0.00001318 769.96845308
0.00001798 -0.00003859 1.00000000 19.15338977
Axis -0.00002608 0.00001134 -1.00000000
Axis point 372.55816731 356.98112744 0.00000000
Rotation angle (degrees) 96.94463716
Shift along axis -19.14631033
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4203, overlap = 6194
steps = 48, shift = 0.0342, angle = 0.00629 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12084586 0.99267128 -0.00004238 63.26670204
-0.99267128 -0.12084586 -0.00001825 769.97406729
-0.00002324 0.00003986 1.00000000 19.11665629
Axis 0.00002927 -0.00000964 -1.00000000
Axis point 372.59530540 356.97078146 0.00000000
Rotation angle (degrees) 96.94092211
Shift along axis -19.12222713
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4202, overlap = 6194
steps = 52, shift = 0.0221, angle = 0.00232 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12088547 0.99266646 -0.00003532 63.27023423
-0.99266646 -0.12088547 -0.00001724 769.97813273
-0.00002138 0.00003297 1.00000000 19.13660594
Axis 0.00002529 -0.00000702 -1.00000000
Axis point 372.58515134 356.97243468 0.00000000
Rotation angle (degrees) 96.94320823
Shift along axis -19.14040956
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4203, overlap = 6194
steps = 64, shift = 0.0177, angle = 0.000357 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12088003 0.99266712 -0.00003234 63.26638038
-0.99266712 -0.12088003 -0.00001698 769.97596996
-0.00002076 0.00003005 1.00000000 19.11972866
Axis 0.00002369 -0.00000583 -1.00000000
Axis point 372.58414159 356.97293052 0.00000000
Rotation angle (degrees) 96.94289456
Shift along axis -19.12271988
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.4199, overlap = 6153
steps = 68, shift = 0.743, angle = 2.14 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08365599 0.99649469 0.00000219 48.63875612
-0.99649469 -0.08365599 0.00001205 758.07449621
0.00001219 -0.00000117 1.00000000 18.37628523
Axis -0.00000664 -0.00000502 -1.00000000
Axis point 372.86956171 356.67395145 0.00000000
Rotation angle (degrees) 94.79874353
Shift along axis -18.38041156
> fitmap #19 inMap #20
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8257, correlation about mean = 0.4202, overlap = 6194
steps = 68, shift = 0.761, angle = 2.15 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.12090858 0.99266364 -0.00002875 63.27816541
-0.99266364 -0.12090858 -0.00001716 769.98642803
-0.00002051 0.00002646 1.00000000 19.13947456
Axis 0.00002197 -0.00000415 -1.00000000
Axis point 372.58478376 356.97378331 0.00000000
Rotation angle (degrees) 96.94454256
Shift along axis -19.14128063
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.4199, overlap = 6152
steps = 76, shift = 0.778, angle = 2.15 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08365076 0.99649513 -0.00000422 48.63906419
-0.99649513 -0.08365076 -0.00004499 758.09821129
-0.00004519 0.00000044 1.00000000 18.37995374
Axis 0.00002280 0.00002056 -1.00000000
Axis point 372.88294234 356.68553600 0.00000000
Rotation angle (degrees) 94.79844276
Shift along axis -18.36326032
Correlation = 0.8294, Correlation about mean = 0.4199, Overlap = 6152
> fitmap #19 inMap #20 metric cam
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8281, correlation about mean = 0.4231, overlap = 6182
steps = 64, shift = 0.0143, angle = 1.31 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.10635482 0.99432824 0.00000190 57.48997417
-0.99432824 -0.10635482 0.00004325 765.37234599
0.00004321 0.00000272 1.00000000 18.36110045
Axis -0.00002038 -0.00002077 -1.00000000
Axis point 372.68100655 356.85180528 0.00000000
Rotation angle (degrees) 96.10522914
Shift along axis -18.37817262
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.4199, overlap = 6153
steps = 76, shift = 0.00714, angle = 1.31 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08365916 0.99649443 -0.00000237 48.64168238
-0.99649442 -0.08365916 -0.00003825 758.09571834
-0.00003832 -0.00000084 1.00000000 18.38455874
Axis 0.00001877 0.00001804 -1.00000000
Axis point 372.88009742 356.68328578 0.00000000
Rotation angle (degrees) 94.79892591
Shift along axis -18.36997114
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.4199, overlap = 6153
steps = 60, shift = 0.0126, angle = 0.00445 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08367200 0.99649335 0.00000469 48.64412199
-0.99649335 -0.08367200 0.00003801 758.07048902
0.00003827 -0.00000150 1.00000000 18.36997538
Axis -0.00001982 -0.00001685 -1.00000000
Axis point 372.86455978 356.66984428 0.00000000
Rotation angle (degrees) 94.79966438
Shift along axis -18.38370955
Correlation = 0.8294, Correlation about mean = 0.4199, Overlap = 6153
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.4199, overlap = 6153
steps = 60, shift = 0.0159, angle = 0.00453 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08365602 0.99649469 -0.00000385 48.64106748
-0.99649469 -0.08365602 -0.00003888 758.09604055
-0.00003906 0.00000058 1.00000000 18.38124056
Axis 0.00001980 0.00001767 -1.00000000
Axis point 372.88104799 356.68364672 0.00000000
Rotation angle (degrees) 94.79874513
Shift along axis -18.36688366
> lighting soft
> select clear
> volume #19 level 0.00616
> select clear
> select #19
3 models selected
> surface style #19 solid
> select clear
> ui mousemode right "move picked models"
> view matrix models
> #19,0.99608,-0.088512,0.00035766,48.247,0.088512,0.99607,-0.00065626,-16.265,-0.00029817,0.00068535,1,18.041
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,804.15,0.98518,-0.17153,-0.00065914,70.63,0.00070404,0.00020092,1,0.081205
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.42, overlap = 6153
steps = 68, shift = 4.86, angle = 0.00539 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08370741 0.99649037 -0.00007465 48.68882393
-0.99649037 -0.08370741 -0.00000432 758.09875726
-0.00001055 0.00007403 0.99999999 18.36789154
Axis 0.00003931 -0.00003216 -1.00000000
Axis point 372.88789449 356.66358306 0.00000000
Rotation angle (degrees) 94.80170003
Shift along axis -18.39035894
> volume #27 level 0.04806
> volume #27 level 0.08725
> surface dust #19 size 9.27
> surface dust #20 size 9.27
> surface dust #27 size 9.27
> volume #27 level 0.07407
> view matrix models
> #27,0.99987,0.015993,-0.00019394,8.5798,-0.015993,0.99987,-0.00069758,26.524,0.00018276,0.00070059,1,29.786
> view matrix models
> #27,0.99987,0.015993,-0.00019394,10.828,-0.015993,0.99987,-0.00069758,31.144,0.00018276,0.00070059,1,18.055
> view matrix models
> #27,0.99987,0.015993,-0.00019394,9.5226,-0.015993,0.99987,-0.00069758,25.844,0.00018276,0.00070059,1,17.08
> volume #17 level 0.01871
> view matrix models
> #19,0.99608,-0.08846,0.00033576,289.44,0.088461,0.99608,-0.00073194,-192.11,-0.0002697,0.00075877,1,-0.38886
> view matrix models
> #17,0.99989,0.014904,-0.0001183,23.681,-0.014904,0.99989,-0.00053085,14.336,0.00011038,0.00053256,1,33.296
> view matrix models
> #17,0.99989,0.014904,-0.0001183,348.96,-0.014904,0.99989,-0.00053085,193.7,0.00011038,0.00053256,1,9.3931
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,811.72,0.98518,-0.17153,-0.00065914,129.68,0.00070404,0.00020092,1,-4.8347
> view matrix models
> #17,0.99989,0.014904,-0.0001183,353.37,-0.014904,0.99989,-0.00053085,204.7,0.00011038,0.00053256,1,9.0178
> select #19
3 models selected
> volume #19 level 0.00154
> select clear
> volume #20 level 0.03238
> select clear
> surface style #20 solid
> select clear
> select #20
2 models selected
> select clear
> select #17
3 models selected
> volume sel style surface
> graphics silhouettes false
> lighting simple
> lighting soft
> select clear
> volume #17 color #54cbfc80
> select clear
> view matrix models
> #19,0.99608,-0.08846,0.00033576,685.36,0.088461,0.99608,-0.00073194,-58.372,-0.0002697,0.00075877,1,-78.591
> view matrix models
> #17,0.99989,0.014904,-0.0001183,354.02,-0.014904,0.99989,-0.00053085,-346.48,0.00011038,0.00053256,1,-20.608
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,877.14,0.98518,-0.17153,-0.00065914,7.393,0.00070404,0.00020092,1,-25.481
> view matrix models
> #19,0.99608,-0.08846,0.00033576,-85.58,0.088461,0.99608,-0.00073194,215.69,-0.0002697,0.00075877,1,102.28
> select #20
2 models selected
> transparency #20.1 10
> transparency #20.1 0
> select clear
Drag select of 20 Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,903.23,0.98518,-0.17153,-0.00065914,10.6,0.00070404,0.00020092,1,81.444
> view matrix models
> #17,0.99989,0.014904,-0.0001183,321.86,-0.014904,0.99989,-0.00053085,-304.98,0.00011038,0.00053256,1,-13.581
> view matrix models
> #19,0.99608,-0.08846,0.00033576,-55.72,0.088461,0.99608,-0.00073194,210.34,-0.0002697,0.00075877,1,99.445
> view matrix models
> #17,0.99989,0.014904,-0.0001183,329.45,-0.014904,0.99989,-0.00053085,-312.72,0.00011038,0.00053256,1,57.875
> view matrix models
> #17,0.99989,0.014904,-0.0001183,331.02,-0.014904,0.99989,-0.00053085,-313.89,0.00011038,0.00053256,1,83.594
> view matrix models
> #17,0.99989,0.014904,-0.0001183,322.24,-0.014904,0.99989,-0.00053085,-311.1,0.00011038,0.00053256,1,75.768
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.01223, correlation about mean = -0.01664, overlap = 1.26e-16
steps = 1128, shift = 57.2, angle = 11 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
0.10820906 0.99403694 -0.01346715 345.32864554
-0.99412815 0.10819796 -0.00155233 809.05185559
-0.00008596 0.01355605 0.99990811 10.04381911
Axis 0.00759877 -0.00673008 -0.99994848
Axis point 623.60115098 211.95938786 0.00000000
Rotation angle (degrees) 83.79088213
Shift along axis -12.86421148
> view matrix models
> #17,0.99989,0.014904,-0.0001183,321.68,-0.014904,0.99989,-0.00053085,-312.65,0.00011038,0.00053256,1,92.943
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,952.52,0.98518,-0.17153,-0.00065914,51.542,0.00070404,0.00020092,1,86.408
> view matrix models
> #19,0.96083,-0.2771,0.004158,92.698,0.27713,0.96074,-0.01366,199.97,-0.00020951,0.014278,0.9999,96.986
> view matrix models
> #17,0.99989,0.014904,-0.0001183,316.93,-0.014904,0.99989,-0.00053085,-294.13,0.00011038,0.00053256,1,91.528
> view matrix models
> #17,0.99989,0.014904,-0.0001183,330.47,-0.014904,0.99989,-0.00053085,-291.07,0.00011038,0.00053256,1,91.754
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1134.1,0.98518,-0.17153,-0.00065914,-230.86,0.00070404,0.00020092,1,111.5
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1123.5,0.98518,-0.17153,-0.00065914,-228.36,0.00070404,0.00020092,1,73.141
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1125.1,0.98518,-0.17153,-0.00065914,-247.18,0.00070404,0.00020092,1,76.777
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1122.1,0.98518,-0.17153,-0.00065914,-237.89,0.00070404,0.00020092,1,77.484
> fitmap #17 inMap #20 metric correlation
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 1376607 points
correlation = 0.8141, correlation about mean = 0.5642, overlap = 6344
steps = 136, shift = 8.88, angle = 5.24 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.09586854 0.99538712 0.00370149 52.73856430
-0.99537543 -0.09588880 0.00575165 761.37838371
0.00608005 -0.00313297 0.99997661 18.07356280
Axis -0.00446288 -0.00119478 -0.99998933
Axis point 372.10035845 356.76600055 0.00000000
Rotation angle (degrees) 95.50256816
Shift along axis -19.21841871
> view matrix models
> #19,0.96083,-0.2771,0.004158,235.78,0.27713,0.96074,-0.01366,-105.9,-0.00020951,0.014278,0.9999,162.69
> volume #17 level 0.002509
> view matrix models
> #19,0.96083,-0.2771,0.004158,448.71,0.27713,0.96074,-0.01366,-370.16,-0.00020951,0.014278,0.9999,144.53
> view matrix models
> #19,0.96083,-0.2771,0.004158,456.39,0.27713,0.96074,-0.01366,-367,-0.00020951,0.014278,0.9999,93.804
> view matrix models
> #17,0.99707,-0.076271,-0.0059826,367.75,0.076285,0.99708,0.0020009,-324.74,0.0058126,-0.0024514,0.99998,96.419
> view matrix models
> #19,0.96083,-0.2771,0.004158,437.34,0.27713,0.96074,-0.01366,-383.31,-0.00020951,0.014278,0.9999,99.637
> fitmap #17 inMap #19 metric correlation
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads.mrc copy using
2023118 points
correlation = 0.943, correlation about mean = 0.9296, overlap = 1.537e+04
steps = 196, shift = 14.4, angle = 11.8 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to
Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.99999977 -0.00063134 -0.00025683 0.29475716
0.00063130 0.99999979 -0.00013110 -0.26393067
0.00025691 0.00013094 0.99999996 -0.11919845
Axis 0.18876994 -0.37010347 0.90960944
Axis point 391.89999393 453.30894778 0.00000000
Rotation angle (degrees) 0.03976648
Shift along axis 0.04489891
> fitmap #17 inMap #19 metric correlation
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads.mrc copy using
2023118 points
correlation = 0.943, correlation about mean = 0.9296, overlap = 1.537e+04
steps = 40, shift = 0.0158, angle = 0.00585 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to
Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.99999982 -0.00053341 -0.00028263 0.26940306
0.00053337 0.99999985 -0.00014461 -0.22322003
0.00028271 0.00014446 0.99999995 -0.11736040
Axis 0.23285213 -0.45538588 0.85930413
Axis point 364.40220190 477.20005314 -0.00000000
Rotation angle (degrees) 0.03556470
Shift along axis 0.06353405
> select clear
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1118.5,0.98518,-0.17153,-0.00065914,-270.68,0.00070404,0.00020092,1,86.626
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1121.8,0.98518,-0.17153,-0.00065914,-262.29,0.00070404,0.00020092,1,99.598
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1111.8,0.98518,-0.17153,-0.00065914,-256.2,0.00070404,0.00020092,1,100.53
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1117.4,0.98518,-0.17153,-0.00065914,-260.59,0.00070404,0.00020092,1,90.587
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1110.8,0.98518,-0.17153,-0.00065914,-253.47,0.00070404,0.00020092,1,90.975
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1116,0.98518,-0.17153,-0.00065914,-259.87,0.00070404,0.00020092,1,91.362
> view matrix models
> #20,-0.17153,-0.98518,0.0003187,1112.1,0.98518,-0.17153,-0.00065914,-256.08,0.00070404,0.00020092,1,91.287
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.30843,-0.94921,-0.062175,1173.1,0.95109,-0.30651,-0.03854,-178.8,0.017525,-0.071021,0.99732,112.61
> select clear
> volume #20 level 0.0329
> select clear
> surface style #20 solid
> select clear
> select #20
2 models selected
> view matrix models
> #20,-0.32111,-0.94035,-0.1124,1193.3,0.9421,-0.32929,0.063365,-204.92,-0.096598,-0.085547,0.99164,162.79
> view matrix models
> #20,-0.30994,-0.95048,-0.022847,1159.5,0.94794,-0.31078,0.069497,-216.3,-0.073156,-0.00011748,0.99732,120
> fitmap #17 inMap #19 metric correlation
Fit map Heads-N-Eclosed_122017.mrc copy gaussian in map Heads.mrc copy using
2023118 points
correlation = 0.9429, correlation about mean = 0.9295, overlap = 1.537e+04
steps = 28, shift = 0.0146, angle = 0.00116 degrees
Position of Heads-N-Eclosed_122017.mrc copy gaussian (#17) relative to
Heads.mrc copy (#19) coordinates:
Matrix rotation and translation
0.99999982 -0.00054025 -0.00027210 0.26777312
0.00054022 0.99999985 -0.00012885 -0.23211798
0.00027217 0.00012870 0.99999995 -0.12255683
Axis 0.20821519 -0.44001552 0.87351747
Axis point 388.40434993 475.91965520 -0.00000000
Rotation angle (degrees) 0.03543522
Shift along axis 0.05083442
Drag select of 19 Heads.mrc copy , 20 Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
> view matrix models
> #19,0.95132,-0.28394,0.11985,401.49,0.23969,0.92608,0.29141,-467.63,-0.19374,-0.2485,0.94906,279.69,#20,-0.32652,-0.94072,0.091836,1119.3,0.88809,-0.27209,0.37049,-320.54,-0.32354,0.20253,0.92429,166.09
> view matrix models
> #19,0.98541,-0.14197,-0.093906,416.15,0.17021,0.82707,0.5357,-496.09,0.0016137,-0.54387,0.83917,355.28,#20,-0.1677,-0.97981,-0.1088,1149.1,0.77062,-0.19912,0.60539,-391.38,-0.61484,0.01768,0.78845,395.58
> view matrix models
> #19,0.98557,-0.13515,-0.10193,416.57,0.16874,0.83232,0.52798,-494.63,0.013479,-0.53756,0.84312,347.4,#20,-0.16022,-0.98022,-0.1162,1149.2,0.77657,-0.19785,0.59816,-391.38,-0.60932,0.0056007,0.79291,396.32
> select clear
> view matrix models
> #20,-0.13256,-0.98988,-0.050582,1118.1,0.82931,-0.13872,0.54129,-411.98,-0.54283,0.029807,0.83931,345.13
> select #20
2 models selected
> select clear
> volume #20 color #457ddb
> select clear
> save /Users/maryamfeghhi/Desktop/image55.png supersample 3
> select clear
> save /Users/maryamfeghhi/Desktop/image56.png supersample 3
> save /Users/maryamfeghhi/Desktop/image57.png supersample 3
> save /Users/maryamfeghhi/Desktop/image58.png supersample 3
> fitmap #19 inMap #20 metric correlation
Fit map Heads.mrc copy in map Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
using 784926 points
correlation = 0.8294, correlation about mean = 0.4199, overlap = 6153
steps = 148, shift = 7.46, angle = 5.79 degrees
Position of Heads.mrc copy (#19) relative to Heads-
Emergedap10.0.927-cryosparc_P7_J622_004_volume-0_region_19671.mrc gaussian
(#20) coordinates:
Matrix rotation and translation
-0.08364709 0.99649544 -0.00002386 48.64624100
-0.99649544 -0.08364709 0.00005109 758.05636716
0.00004892 0.00002805 1.00000000 18.33992585
Axis -0.00001156 -0.00003652 -1.00000000
Axis point 372.86778060 356.66099793 0.00000000
Rotation angle (degrees) 94.79823200
Shift along axis -18.36816942
> select clear
> select #20
2 models selected
> save /Users/maryamfeghhi/Desktop/image59.png supersample 3
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
QPainter::begin: Paint device returned engine == 0, type: 2
QPainter::translate: Painter not active
QPainter::setPen: Painter not active
QPainter::setBrush: Painter not active
QPainter::drawPoints: Painter not active
QPainter::end: Painter not active, aborted
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,13
Model Number: MC9E4LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 1 day, 7 hours, 10 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.8.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202501142332
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.15
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.43
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.6.10
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.11
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.5
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
pluggy: 1.5.0
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.0
PyQt6-Qt6: 6.8.1
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.1
PyQt6_sip: 13.9.1
pytest: 8.3.4
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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6.8.1, not 6.8.2