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Opened 8 months ago
Closed 8 months ago
#17037 closed defect (duplicate)
Mac multi-display crash
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.7.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001f9a78f80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 65)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac14,6",
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"codeSigningMonitor" : 1,
"incident" : "7DED01CE-C246-46FC-9134-EC9AC0D28D36",
"pid" : 16551,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-19 16:33:07.8962 -0500",
"procStartAbsTime" : 29253478198556,
"procExitAbsTime" : 38029001375900,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2004EEB0-6CE4-B69C-55BC-8DB5DE4ACC9C",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 28391,
"sleepWakeUUID" : "F8E2DF71-97C3-4CF0-9AE8-90E40F81A0FF",
"sip" : "enabled",
"vmRegionInfo" : "0xffff81276816b30e is not in any region. Bytes after previous region: 18446499047034761999 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600100000000-600120000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x9ab601276816b30e","rawCodes":[1,-7298644877345639666],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x9ab601276816b30e -> 0xffff81276816b30e (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":16551},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> set bgColor white
> graphics silhouettes true
> alias newcolor color $1 darkseagreen ; color $2 burlywood ; color $3 coral ;
> color $4 #498cff ; color $5 mediumslateblue ; color $6 grey ; color $7
> #ff69b4 ; color $8 #20B2AA ; color $9 #20B2AA
> alias propercolor color $1 mediumslateblue ; color $2 lightcoral ; color $3
> darkseagreen ; color $4 burlywood ; color $5 coral ; color $6 grey ; color
> $7 #bb57a1ff ; color $8 #0080ffff ; color $9 #004080ff
> alias removeatom select main ; style stick ; color sel byhetero ; hide sel
> atoms ; show sel cartoons ; select clear
> alias showATP select ::name="ATP" ; show sel ; color sel byhetero ; select
> clear
> alias modelfix style stick ; newcolor /A /B /C /D /E /F /G /H /I ; color
> byhetero ; show cartoons ; select clear ; select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
> ; hide sel atoms ; select clear
> lighting soft
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/apo_ylORC1-6_autoinhibited_O1AAA/fragmented from
> 2.3A map/apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc"
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc as #1, grid size
100,75,99, pixel 0.827,0.827,0.827, shown at level 0.351, step 1, values
float32
> volume #1 level 0.09834
> volume #1 level 0.1
> ui mousemode right "map eraser"
> volume erase #1 center 163.89,176.39,145.09 radius 12.448
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy as #3, grid size
100,75,99, pixel 0.827,0.827,0.827, shown at step 1, values float32
> volume erase #3 center 160.72,178.6,147.14 radius 25.099
> volume erase #3 center 153.84,165.37,159.35 radius 25.099
> volume erase #3 center 186.28,218.17,168.98 radius 18.318
> volume erase #3 center 177.17,206.22,131.59 radius 34.403
> volume erase #3 center 218.68,194.01,175.8 radius 34.403
> volume erase #3 center 189.93,162.62,149.15 radius 34.403
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylODC_54bp-
> oriC061_complete/ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc"
Opened ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc as #2, grid size 440,440,440,
pixel 0.827, shown at level 0.0339, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1
> ui mousemode right select
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-6.5437,0,1,0,-39.682,0,0,1,32.694
> view matrix models #3,1,0,0,63.882,0,1,0,-59.979,0,0,1,-62.393
> view matrix models #3,1,0,0,38.347,0,1,0,-95.198,0,0,1,-13.033
> view matrix models #3,1,0,0,16.509,0,1,0,-66.14,0,0,1,-0.99619
> view matrix models #3,1,0,0,20.128,0,1,0,-62.33,0,0,1,-2.0463
> close #1
> fitmap #3 inMap #2
Fit map apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy in map
ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc using 11600 points
correlation = 0.9405, correlation about mean = 0.5992, overlap = 241.7
steps = 200, shift = 2.29, angle = 36.2 degrees
Position of apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy (#3)
relative to ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.84572459 -0.49295295 0.20432158 104.99315114
0.53093078 0.81572589 -0.22957303 -70.02432300
-0.05350170 0.30263617 0.95160334 -43.34359941
Axis 0.45011126 0.21805178 0.86594069
Axis point 185.17878159 160.09585855 0.00000000
Rotation angle (degrees) 36.24202405
Shift along axis -5.54331477
> ui mousemode right select
> select clear
> vop resample #3 onGrid #2
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled as #1,
grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> volume #1 level 0.0764
> volume #1 level 0.1
> volume #1 level 0.15
> volume #2 level 0.05442
> volume #2 level 0.1
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99933,-0.018848,0.031243,-3.0076,0.018589,0.99979,0.0085722,-4.9693,-0.031398,-0.0079858,0.99948,6.9845
> fitmap #3 inMap #2
Fit map apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy in map
ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc using 11600 points
correlation = 0.9405, correlation about mean = 0.5991, overlap = 241.7
steps = 160, shift = 0.0161, angle = 0.0151 degrees
Position of apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy (#3)
relative to ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.84577508 -0.49297133 0.20406808 105.02263727
0.53087390 0.81574712 -0.22962913 -70.01411447
-0.05326738 0.30254901 0.95164420 -43.38215291
Axis 0.45014347 0.21766749 0.86602062
Axis point 185.20083727 160.15397652 0.00000000
Rotation angle (degrees) 36.23656846
Shift along axis -5.53438078
> ui mousemode right select
> select #3
2 models selected
> volume #3 level 0.15
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select clear
> close #1
> vop resample #3 onGrid #2
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled as #1,
grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> volume #1 level 0.2
> volume #1 level 0.15
> vop flip #1
Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled z flip
as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32
> vop flip #2
Opened ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc z flip as #5, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> save /Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/High-Res-ORC2WHD-
> mask_BASE_notBinary.mrc models #4
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_frame4_J411_003_volume_map.mrc"
Opened cryosparc_frame4_J411_003_volume_map.mrc as #6, grid size 440,440,440,
pixel 0.827, shown at level 0.0169, step 2, values float32
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/frame2_J413.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_P370_J410_005_volume_map.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate results/cryosparc_frame4_J411_003_volume_map.mrc"
Opened frame2_J413.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at
level 0.022, step 2, values float32
Opened cryosparc_P370_J410_005_volume_map.mrc as #1.2, grid size 440,440,440,
pixel 0.827, shown at level 0.019, step 2, values float32
Opened cryosparc_frame4_J411_003_volume_map.mrc as #1.3, grid size
440,440,440, pixel 0.827, shown at level 0.0169, step 2, values float32
> vop step 1
> vop level 0.1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-maps/ylORC1-6_oriC061_OPEN_noO1AAA/ORC-
> OPEN_DNA_P370_J167_FLIPPED.mrc"
Opened ORC-OPEN_DNA_P370_J167_FLIPPED.mrc as #2, grid size 440,440,440, pixel
0.827, shown at level 0.0182, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1
> vop flip #1
Opened frame2_J413.mrc z flip as #3, grid size 440,440,440, pixel 0.827, shown
at step 1, values float32
Opened cryosparc_P370_J410_005_volume_map.mrc z flip as #4, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened cryosparc_frame4_J411_003_volume_map.mrc z flip as #5, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> close #1#1.1-3
> fitmap #3 inMap #2
Fit map frame2_J413.mrc z flip in map ORC-OPEN_DNA_P370_J167_FLIPPED.mrc using
209824 points
correlation = 0.8749, correlation about mean = 0.6459, overlap = 5044
steps = 348, shift = 6.71, angle = 15.5 degrees
Position of frame2_J413.mrc z flip (#3) relative to ORC-
OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.97446697 0.02860606 0.22270119 -35.49808469
0.00472647 0.98901775 -0.14772120 23.54512380
-0.22448115 0.14500202 0.96362992 17.88035991
Axis 0.54714223 0.83584876 -0.04463441
Axis point 52.95063289 0.00000000 164.14097100
Rotation angle (degrees) 15.51567190
Shift along axis -0.54041832
> fitmap #4 inMap #2
Fit map cryosparc_P370_J410_005_volume_map.mrc z flip in map ORC-
OPEN_DNA_P370_J167_FLIPPED.mrc using 160211 points
correlation = 0.9112, correlation about mean = 0.6738, overlap = 4054
steps = 220, shift = 2.82, angle = 8.58 degrees
Position of cryosparc_P370_J410_005_volume_map.mrc z flip (#4) relative to
ORC-OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.99234355 -0.00562414 0.12338008 -16.99642910
0.01597062 0.99641901 -0.08303075 10.54881173
-0.12247128 0.08436548 0.98887980 8.05853927
Axis 0.56133195 0.82441655 0.07241400
Axis point 53.25288131 0.00000000 139.87627102
Rotation angle (degrees) 8.57513729
Shift along axis -0.26047268
> fitmap #5 inMap #2
Fit map cryosparc_frame4_J411_003_volume_map.mrc z flip in map ORC-
OPEN_DNA_P370_J167_FLIPPED.mrc using 154100 points
correlation = 0.9198, correlation about mean = 0.6573, overlap = 4122
steps = 120, shift = 1.21, angle = 4.97 degrees
Position of cryosparc_frame4_J411_003_volume_map.mrc z flip (#5) relative to
ORC-OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates:
Matrix rotation and translation
0.99738968 -0.01045075 0.07144651 -9.18473790
0.01387007 0.99877345 -0.04753118 5.34475067
-0.07086214 0.04839807 0.99631129 4.38863766
Axis 0.55342664 0.82099463 0.14030953
Axis point 55.32397495 0.00000000 129.96106991
Rotation angle (degrees) 4.97197356
Shift along axis -0.07929937
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!5 models
> hide #!2 models
> show #!4 models
> show #!3 models
> hide #!5 models
> volume #3 level 0.171
> volume #4 level 0.1381
> volume #4 level 0.1
> volume #3 level 0.1
> hide #!3 models
> show #!3 models
> volume #3 level 0.1121
> volume #3 level 0.08
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylORC1-6_oriC061_closed_noO1AAA/ORC-DNA-closed-
> noCdc6-noO1AAA_rev2_sidechains-not-done.pdb"
Chain information for ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-
done.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
> modelfix
Changed 18185 atom styles
16772 atoms, 17104 bonds, 8 pseudobonds, 2086 residues, 2 models selected
> hide #!1 models
> show #!1 models
> fitmap #1 inMap #3
Fit molecule ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-done.pdb (#1)
to map frame2_J413.mrc z flip (#3) using 18185 atoms
average map value = 0.1748, steps = 108
shifted from previous position = 3.5
rotated from previous position = 6.13 degrees
atoms outside contour = 2411, contour level = 0.08
Position of ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-done.pdb (#1)
relative to frame2_J413.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99078521 -0.01123591 -0.13497562 25.44161891
0.02375867 0.99551894 0.09152899 -17.35760278
0.13334237 -0.09389241 0.98661240 -3.43448090
Axis -0.56526644 -0.81798084 0.10668273
Axis point 43.71104119 0.00000000 183.20504019
Rotation angle (degrees) 9.43986719
Shift along axis -0.54950672
> select /C:220
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:171
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> volume #3 level 0.06943
> close #1
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb"
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25299 atom styles
23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected
> fitmap #1 inMap #3
Fit molecule ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) to map
frame2_J413.mrc z flip (#3) using 25299 atoms
average map value = 0.124, steps = 184
shifted from previous position = 4.41
rotated from previous position = 6.1 degrees
atoms outside contour = 9398, contour level = 0.06943
Position of ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) relative to
frame2_J413.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99093954 -0.00429549 -0.13423996 23.99797706
0.01699922 0.99546171 0.09363235 -16.70012343
0.13322855 -0.09506597 0.98651539 -3.03142526
Axis -0.57525720 -0.81539242 0.06491808
Axis point 40.21853239 0.00000000 174.40638339
Rotation angle (degrees) 9.43985245
Shift along axis -0.38464920
> select /D:168
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> volume #3 level 0.06037
> select clear
Unsupported scale factor (0.000000) detected on Display0
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/Projects-
> maps/apo_ylORC1-6_autoinhibited_O1AAA/cryosparc_P370_J421_map_sharp.mrc"
Opened cryosparc_P370_J421_map_sharp.mrc as #6, grid size 480,480,480, pixel
0.84, shown at level 0.0726, step 2, values float32
> hide #!1 models
> volume #6 step 1
> volume #6 level 0.1165
> volume #6 level 0.2042
> vop flip #6
Opened cryosparc_P370_J421_map_sharp.mrc z flip as #7, grid size 480,480,480,
pixel 0.84, shown at step 1, values float32
> close #6
> volume #7 level 0.2919
> volume #7 level 0.2656
> close #7
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_024.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_023.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_022.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_021.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_020.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_019.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_018.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_017.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_016.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_015.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_014.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_013.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_012.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_011.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_010.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_009.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_008.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_007.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_006.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_005.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_004.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_003.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_002.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_001.mrc"
> "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/intermediate
> results/cryosparc_P370_J407_component_000/J407_component_000_frame_000.mrc"
Opened J407_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J407_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel
0.827, shown at level 0.0247, step 2, values float32
Opened J407_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel
0.827, shown at level 0.0246, step 2, values float32
Opened J407_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel
0.827, shown at level 0.0248, step 2, values float32
Opened J407_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel
0.827, shown at level 0.025, step 2, values float32
Opened J407_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel
0.827, shown at level 0.0253, step 2, values float32
Opened J407_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel
0.827, shown at level 0.0256, step 2, values float32
Opened J407_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel
0.827, shown at level 0.0259, step 2, values float32
Opened J407_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel
0.827, shown at level 0.0262, step 2, values float32
Opened J407_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel
0.827, shown at level 0.0267, step 2, values float32
Opened J407_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel
0.827, shown at level 0.0269, step 2, values float32
Opened J407_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel
0.827, shown at level 0.0268, step 2, values float32
Opened J407_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel
0.827, shown at level 0.0266, step 2, values float32
Opened J407_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel
0.827, shown at level 0.0265, step 2, values float32
Opened J407_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel
0.827, shown at level 0.0263, step 2, values float32
Opened J407_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel
0.827, shown at level 0.0261, step 2, values float32
Opened J407_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel
0.827, shown at level 0.026, step 2, values float32
Opened J407_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
Opened J407_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel
0.827, shown at level 0.0257, step 2, values float32
Opened J407_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel
0.827, shown at level 0.0258, step 2, values float32
> vop step 1
> vop level 0.1
> fitmap #1.2 inMap #1.1
Fit map J407_component_000_frame_023.mrc in map
J407_component_000_frame_024.mrc using 209250 points
correlation = 0.9997, correlation about mean = 0.998, overlap = 8175
steps = 44, shift = 0.00683, angle = 0.0107 degrees
Position of J407_component_000_frame_023.mrc (#1.2) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999999 -0.00012647 -0.00005333 0.03293876
0.00012647 0.99999998 0.00012643 -0.05198641
0.00005331 -0.00012643 0.99999999 0.01305327
Axis -0.67751845 -0.28572825 0.67773749
Axis point 407.94854492 267.83546595 0.00000000
Rotation angle (degrees) 0.01069187
Shift along axis 0.00138407
> fitmap #1.3 inMap #1.1
Fit map J407_component_000_frame_022.mrc in map
J407_component_000_frame_024.mrc using 203717 points
correlation = 0.9986, correlation about mean = 0.9908, overlap = 7802
steps = 40, shift = 0.0172, angle = 0.0261 degrees
Position of J407_component_000_frame_022.mrc (#1.3) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999990 -0.00019261 -0.00039264 0.12474433
0.00019266 0.99999997 0.00012757 -0.06314784
0.00039262 -0.00012765 0.99999991 -0.04255682
Axis -0.28010520 -0.86182612 0.42284371
Axis point 110.06260037 0.00000000 318.73939640
Rotation angle (degrees) 0.02610266
Shift along axis 0.00148604
> fitmap #1.4 inMap #1.1
Fit map J407_component_000_frame_021.mrc in map
J407_component_000_frame_024.mrc using 198335 points
correlation = 0.9964, correlation about mean = 0.9756, overlap = 7418
steps = 44, shift = 0.0346, angle = 0.0352 degrees
Position of J407_component_000_frame_021.mrc (#1.4) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999985 -0.00028033 -0.00047313 0.15686283
0.00028046 0.99999992 0.00027270 -0.11547011
0.00047306 -0.00027283 0.99999985 -0.00564243
Axis -0.44433259 -0.77067092 0.45676569
Axis point 28.17446960 0.00000000 347.22791612
Rotation angle (degrees) 0.03517232
Shift along axis 0.01671292
> fitmap #1.5 inMap #1.1
Fit map J407_component_000_frame_020.mrc in map
J407_component_000_frame_024.mrc using 193267 points
correlation = 0.9926, correlation about mean = 0.9494, overlap = 7047
steps = 60, shift = 0.0446, angle = 0.0543 degrees
Position of J407_component_000_frame_020.mrc (#1.5) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999970 -0.00057369 -0.00052292 0.22913926
0.00057398 0.99999969 0.00054339 -0.22570178
0.00052261 -0.00054369 0.99999972 0.04101180
Axis -0.57357699 -0.55165719 0.60554420
Axis point 376.23364392 417.12641997 0.00000000
Rotation angle (degrees) 0.05429535
Shift along axis 0.01791546
> fitmap #1.6 inMap #1.1
Fit map J407_component_000_frame_019.mrc in map
J407_component_000_frame_024.mrc using 188984 points
correlation = 0.9863, correlation about mean = 0.9083, overlap = 6678
steps = 48, shift = 0.0575, angle = 0.0736 degrees
Position of J407_component_000_frame_019.mrc (#1.6) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999937 -0.00074520 -0.00084161 0.32749078
0.00074572 0.99999953 0.00062002 -0.28019774
0.00084115 -0.00062065 0.99999945 0.00597028
Axis -0.48315481 -0.65532311 0.58061438
Axis point 13.08513741 0.00000000 405.67912733
Rotation angle (degrees) 0.07356325
Shift along axis 0.02885774
> fitmap #1.7 inMap #1.1
Fit map J407_component_000_frame_018.mrc in map
J407_component_000_frame_024.mrc using 185458 points
correlation = 0.976, correlation about mean = 0.8493, overlap = 6310
steps = 48, shift = 0.0664, angle = 0.101 degrees
Position of J407_component_000_frame_018.mrc (#1.7) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999880 -0.00101281 -0.00116866 0.44242428
0.00101380 0.99999913 0.00084596 -0.38421046
0.00116780 -0.00084714 0.99999896 -0.01109545
Axis -0.48017506 -0.66263457 0.57475851
Axis point 27.45801527 0.00000000 393.24528287
Rotation angle (degrees) 0.10101276
Shift along axis 0.03577283
> fitmap #1.8 inMap #1.1
Fit map J407_component_000_frame_017.mrc in map
J407_component_000_frame_024.mrc using 183289 points
correlation = 0.9601, correlation about mean = 0.7729, overlap = 5913
steps = 48, shift = 0.0993, angle = 0.147 degrees
Position of J407_component_000_frame_017.mrc (#1.8) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999771 -0.00151197 -0.00151334 0.63051172
0.00151411 0.99999786 0.00140855 -0.58580425
0.00151121 -0.00141083 0.99999786 0.05858363
Axis -0.55024534 -0.59028684 0.59058573
Axis point 374.46052800 428.62087361 0.00000000
Rotation angle (degrees) 0.14678795
Shift along axis 0.03345506
> fitmap #1.9 inMap #1.1
Fit map J407_component_000_frame_016.mrc in map
J407_component_000_frame_024.mrc using 182675 points
correlation = 0.9355, correlation about mean = 0.6834, overlap = 5515
steps = 60, shift = 0.127, angle = 0.201 degrees
Position of J407_component_000_frame_016.mrc (#1.9) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999541 -0.00199889 -0.00227570 0.88265488
0.00200291 0.99999644 0.00176426 -0.75951590
0.00227217 -0.00176881 0.99999585 0.00414204
Axis -0.50380000 -0.64850507 0.57063713
Axis point 11.52035137 0.00000000 398.95768312
Rotation angle (degrees) 0.20090381
Shift along axis 0.05023198
> fitmap #1.10 inMap #1.1
Fit map J407_component_000_frame_015.mrc in map
J407_component_000_frame_024.mrc using 183507 points
correlation = 0.9007, correlation about mean = 0.5875, overlap = 5095
steps = 64, shift = 0.173, angle = 0.289 degrees
Position of J407_component_000_frame_015.mrc (#1.10) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99999101 -0.00276858 -0.00321317 1.22924900
0.00277736 0.99999241 0.00273204 -1.11683070
0.00320558 -0.00274094 0.99999111 0.04432005
Axis -0.54214099 -0.63582814 0.54936848
Axis point -1.07295593 0.00000000 394.04766813
Rotation angle (degrees) 0.28920482
Shift along axis 0.06803416
> fitmap #1.11 inMap #1.1
Fit map J407_component_000_frame_014.mrc in map
J407_component_000_frame_024.mrc using 185464 points
correlation = 0.8576, correlation about mean = 0.4935, overlap = 4658
steps = 68, shift = 0.257, angle = 0.451 degrees
Position of J407_component_000_frame_014.mrc (#1.11) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99997838 -0.00387997 -0.00530947 1.90413629
0.00390287 0.99998310 0.00431009 -1.66245856
0.00529266 -0.00433072 0.99997662 0.00352928
Axis -0.54908908 -0.67372352 0.49456830
Axis point 8.07677421 0.00000000 366.48177817
Rotation angle (degrees) 0.45082580
Shift along axis 0.07624247
> fitmap #1.12 inMap #1.1
Fit map J407_component_000_frame_013.mrc in map
J407_component_000_frame_024.mrc using 188095 points
correlation = 0.8117, correlation about mean = 0.4088, overlap = 4242
steps = 72, shift = 0.438, angle = 0.846 degrees
Position of J407_component_000_frame_013.mrc (#1.12) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99992647 -0.00628818 -0.01036874 3.45771106
0.00637521 0.99994455 0.00838211 -2.99419606
0.01031546 -0.00844760 0.99991111 -0.07122117
Axis -0.57011020 -0.70068168 0.42897500
Axis point 13.82106219 -0.00000000 338.66317537
Rotation angle (degrees) 0.84571953
Shift along axis 0.09614987
> fitmap #1.13 inMap #1.1
Fit map J407_component_000_frame_012.mrc in map
J407_component_000_frame_024.mrc using 190432 points
correlation = 0.826, correlation about mean = 0.4787, overlap = 4037
steps = 116, shift = 2.59, angle = 5.32 degrees
Position of J407_component_000_frame_012.mrc (#1.13) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99693363 -0.00485375 -0.07810112 18.39674331
0.00874835 0.99873077 0.04960155 -12.12187935
0.07776124 -0.05013271 0.99571075 -3.59284498
Axis -0.53753568 -0.84004816 0.07331093
Axis point 59.10885375 0.00000000 233.44064050
Rotation angle (degrees) 5.32297724
Shift along axis 0.03066174
> fitmap #1.14 inMap #1.1
Fit map J407_component_000_frame_011.mrc in map
J407_component_000_frame_024.mrc using 192986 points
correlation = 0.8264, correlation about mean = 0.5097, overlap = 4134
steps = 180, shift = 3.25, angle = 6.55 degrees
Position of J407_component_000_frame_011.mrc (#1.14) relative to
J407_component_000_frame_024.mrc (#1.1) coordinates:
Matrix rotation and translation
0.99536641 -0.00257223 -0.09612019 22.16708898
0.00847171 0.99810069 0.06101846 -14.42324176
0.09578068 -0.06155003 0.99349769 -4.19909428
Axis -0.53764860 -0.84177617 0.04844440
Axis point 59.32007584 0.00000000 227.86856058
Rotation angle (degrees) 6.54512439
Shift along axis 0.01961419
> vop flip #1
Opened J407_component_000_frame_024.mrc z flip as #2, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_023.mrc z flip as #3, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_022.mrc z flip as #4, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_021.mrc z flip as #5, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_020.mrc z flip as #6, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_019.mrc z flip as #7, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_018.mrc z flip as #8, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_017.mrc z flip as #9, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_016.mrc z flip as #10, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_015.mrc z flip as #11, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_014.mrc z flip as #12, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_013.mrc z flip as #13, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_012.mrc z flip as #14, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_011.mrc z flip as #15, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_010.mrc z flip as #16, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_009.mrc z flip as #17, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_008.mrc z flip as #18, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_007.mrc z flip as #19, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_006.mrc z flip as #20, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_005.mrc z flip as #21, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_004.mrc z flip as #22, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_003.mrc z flip as #23, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_002.mrc z flip as #24, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_001.mrc z flip as #25, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_000.mrc z flip as #26, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
> close #1
> fitmap #3 inMap #2
Fit map J407_component_000_frame_023.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 209250 points
correlation = 0.9997, correlation about mean = 0.998, overlap = 8159
steps = 44, shift = 0.0122, angle = 0.0166 degrees
Position of J407_component_000_frame_023.mrc z flip (#3) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999998 -0.00007198 0.00017080 -0.01218363
0.00007199 1.00000000 -0.00004990 -0.01272519
-0.00017079 0.00004991 0.99999998 0.00861980
Axis 0.26000175 0.88979882 0.37504286
Axis point 75.18576895 0.00000000 54.20442455
Rotation angle (degrees) 0.01099771
Shift along axis -0.01125783
> fitmap #4 inMap #2
Fit map J407_component_000_frame_022.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 203717 points
correlation = 0.9986, correlation about mean = 0.9908, overlap = 7804
steps = 44, shift = 0.00922, angle = 0.043 degrees
Position of J407_component_000_frame_022.mrc z flip (#4) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999993 -0.00018708 0.00032120 -0.00987873
0.00018712 0.99999998 -0.00010622 -0.01960247
-0.00032118 0.00010628 0.99999994 0.03150743
Axis 0.27483331 0.83080943 0.48396524
Axis point 103.74870000 0.00000000 27.56737164
Rotation angle (degrees) 0.02215041
Shift along axis -0.00375242
> fitmap #5 inMap #2
Fit map J407_component_000_frame_021.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 198335 points
correlation = 0.9964, correlation about mean = 0.9756, overlap = 7433
steps = 48, shift = 0.0353, angle = 0.0607 degrees
Position of J407_component_000_frame_021.mrc z flip (#5) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999983 -0.00035430 0.00045957 -0.00246458
0.00035440 0.99999991 -0.00022596 -0.04001364
-0.00045949 0.00022612 0.99999987 0.02969192
Axis 0.36297181 0.73789422 0.56900227
Axis point 81.37020887 0.00000000 -5.29006039
Rotation angle (degrees) 0.03568139
Shift along axis -0.01352564
> fitmap #6 inMap #2
Fit map J407_component_000_frame_020.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 193267 points
correlation = 0.9926, correlation about mean = 0.9494, overlap = 7051
steps = 48, shift = 0.0572, angle = 0.091 degrees
Position of J407_component_000_frame_020.mrc z flip (#6) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999963 -0.00049347 0.00070005 -0.00617347
0.00049379 0.99999977 -0.00046712 -0.02146966
-0.00069982 0.00046747 0.99999965 0.00864692
Axis 0.47894449 0.71738422 0.50593682
Axis point 22.46606534 -0.00000000 -0.73683347
Rotation angle (degrees) 0.05590211
Shift along axis -0.01398395
> fitmap #7 inMap #2
Fit map J407_component_000_frame_019.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 188984 points
correlation = 0.9863, correlation about mean = 0.9084, overlap = 6677
steps = 44, shift = 0.0751, angle = 0.121 degrees
Position of J407_component_000_frame_019.mrc z flip (#7) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999936 -0.00073951 0.00086022 0.01917742
0.00074004 0.99999953 -0.00062080 -0.05247554
-0.00085976 0.00062143 0.99999944 -0.00306149
Axis 0.48025379 0.66495781 0.57200298
Axis point 14.71644850 0.00000000 -37.59932412
Rotation angle (degrees) 0.07410093
Shift along axis -0.02743518
> fitmap #8 inMap #2
Fit map J407_component_000_frame_018.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 185458 points
correlation = 0.976, correlation about mean = 0.8495, overlap = 6307
steps = 48, shift = 0.0762, angle = 0.166 degrees
Position of J407_component_000_frame_018.mrc z flip (#8) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999889 -0.00109466 0.00101112 0.06239608
0.00109572 0.99999885 -0.00105131 -0.05426405
-0.00100997 0.00105242 0.99999894 -0.06011444
Axis 0.57667175 0.55401943 0.60042665
Axis point 34.34276710 72.86216565 0.00000000
Rotation angle (degrees) 0.10450891
Shift along axis -0.03017559
> fitmap #9 inMap #2
Fit map J407_component_000_frame_017.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 183289 points
correlation = 0.9601, correlation about mean = 0.7729, overlap = 5915
steps = 64, shift = 0.122, angle = 0.236 degrees
Position of J407_component_000_frame_017.mrc z flip (#9) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999771 -0.00148690 0.00153937 0.06533420
0.00148900 0.99999796 -0.00136750 -0.08041576
-0.00153733 0.00136979 0.99999788 -0.04587663
Axis 0.53874971 0.60555051 0.58571096
Axis point -14.38402550 0.00000000 -56.59152311
Rotation angle (degrees) 0.14555510
Shift along axis -0.04036747
> fitmap #10 inMap #2
Fit map J407_component_000_frame_016.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 182675 points
correlation = 0.9352, correlation about mean = 0.6832, overlap = 5522
steps = 52, shift = 0.145, angle = 0.328 degrees
Position of J407_component_000_frame_016.mrc z flip (#10) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999558 -0.00205030 0.00215508 0.07345453
0.00205433 0.99999614 -0.00186887 -0.11702549
-0.00215124 0.00187329 0.99999593 -0.03493961
Axis 0.53244610 0.61271628 0.58402047
Axis point -1.76436098 0.00000000 -47.18208786
Rotation angle (degrees) 0.20134459
Shift along axis -0.05299829
> fitmap #11 inMap #2
Fit map J407_component_000_frame_015.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 183507 points
correlation = 0.9009, correlation about mean = 0.5877, overlap = 5090
steps = 48, shift = 0.208, angle = 0.483 degrees
Position of J407_component_000_frame_015.mrc z flip (#11) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99999091 -0.00273836 0.00326767 0.05590994
0.00274708 0.99999267 -0.00266766 -0.12998441
-0.00326034 0.00267661 0.99999110 -0.02714748
Axis 0.53107566 0.64870698 0.54510357
Axis point 3.35863162 0.00000000 -28.38436861
Rotation angle (degrees) 0.28828800
Shift along axis -0.06942757
> fitmap #12 inMap #2
Fit map J407_component_000_frame_014.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 185464 points
correlation = 0.8578, correlation about mean = 0.4936, overlap = 4655
steps = 56, shift = 0.29, angle = 0.782 degrees
Position of J407_component_000_frame_014.mrc z flip (#12) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99997895 -0.00391909 0.00517094 0.00256972
0.00394209 0.99998236 -0.00444391 -0.08633596
-0.00515344 0.00446420 0.99997676 -0.05838787
Axis 0.56595594 0.65593568 0.49944195
Axis point -3.11241061 0.00000000 -9.74033626
Rotation angle (degrees) 0.45092040
Shift along axis -0.08433783
> fitmap #13 inMap #2
Fit map J407_component_000_frame_013.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 188095 points
correlation = 0.8116, correlation about mean = 0.4086, overlap = 4243
steps = 96, shift = 0.393, angle = 1.53 degrees
Position of J407_component_000_frame_013.mrc z flip (#13) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99992688 -0.00630498 0.01031927 -0.30501394
0.00639187 0.99994421 -0.00840964 0.04351622
-0.01026567 0.00847499 0.99991139 0.09565506
Axis 0.57242910 0.69787876 0.43045344
Axis point 13.43257006 0.00000000 23.93624556
Rotation angle (degrees) 0.84504164
Shift along axis -0.10305476
> fitmap #14 inMap #2
Fit map J407_component_000_frame_012.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 190432 points
correlation = 0.8261, correlation about mean = 0.4787, overlap = 4037
steps = 176, shift = 1.44, angle = 10.6 degrees
Position of J407_component_000_frame_012.mrc z flip (#14) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99694118 -0.00490893 0.07800121 -9.93956782
0.00881435 0.99872014 -0.04980352 5.90096487
-0.07765690 0.05033871 0.99570850 5.09045949
Axis 0.53956818 0.83868878 0.07394129
Axis point 58.43220848 0.00000000 129.45965602
Rotation angle (degrees) 5.32462315
Shift along axis -0.03760638
> fitmap #15 inMap #2
Fit map J407_component_000_frame_011.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 192986 points
correlation = 0.8264, correlation about mean = 0.5098, overlap = 4134
steps = 292, shift = 1.7, angle = 13.1 degrees
Position of J407_component_000_frame_011.mrc z flip (#15) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99535227 -0.00254091 0.09626734 -12.75691240
0.00845357 0.99809823 -0.06106117 7.73661469
-0.09592911 0.06159118 0.99348082 6.58346657
Axis 0.53732932 0.84199599 0.04816585
Axis point 59.44846482 0.00000000 135.25518533
Rotation angle (degrees) 6.55353132
Shift along axis -0.02336624
> fitmap #16 inMap #2
Fit map J407_component_000_frame_010.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 196011 points
correlation = 0.8258, correlation about mean = 0.5264, overlap = 4268
steps = 196, shift = 3.64, angle = 7.16 degrees
Position of J407_component_000_frame_010.mrc z flip (#16) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99443723 -0.00129423 0.10532294 -14.14446568
0.00834325 0.99775057 -0.06651460 8.62606466
-0.10499994 0.06702333 0.99221111 7.38173986
Axis 0.53560639 0.84358259 0.03865489
Axis point 60.11494959 0.00000000 137.40139033
Rotation angle (degrees) 7.16115140
Shift along axis -0.01372784
> fitmap #17 inMap #2
Fit map J407_component_000_frame_009.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 199261 points
correlation = 0.8232, correlation about mean = 0.5306, overlap = 4420
steps = 136, shift = 3.94, angle = 7.55 degrees
Position of J407_component_000_frame_009.mrc z flip (#17) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99383750 -0.00051591 0.11084568 -14.99048576
0.00835653 0.99749218 -0.07028168 9.22600775
-0.11053144 0.07077485 0.99134944 7.80629725
Axis 0.53705726 0.84286912 0.03378085
Axis point 59.78820314 0.00000000 138.50939775
Rotation angle (degrees) 7.54608177
Shift along axis -0.01072884
> fitmap #18 inMap #2
Fit map J407_component_000_frame_008.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 203831 points
correlation = 0.8153, correlation about mean = 0.52, overlap = 4559
steps = 2000, shift = 4.22, angle = 7.99 degrees
Position of J407_component_000_frame_008.mrc z flip (#18) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99311478 0.00036012 0.11714484 -15.91996779
0.00844044 0.99717627 -0.07462070 10.01782949
-0.11684093 0.07509567 0.99030745 8.49776599
Axis 0.53873766 0.84197168 0.02907615
Axis point 61.09163915 0.00000000 139.97400207
Rotation angle (degrees) 7.98715498
Shift along axis 0.10512492
> fitmap #19 inMap #2
Fit map J407_component_000_frame_007.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 209283 points
correlation = 0.8104, correlation about mean = 0.5166, overlap = 4743
steps = 2000, shift = 4.27, angle = 7.92 degrees
Position of J407_component_000_frame_007.mrc z flip (#19) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99298926 0.00085186 0.11820153 -16.25189613
0.00754817 0.99747619 -0.07059942 9.40986459
-0.11796335 0.07099668 0.99047671 9.37694002
Axis 0.51406917 0.85740414 0.02431115
Axis point 68.09691265 0.00000000 141.27730169
Rotation angle (degrees) 7.91598383
Shift along axis -0.05857770
> fitmap #20 inMap #2
Fit map J407_component_000_frame_006.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 215308 points
correlation = 0.803, correlation about mean = 0.509, overlap = 4911
steps = 2000, shift = 4.59, angle = 7.95 degrees
Position of J407_component_000_frame_006.mrc z flip (#20) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99338714 0.00062278 0.11481118 -15.65271922
0.00828418 0.99699005 -0.07708568 10.23612069
-0.11451362 0.07752704 0.99039194 7.15534657
Axis 0.55880756 0.82883495 0.02769014
Axis point 50.84212432 0.00000000 138.94807270
Rotation angle (degrees) 7.95189644
Shift along axis -0.06467064
> fitmap #21 inMap #2
Fit map J407_component_000_frame_005.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 221943 points
correlation = 0.7975, correlation about mean = 0.5036, overlap = 5120
steps = 2000, shift = 4.83, angle = 8.46 degrees
Position of J407_component_000_frame_005.mrc z flip (#21) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99245648 0.00133502 0.12259016 -16.74608631
0.00870219 0.99665134 -0.08130423 11.00789413
-0.12228819 0.08175771 0.98912147 8.37528140
Axis 0.55407863 0.83208786 0.02503340
Axis point 55.97483404 -0.00000000 140.45584472
Rotation angle (degrees) 8.46162297
Shift along axis 0.09054828
> fitmap #22 inMap #2
Fit map J407_component_000_frame_004.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 228675 points
correlation = 0.7942, correlation about mean = 0.505, overlap = 5345
steps = 128, shift = 4.86, angle = 8.35 degrees
Position of J407_component_000_frame_004.mrc z flip (#22) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99249124 0.00154071 0.12230601 -16.79973741
0.00809048 0.99690400 -0.07821101 10.55194435
-0.12204785 0.07861326 0.98940602 8.69406762
Axis 0.53998559 0.84137207 0.02255251
Axis point 58.99611311 0.00000000 140.99153578
Rotation angle (degrees) 8.34952877
Shift along axis 0.00256822
> fitmap #23 inMap #2
Fit map J407_component_000_frame_003.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 235349 points
correlation = 0.7882, correlation about mean = 0.5, overlap = 5547
steps = 212, shift = 4.98, angle = 8.42 degrees
Position of J407_component_000_frame_003.mrc z flip (#23) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99239157 0.00173360 0.12310956 -16.93547458
0.00807332 0.99683268 -0.07911654 10.70058751
-0.12285679 0.07950849 0.98923436 8.68387043
Axis 0.54184790 0.84019752 0.02165588
Axis point 58.31141283 -0.00000000 141.17775832
Rotation angle (degrees) 8.41685965
Shift along axis 0.00221262
> fitmap #24 inMap #2
Fit map J407_component_000_frame_002.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 242114 points
correlation = 0.7826, correlation about mean = 0.4956, overlap = 5752
steps = 208, shift = 5.08, angle = 8.48 degrees
Position of J407_component_000_frame_002.mrc z flip (#24) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99225263 0.00189051 0.12422215 -17.10140627
0.00804439 0.99680826 -0.07942660 10.75407774
-0.12397582 0.07981055 0.98907041 8.85014965
Axis 0.53987514 0.84148650 0.02086400
Axis point 58.92464501 0.00000000 141.34912975
Rotation angle (degrees) 8.48068000
Shift along axis 0.00143673
> fitmap #25 inMap #2
Fit map J407_component_000_frame_001.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 249113 points
correlation = 0.7772, correlation about mean = 0.4915, overlap = 5962
steps = 188, shift = 5.18, angle = 8.55 degrees
Position of J407_component_000_frame_001.mrc z flip (#25) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99214829 0.00207808 0.12504976 -17.23705108
0.00803389 0.99673797 -0.08030494 10.89836189
-0.12480873 0.08067904 0.98889518 8.86701028
Axis 0.54150720 0.84045738 0.02003374
Axis point 58.45205449 0.00000000 141.52577979
Rotation angle (degrees) 8.54837308
Shift along axis 0.00326072
> fitmap #26 inMap #2
Fit map J407_component_000_frame_000.mrc z flip in map
J407_component_000_frame_024.mrc z flip using 256043 points
correlation = 0.7721, correlation about mean = 0.488, overlap = 6173
steps = 148, shift = 5.26, angle = 8.6 degrees
Position of J407_component_000_frame_000.mrc z flip (#26) relative to
J407_component_000_frame_024.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.99206661 0.00217833 0.12569448 -17.33798987
0.00806440 0.99668776 -0.08092267 10.99552196
-0.12545442 0.08129433 0.98876308 8.89667575
Axis 0.54245968 0.83985122 0.01968325
Axis point 58.22890126 -0.00000000 141.63243770
Rotation angle (degrees) 8.59910356
Shift along axis 0.00455761
> color grey
> volume morph #2-26
Map positions are not the same, J407_component_000_frame_023.mrc z flip #3 and
J407_component_000_frame_024.mrc z flip #2. Use the "volume resample" command
to make a copy of one map with the same grid as the other map.
> volume resample #3-26 onGrid #2
Opened J407_component_000_frame_023.mrc z flip resampled as #1, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_022.mrc z flip resampled as #27, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_021.mrc z flip resampled as #28, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_020.mrc z flip resampled as #29, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_019.mrc z flip resampled as #30, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_018.mrc z flip resampled as #31, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_017.mrc z flip resampled as #32, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_016.mrc z flip resampled as #33, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_015.mrc z flip resampled as #34, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_014.mrc z flip resampled as #35, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_013.mrc z flip resampled as #36, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_012.mrc z flip resampled as #37, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_011.mrc z flip resampled as #38, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_010.mrc z flip resampled as #39, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_009.mrc z flip resampled as #40, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_008.mrc z flip resampled as #41, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_007.mrc z flip resampled as #42, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_006.mrc z flip resampled as #43, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_005.mrc z flip resampled as #44, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_004.mrc z flip resampled as #45, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_003.mrc z flip resampled as #46, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_002.mrc z flip resampled as #47, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_001.mrc z flip resampled as #48, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
Opened J407_component_000_frame_000.mrc z flip resampled as #49, grid size
440,440,440, pixel 0.827, shown at step 1, values float32
> close #3-26
> rename #2 id #500
> rename #1 id #2
> rename #500 id #1
> color grey
> volume morph #2-49
Opened morph as #3, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> hide #!1 models
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
Unsupported scale factor (0.000000) detected on Display1
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
Unsupported scale factor (0.000000) detected on Display1
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_54bp-
> oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb" format pdb
Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J339_component_002_frame_017.mrc z flip as #19, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_018.mrc z flip as #20, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
Opened J339_component_002_frame_019.mrc z flip as #21, grid size 440,440,440,
pixel 0.827, shown at step 1, values float32
> vop level 0.1
> hide #!1 models
> vop morph #2-21
Opened morph as #22, grid size 440,440,440, pixel 0.827, shown at step 1,
values float32
> show #!21 models
> hide #!22 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> hide #!20 models
> hide #!21 models
> close #22
> close
> open "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
> structures/PDBs/ylODC_45bp-
> oriC061_complete/ODC1-6_45bpOriC061_DNApucker_rev3.cif"
Summary of feedback from opening /Users/jtbauer/Library/CloudStorage/OneDrive-
Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize
structures/PDBs/ylODC_45bp-
oriC061_complete/ODC1-6_45bpOriC061_DNApucker_rev3.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 19
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for ODC1-6_45bpOriC061_DNApucker_rev3.cif #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> modelfix
Changed 25273 atom styles
23792 atoms, 24240 bonds, 9 pseudobonds, 2982 residues, 2 models selected
Computing secondary structure
> lighting soft
> graphics silhouettes true
> save "/Users/jtbauer/Library/CloudStorage/OneDrive-
> Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for
> posterpub/45bp_too_short.png" supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
> set bgColor white
> graphics silhouettes true
> alias newcolor color $1 darkseagreen ; color $2 burlywood ; color $3 coral ;
> color $4 #498cff ; color $5 mediumslateblue ; color $6 grey ; color $7
> #ff69b4 ; color $8 #20B2AA ; color $9 #20B2AA
> alias propercolor color $1 mediumslateblue ; color $2 lightcoral ; color $3
> darkseagreen ; color $4 burlywood ; color $5 coral ; color $6 grey ; color
> $7 #bb57a1ff ; color $8 #0080ffff ; color $9 #004080ff
> alias removeatom select main ; style stick ; color sel byhetero ; hide sel
> atoms ; show sel cartoons ; select clear
> alias showATP select ::name="ATP" ; show sel ; color sel byhetero ; select
> clear
> alias modelfix style stick ; newcolor /A /B /C /D /E /F /G /H /I ; color
> byhetero ; show cartoons ; select clear ; select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
> ; hide sel atoms ; select clear
> lighting soft
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: Z176000HCLL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 11881.61.3
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 51 days, 21 hours, 52 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
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: 3.4.0
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: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
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: 1.0.1
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: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
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: 1.2.6
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: 1.2.1
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: 2.7.6
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-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
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: 1.18.1
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
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: 1.41
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
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
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
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
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
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
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: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
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: 2.2.3
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 , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Mac multi-display crash |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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