![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15711 closed defect (nonchimerax)
Crash in event loop, setting volume level, probable Apple AMD graphics crash
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | 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-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff8458d6fc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 59)
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{
"uptime" : 230000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"coalitionID" : 1294,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-08-01 09:18:07.5224 +0200",
"codeSigningMonitor" : 0,
"incident" : "A72C64CA-E3CE-4EF1-A371-F69537FAE2A1",
"pid" : 62772,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-31 08:56:40.8658 +0200",
"procStartAbsTime" : 194227310086464,
"procExitAbsTime" : 234201071816027,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B371D212-791B-571F-B34F-C7FBE1E30786","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "81900405-2890-8286-C35F-B86F1DDE70AD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 12,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "E776EA31-B6C0-4CFA-8C25-1C853738FCF8",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4482916352\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b33e000-10b342000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":62772},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4482916352\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b33e000-10b342000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/cristianrosales/Downloads/cryosparc_P380_J1324_008_volume_map
> (1).mrc"
Opened cryosparc_P380_J1324_008_volume_map (1).mrc as #1, grid size
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> ui tool show "Side View"
> volume #1 level 0.105
> volume #1 level 0.2078
> volume #1 level 0.3105
> open "/Users/cristianrosales/Library/CloudStorage/OneDrive-
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Chain information for Bcs1-ATPgS_V2(r31).pdb #2
---
Chain | Description
A B C D E F G | No description available
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule Bcs1-ATPgS_V2(r31).pdb (#2) to map
cryosparc_P380_J1324_008_volume_map (1).mrc (#1) using 46321 atoms
average map value = 0.456, steps = 276
shifted from previous position = 5.49
rotated from previous position = 52 degrees
atoms outside contour = 18301, contour level = 0.31054
Position of Bcs1-ATPgS_V2(r31).pdb (#2) relative to
cryosparc_P380_J1324_008_volume_map (1).mrc (#1) coordinates:
Matrix rotation and translation
0.62201996 0.54374379 0.56341270 -100.16954163
-0.61284216 0.78594770 -0.08191886 120.66952939
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Axis -0.13469200 0.66630929 -0.73340985
Axis point 107.08703555 258.79421417 0.00000000
Rotation angle (degrees) 52.04546638
Shift along axis -0.53040937
> hide atoms
> show cartoons
> volume #1 level 0.377
> close
> open "/Users/cristianrosales/Downloads/cryosparc_P448_J103_004_volume_map
> (1).mrc"
Opened cryosparc_P448_J103_004_volume_map (1).mrc as #1, grid size
256,256,256, pixel 1.05, shown at level 0.272, step 1, values float32
> volume #1 level 0.1677
> close
> open "/Users/cristianrosales/Downloads/cryosparc_P445_J155_007_volume_map
> (3).mrc"
Opened cryosparc_P445_J155_007_volume_map (3).mrc as #1, grid size
180,180,180, pixel 1.45, shown at level 0.352, step 1, values float32
> volume #1 level 0.2264
> volume #1 level 0.2663
> volume #1 level 0.392
> volume #1 level 0.2203
> volume #1 level 0.343
> open "/Users/cristianrosales/Downloads/cryosparc_P445_J154_011_volume_map
> (2).mrc"
Opened cryosparc_P445_J154_011_volume_map (2).mrc as #2, grid size
180,180,180, pixel 1.45, shown at level 0.362, step 1, values float32
> fitmap #2 inMap #1
Fit map cryosparc_P445_J154_011_volume_map (2).mrc in map
cryosparc_P445_J155_007_volume_map (3).mrc using 58257 points
correlation = 0.8301, correlation about mean = 0.2214, overlap = 1.28e+04
steps = 48, shift = 0.199, angle = 1.36 degrees
Position of cryosparc_P445_J154_011_volume_map (2).mrc (#2) relative to
cryosparc_P445_J155_007_volume_map (3).mrc (#1) coordinates:
Matrix rotation and translation
0.99992430 0.00573059 0.01088817 -2.20008894
-0.00594948 0.99977868 0.02017884 -1.85932451
-0.01077013 -0.02024209 0.99973710 3.82137082
Axis -0.85417053 0.45768078 -0.24682181
Axis point 0.00000000 188.57214637 96.14014441
Rotation angle (degrees) 1.35579748
Shift along axis 0.08507639
> volume #1 level 0.2968
> select add #2
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99981,0.0011338,0.019665,-2.7341,-0.014365,0.72505,0.68854,-52.602,-0.013478,-0.68869,0.72493,129.22
> view matrix models
> #2,0.9846,-0.13175,0.1149,4.3971,0.0062212,0.68327,0.73014,-55.384,-0.17471,-0.71818,0.67357,162.06
> view matrix models
> #2,0.98067,-0.067039,0.18381,-12.759,-0.077085,0.73108,0.67792,-43.385,-0.17982,-0.67899,0.71178,152.52
> vop flip #2
Opened cryosparc_P445_J154_011_volume_map (2).mrc z flip as #3, grid size
180,180,180, pixel 1.45, shown at step 1, values float32
> fitmap #3 inMap #1
Fit map cryosparc_P445_J154_011_volume_map (2).mrc z flip in map
cryosparc_P445_J155_007_volume_map (3).mrc using 58257 points
correlation = 0.9571, correlation about mean = 0.7132, overlap = 1.776e+04
steps = 120, shift = 4.3, angle = 18.9 degrees
Position of cryosparc_P445_J154_011_volume_map (2).mrc z flip (#3) relative to
cryosparc_P445_J155_007_volume_map (3).mrc (#1) coordinates:
Matrix rotation and translation
0.99912074 -0.00362330 0.04176861 -4.75175121
-0.01540842 0.89480227 0.44619668 -42.44648449
-0.03899135 -0.44644795 0.89395968 76.88883989
Axis -0.99584622 0.09009689 -0.01314764
Axis point 0.00000000 141.69546355 128.51558738
Rotation angle (degrees) 26.62722909
Shift along axis -0.10318935
> volume #3 level 0.224
> close
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1372_009_volume_map.mrc
Opened cryosparc_P380_J1372_009_volume_map.mrc as #1, grid size 180,180,180,
pixel 1.45, shown at level 0.377, step 1, values float32
> volume #1 level 0.3258
> volume #1 level 0.3077
> volume #1 level 0.2823
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1373_008_volume_map.mrc
Opened cryosparc_P380_J1373_008_volume_map.mrc as #2, grid size 180,180,180,
pixel 1.45, shown at level 0.374, step 1, values float32
> volume #2 level 0.2014
> volume #2 level 0.3474
> volume #2 level 0.259
> volume #1 level 0.1662
> volume #1 level 0.2533
> volume #1 level 0.1626
> volume #1 level 0.2134
> volume #1 level 0.1553
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1374_008_volume_map.mrc
Opened cryosparc_P380_J1374_008_volume_map.mrc as #3, grid size 180,180,180,
pixel 1.45, shown at level 0.376, step 1, values float32
> volume #3 level 0.1943
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1375_008_volume_map.mrc
Opened cryosparc_P380_J1375_008_volume_map.mrc as #4, grid size 180,180,180,
pixel 1.45, shown at level 0.374, step 1, values float32
> volume #4 level 0.183
> volume #4 level 0.2904
> volume #3 level 0.144
> volume #3 level 0.2716
> open "/Users/cristianrosales/Library/CloudStorage/OneDrive-
> Personal/LMU/PhD/Lab/Data/CryoEM Data/Coot/Bcs1 Legacy/dn82Rip1_1kb9.pdb"
Chain information for dn82Rip1_1kb9.pdb #5
---
Chain | Description
E | No description available
> select add #5
1026 atoms, 1053 bonds, 4 pseudobonds, 135 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,41.562,0,1,0,-38.602,0,0,1,88
> volume #1 level 0.3333
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.1399,0.66418,0.73437,-10.215,0.81601,0.34276,-0.46545,-8.9921,-0.56086,0.66437,-0.49402,220.69
> view matrix models
> #5,-0.77028,0.29479,0.56547,178.35,0.1487,-0.77926,0.60881,126.42,0.62012,0.55304,0.55642,-25.948
> view matrix models
> #5,-0.31917,0.19734,0.92692,95.739,-0.45362,-0.89057,0.033401,279.44,0.83208,-0.40981,0.37376,97.45
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.31917,0.19734,0.92692,95.096,-0.45362,-0.89057,0.033401,271.94,0.83208,-0.40981,0.37376,35.365
> view matrix models
> #5,-0.31917,0.19734,0.92692,103.44,-0.45362,-0.89057,0.033401,291.92,0.83208,-0.40981,0.37376,38.753
> view matrix models
> #5,-0.31917,0.19734,0.92692,79.543,-0.45362,-0.89057,0.033401,299.76,0.83208,-0.40981,0.37376,45.103
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.84126,-0.49272,-0.22249,359.66,-0.10664,-0.25222,0.96178,72.208,-0.53001,0.83283,0.15963,75.23
> view matrix models
> #5,-0.15002,0.31709,-0.93646,228,-0.9658,-0.2496,0.070205,275.28,-0.21148,0.91496,0.34369,3.1883
> view matrix models
> #5,-0.31635,0.5313,-0.7859,205.27,-0.93041,-0.01213,0.36632,207.99,0.18509,0.8471,0.49816,-55.479
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.31635,0.5313,-0.7859,209.42,-0.93041,-0.01213,0.36632,212.98,0.18509,0.8471,0.49816,-55.383
> view matrix models
> #5,-0.31635,0.5313,-0.7859,208.42,-0.93041,-0.01213,0.36632,211.43,0.18509,0.8471,0.49816,-54.255
> view matrix models
> #5,-0.31635,0.5313,-0.7859,210.79,-0.93041,-0.01213,0.36632,213.51,0.18509,0.8471,0.49816,-53.72
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.5759,-0.35083,-0.73842,209.8,0.66717,-0.32031,0.67252,13.771,-0.47246,-0.87995,0.049595,317.2
> view matrix models
> #5,-0.23703,-0.64688,0.72482,211.21,-0.72995,-0.37375,-0.57227,331.35,0.64109,-0.66472,-0.3836,183.56
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.23703,-0.64688,0.72482,211.52,-0.72995,-0.37375,-0.57227,321.51,0.64109,-0.66472,-0.3836,175.88
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.44462,-0.55501,0.70305,228.5,-0.50579,-0.49223,-0.70844,321.9,0.73925,-0.67058,-0.061866,131.33
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.44462,-0.55501,0.70305,230.14,-0.50579,-0.49223,-0.70844,319.39,0.73925,-0.67058,-0.061866,129.47
> view matrix models
> #5,-0.44462,-0.55501,0.70305,229.74,-0.50579,-0.49223,-0.70844,320.71,0.73925,-0.67058,-0.061866,128.4
> volume #1 level 0.5001
> volume #1 level 0.311
> view matrix models
> #5,-0.44462,-0.55501,0.70305,220.58,-0.50579,-0.49223,-0.70844,263.07,0.73925,-0.67058,-0.061866,138.83
> molmap #5 20
Opened dn82Rip1_1kb9.pdb map 20 as #6, grid size 23,25,25, pixel 6.67, shown
at level 0.018, step 1, values float32
> volume #6 level 0.1092
> close #6
> molmap #5 10
Opened dn82Rip1_1kb9.pdb map 10 as #6, grid size 27,32,32, pixel 3.33, shown
at level 0.0462, step 1, values float32
> volume #6 level 0.3202
> select add #6
1026 atoms, 1053 bonds, 4 pseudobonds, 135 residues, 5 models selected
> view matrix models
> #5,-0.44462,-0.55501,0.70305,228.58,-0.50579,-0.49223,-0.70844,269.4,0.73925,-0.67058,-0.061866,143.23,#6,-0.44462,-0.55501,0.70305,228.58,-0.50579,-0.49223,-0.70844,269.4,0.73925,-0.67058,-0.061866,143.23
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.38804,0.90214,0.18862,-31.358,-0.86049,0.42793,-0.27646,145.73,-0.33012,-0.055029,0.94233,98.75,#6,0.38804,0.90214,0.18862,-31.358,-0.86049,0.42793,-0.27646,145.73,-0.33012,-0.055029,0.94233,98.75
> view matrix models
> #5,-0.0095495,0.84672,0.53195,-5.5842,0.69687,0.38715,-0.60373,-21.938,-0.71713,0.36494,-0.59375,246.42,#6,-0.0095495,0.84672,0.53195,-5.5842,0.69687,0.38715,-0.60373,-21.938,-0.71713,0.36494,-0.59375,246.42
> view matrix models
> #5,0.55433,0.061037,-0.83006,165.34,0.50344,-0.81876,0.276,81.89,-0.66277,-0.57088,-0.48459,357.6,#6,0.55433,0.061037,-0.83006,165.34,0.50344,-0.81876,0.276,81.89,-0.66277,-0.57088,-0.48459,357.6
> view matrix models
> #5,0.70508,0.1465,-0.69383,119.86,0.42796,-0.86807,0.2516,101.16,-0.56543,-0.47433,-0.67476,350.49,#6,0.70508,0.1465,-0.69383,119.86,0.42796,-0.86807,0.2516,101.16,-0.56543,-0.47433,-0.67476,350.49
> view matrix models
> #5,0.72121,0.030003,-0.69207,133.65,0.64751,-0.38421,0.65812,-35.684,-0.24616,-0.92276,-0.29652,332.16,#6,0.72121,0.030003,-0.69207,133.65,0.64751,-0.38421,0.65812,-35.684,-0.24616,-0.92276,-0.29652,332.16
> view matrix models
> #5,0.4701,0.031613,-0.88205,185.79,0.86987,-0.18578,0.45695,-72.327,-0.14942,-0.98208,-0.11484,309.28,#6,0.4701,0.031613,-0.88205,185.79,0.86987,-0.18578,0.45695,-72.327,-0.14942,-0.98208,-0.11484,309.28
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.4701,0.031613,-0.88205,180.26,0.86987,-0.18578,0.45695,-84.097,-0.14942,-0.98208,-0.11484,312.34,#6,0.4701,0.031613,-0.88205,180.26,0.86987,-0.18578,0.45695,-84.097,-0.14942,-0.98208,-0.11484,312.34
> view matrix models
> #5,0.4701,0.031613,-0.88205,175.17,0.86987,-0.18578,0.45695,-86.204,-0.14942,-0.98208,-0.11484,305.6,#6,0.4701,0.031613,-0.88205,175.17,0.86987,-0.18578,0.45695,-86.204,-0.14942,-0.98208,-0.11484,305.6
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.46044,-0.16305,-0.87259,202.41,0.75647,-0.44229,0.48181,-38.23,-0.46449,-0.88193,-0.080308,330,#6,0.46044,-0.16305,-0.87259,202.41,0.75647,-0.44229,0.48181,-38.23,-0.46449,-0.88193,-0.080308,330
> volume #6 level 0.3285
> view matrix models
> #5,0.25309,0.10814,-0.96138,201.31,0.96006,0.094492,0.26337,-117.42,0.11932,-0.98963,-0.079909,267.54,#6,0.25309,0.10814,-0.96138,201.31,0.96006,0.094492,0.26337,-117.42,0.11932,-0.98963,-0.079909,267.54
> view matrix models
> #5,0.88102,0.053513,-0.47005,76.295,0.32122,-0.79711,0.51131,65.483,-0.34732,-0.60146,-0.71945,340,#6,0.88102,0.053513,-0.47005,76.295,0.32122,-0.79711,0.51131,65.483,-0.34732,-0.60146,-0.71945,340
> view matrix models
> #5,0.70511,-0.017585,-0.70888,133.44,0.53334,-0.64565,0.54652,12.919,-0.4673,-0.76343,-0.44588,350.76,#6,0.70511,-0.017585,-0.70888,133.44,0.53334,-0.64565,0.54652,12.919,-0.4673,-0.76343,-0.44588,350.76
> view matrix models
> #5,0.4256,0.21742,-0.87841,155.01,0.78978,-0.56308,0.24329,-1.9542,-0.44172,-0.79729,-0.41136,348.58,#6,0.4256,0.21742,-0.87841,155.01,0.78978,-0.56308,0.24329,-1.9542,-0.44172,-0.79729,-0.41136,348.58
> view matrix models
> #5,0.48908,0.3212,-0.81094,125.48,0.72939,-0.66045,0.17831,26.035,-0.47831,-0.67871,-0.55729,351.71,#6,0.48908,0.3212,-0.81094,125.48,0.72939,-0.66045,0.17831,26.035,-0.47831,-0.67871,-0.55729,351.71
> view matrix models
> #5,0.022261,0.83894,-0.54376,88.852,0.8575,-0.29565,-0.42105,18.926,-0.514,-0.4569,-0.72598,342.74,#6,0.022261,0.83894,-0.54376,88.852,0.8575,-0.29565,-0.42105,18.926,-0.514,-0.4569,-0.72598,342.74
> view matrix models
> #5,0.0279,0.83871,-0.54386,88.146,0.83135,-0.32157,-0.45327,29.212,-0.55505,-0.43949,-0.70624,343.78,#6,0.0279,0.83871,-0.54386,88.146,0.83135,-0.32157,-0.45327,29.212,-0.55505,-0.43949,-0.70624,343.78
> view matrix models
> #5,0.28221,0.6148,-0.73647,104.8,0.79419,-0.58035,-0.18016,42.437,-0.53817,-0.53405,-0.65205,349.17,#6,0.28221,0.6148,-0.73647,104.8,0.79419,-0.58035,-0.18016,42.437,-0.53817,-0.53405,-0.65205,349.17
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.28221,0.6148,-0.73647,115.59,0.79419,-0.58035,-0.18016,95.64,-0.53817,-0.53405,-0.65205,329.17,#6,0.28221,0.6148,-0.73647,115.59,0.79419,-0.58035,-0.18016,95.64,-0.53817,-0.53405,-0.65205,329.17
> view matrix models
> #5,0.28221,0.6148,-0.73647,115.32,0.79419,-0.58035,-0.18016,108.36,-0.53817,-0.53405,-0.65205,330.05,#6,0.28221,0.6148,-0.73647,115.32,0.79419,-0.58035,-0.18016,108.36,-0.53817,-0.53405,-0.65205,330.05
> view matrix models
> #5,0.28221,0.6148,-0.73647,112.46,0.79419,-0.58035,-0.18016,104.64,-0.53817,-0.53405,-0.65205,341.06,#6,0.28221,0.6148,-0.73647,112.46,0.79419,-0.58035,-0.18016,104.64,-0.53817,-0.53405,-0.65205,341.06
> view matrix models
> #5,0.28221,0.6148,-0.73647,114.38,0.79419,-0.58035,-0.18016,106.2,-0.53817,-0.53405,-0.65205,340.36,#6,0.28221,0.6148,-0.73647,114.38,0.79419,-0.58035,-0.18016,106.2,-0.53817,-0.53405,-0.65205,340.36
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.33089,0.8519,-0.40593,41.921,0.88293,-0.43132,-0.18548,74.388,-0.3331,-0.29703,-0.89488,304.87,#6,0.33089,0.8519,-0.40593,41.921,0.88293,-0.43132,-0.18548,74.388,-0.3331,-0.29703,-0.89488,304.87
> view matrix models
> #5,0.28288,0.84484,-0.45412,54.101,0.85492,-0.43673,-0.27994,88.344,-0.43484,-0.30905,-0.84581,315.07,#6,0.28288,0.84484,-0.45412,54.101,0.85492,-0.43673,-0.27994,88.344,-0.43484,-0.30905,-0.84581,315.07
> view matrix models
> #5,0.19656,0.94363,-0.26631,32.985,0.89298,-0.28445,-0.34882,69.181,-0.40491,-0.16925,-0.89856,297.08,#6,0.19656,0.94363,-0.26631,32.985,0.89298,-0.28445,-0.34882,69.181,-0.40491,-0.16925,-0.89856,297.08
> view matrix models
> #5,0.12085,0.91107,-0.39415,60.37,0.8769,-0.28407,-0.38776,75.176,-0.46524,-0.29877,-0.83324,316.41,#6,0.12085,0.91107,-0.39415,60.37,0.8769,-0.28407,-0.38776,75.176,-0.46524,-0.29877,-0.83324,316.41
> view matrix models
> #5,0.080495,0.93772,-0.33792,56.373,0.88898,-0.22088,-0.40117,66.189,-0.45082,-0.26812,-0.85139,312.09,#6,0.080495,0.93772,-0.33792,56.373,0.88898,-0.22088,-0.40117,66.189,-0.45082,-0.26812,-0.85139,312.09
> view matrix models
> #5,0.21097,0.89961,-0.38236,48.834,0.94101,-0.29278,-0.16963,45.951,-0.26455,-0.32402,-0.90831,300.87,#6,0.21097,0.89961,-0.38236,48.834,0.94101,-0.29278,-0.16963,45.951,-0.26455,-0.32402,-0.90831,300.87
> view matrix models
> #5,0.30829,0.86047,-0.40564,43.697,0.90636,-0.39519,-0.14947,62.669,-0.28892,-0.32157,-0.90173,303.1,#6,0.30829,0.86047,-0.40564,43.697,0.90636,-0.39519,-0.14947,62.669,-0.28892,-0.32157,-0.90173,303.1
> view matrix models
> #5,0.28081,0.90014,-0.33302,34.55,0.9053,-0.36364,-0.21954,65.495,-0.31871,-0.23983,-0.91701,297.28,#6,0.28081,0.90014,-0.33302,34.55,0.9053,-0.36364,-0.21954,65.495,-0.31871,-0.23983,-0.91701,297.28
> volume #1 level 0.159
> volume #1 level 0.1182
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1365_004_volume_map.mrc
Opened cryosparc_P380_J1365_004_volume_map.mrc as #7, grid size 180,180,180,
pixel 1.45, shown at level 0.362, step 1, values float32
> volume #7 level 0.1284
> volume #7 level 0.1793
> volume #7 level 0.2896
> view matrix models
> #5,0.41974,-0.15502,-0.89431,218.46,0.8749,0.33137,0.35319,-84.152,0.2416,-0.93068,0.27471,198.73,#6,0.41974,-0.15502,-0.89431,218.46,0.8749,0.33137,0.35319,-84.152,0.2416,-0.93068,0.27471,198.73
> view matrix models
> #5,0.72441,-0.26148,-0.63786,167.04,-0.031592,-0.93689,0.34819,211.7,-0.68865,-0.23208,-0.68695,322.06,#6,0.72441,-0.26148,-0.63786,167.04,-0.031592,-0.93689,0.34819,211.7,-0.68865,-0.23208,-0.68695,322.06
> view matrix models
> #5,0.73963,-0.30322,-0.60084,167.07,0.051974,-0.86436,0.50018,175.32,-0.67101,-0.40118,-0.62354,336.72,#6,0.73963,-0.30322,-0.60084,167.07,0.051974,-0.86436,0.50018,175.32,-0.67101,-0.40118,-0.62354,336.72
> view matrix models
> #5,0.68462,-0.13364,-0.71654,162.55,0.18206,-0.92054,0.34563,181.4,-0.7058,-0.36708,-0.60589,334.84,#6,0.68462,-0.13364,-0.71654,162.55,0.18206,-0.92054,0.34563,181.4,-0.7058,-0.36708,-0.60589,334.84
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.68462,-0.13364,-0.71654,158.64,0.18206,-0.92054,0.34563,183.38,-0.7058,-0.36708,-0.60589,331.6,#6,0.68462,-0.13364,-0.71654,158.64,0.18206,-0.92054,0.34563,183.38,-0.7058,-0.36708,-0.60589,331.6
> view matrix models
> #5,0.68462,-0.13364,-0.71654,158.7,0.18206,-0.92054,0.34563,181.47,-0.7058,-0.36708,-0.60589,336.28,#6,0.68462,-0.13364,-0.71654,158.7,0.18206,-0.92054,0.34563,181.47,-0.7058,-0.36708,-0.60589,336.28
> view matrix models
> #5,0.68462,-0.13364,-0.71654,157.18,0.18206,-0.92054,0.34563,182.74,-0.7058,-0.36708,-0.60589,335.8,#6,0.68462,-0.13364,-0.71654,157.18,0.18206,-0.92054,0.34563,182.74,-0.7058,-0.36708,-0.60589,335.8
> view matrix models
> #5,0.68462,-0.13364,-0.71654,157.09,0.18206,-0.92054,0.34563,182.13,-0.7058,-0.36708,-0.60589,335.57,#6,0.68462,-0.13364,-0.71654,157.09,0.18206,-0.92054,0.34563,182.13,-0.7058,-0.36708,-0.60589,335.57
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.59376,-0.24812,-0.76543,189.87,0.1009,-0.9208,0.37676,189.78,-0.79829,-0.30094,-0.5217,330.21,#6,0.59376,-0.24812,-0.76543,189.87,0.1009,-0.9208,0.37676,189.78,-0.79829,-0.30094,-0.5217,330.21
> view matrix models
> #5,0.61761,-0.2918,-0.73035,189.22,0.0084415,-0.92612,0.37715,202.72,-0.78644,-0.23909,-0.56951,324.9,#6,0.61761,-0.2918,-0.73035,189.22,0.0084415,-0.92612,0.37715,202.72,-0.78644,-0.23909,-0.56951,324.9
> view matrix models
> #5,0.039811,-0.4937,-0.86872,307.55,0.42727,-0.7775,0.46144,118.24,-0.90325,-0.38955,0.17999,285.78,#6,0.039811,-0.4937,-0.86872,307.55,0.42727,-0.7775,0.46144,118.24,-0.90325,-0.38955,0.17999,285.78
> view matrix models
> #5,0.7274,0.026358,-0.68571,126.21,0.28383,-0.92133,0.26567,176.8,-0.62476,-0.38788,-0.67766,334.93,#6,0.7274,0.026358,-0.68571,126.21,0.28383,-0.92133,0.26567,176.8,-0.62476,-0.38788,-0.67766,334.93
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.7274,0.026358,-0.68571,126.83,0.28383,-0.92133,0.26567,178.71,-0.62476,-0.38788,-0.67766,334.77,#6,0.7274,0.026358,-0.68571,126.83,0.28383,-0.92133,0.26567,178.71,-0.62476,-0.38788,-0.67766,334.77
> view matrix models
> #5,0.7274,0.026358,-0.68571,127.21,0.28383,-0.92133,0.26567,178.4,-0.62476,-0.38788,-0.67766,335.59,#6,0.7274,0.026358,-0.68571,127.21,0.28383,-0.92133,0.26567,178.4,-0.62476,-0.38788,-0.67766,335.59
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.84906,-0.10724,-0.5173,112.63,0.026518,-0.96929,0.24447,221.24,-0.52763,-0.22129,-0.82015,314.03,#6,0.84906,-0.10724,-0.5173,112.63,0.026518,-0.96929,0.24447,221.24,-0.52763,-0.22129,-0.82015,314.03
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.84906,-0.10724,-0.5173,110.65,0.026518,-0.96929,0.24447,220.64,-0.52763,-0.22129,-0.82015,317.52,#6,0.84906,-0.10724,-0.5173,110.65,0.026518,-0.96929,0.24447,220.64,-0.52763,-0.22129,-0.82015,317.52
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.51218,-0.55776,-0.65313,231.19,-0.13099,-0.80227,0.58241,184.42,-0.84883,-0.21275,-0.48397,325.06,#6,0.51218,-0.55776,-0.65313,231.19,-0.13099,-0.80227,0.58241,184.42,-0.84883,-0.21275,-0.48397,325.06
> view matrix models
> #5,0.55986,-0.42804,-0.70946,212.61,0.075585,-0.82628,0.55816,162.82,-0.82513,-0.36612,-0.43025,337.72,#6,0.55986,-0.42804,-0.70946,212.61,0.075585,-0.82628,0.55816,162.82,-0.82513,-0.36612,-0.43025,337.72
> vop resample #6 ongrid #7
Opened dn82Rip1_1kb9.pdb map 10 resampled as #8, grid size 180,180,180, pixel
1.45, shown at step 1, values float32
> close #6
> select add #8
1026 atoms, 1053 bonds, 4 pseudobonds, 135 residues, 5 models selected
> fitmap #8 inMap #7
Fit map dn82Rip1_1kb9.pdb map 10 resampled in map
cryosparc_P380_J1365_004_volume_map.mrc using 1829 points
correlation = 0.9198, correlation about mean = 0.3853, overlap = 195.5
steps = 228, shift = 13.8, angle = 86.5 degrees
Position of dn82Rip1_1kb9.pdb map 10 resampled (#8) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.64538348 0.71151089 0.27790722 -50.28461150
0.06006777 0.31542036 -0.94704903 203.63106504
-0.76149329 0.62790306 0.16082822 162.06990588
Axis 0.78893637 0.52066401 -0.32632559
Axis point 0.00000000 6.28600024 203.07010241
Rotation angle (degrees) 86.51334659
Shift along axis 13.46444974
> undo
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.2044, steps = 72
shifted from previous position = 8.76
rotated from previous position = 12.3 degrees
atoms outside contour = 739, contour level = 0.28964
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.91145451 0.01556008 -0.41110655 81.35580411
0.05744679 -0.99430800 0.08973010 228.58095280
-0.40737032 -0.10540166 -0.90716037 294.17667277
Axis -0.97755636 -0.01871749 0.20984092
Axis point 0.00000000 121.15760986 149.98179556
Rotation angle (degrees) 174.27200721
Shift along axis -22.07804305
> view matrix models
> #5,0.50792,-0.30752,-0.80464,219.03,0.31523,-0.80295,0.50586,126.14,-0.80165,-0.51059,-0.3109,342.43
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.50792,-0.30752,-0.80464,215.01,0.31523,-0.80295,0.50586,134.54,-0.80165,-0.51059,-0.3109,338.43
> view matrix models
> #5,0.50792,-0.30752,-0.80464,213.55,0.31523,-0.80295,0.50586,132.85,-0.80165,-0.51059,-0.3109,340.49
> view matrix models
> #5,0.50792,-0.30752,-0.80464,212.58,0.31523,-0.80295,0.50586,134.12,-0.80165,-0.51059,-0.3109,339.51
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.68038,-0.41326,-0.60523,184.31,-0.015122,-0.83358,0.55219,177.44,-0.7327,-0.36655,-0.5734,336.87
> view matrix models
> #5,0.46909,-0.53392,-0.70348,238.85,0.35481,-0.61551,0.70374,83.065,-0.80874,-0.57972,-0.099291,328.73
> volume #7 level 0.1866
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.1965, steps = 100
shifted from previous position = 4.8
rotated from previous position = 32.2 degrees
atoms outside contour = 476, contour level = 0.18665
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.28067994 -0.18036278 -0.94270252 242.84724452
0.75200422 -0.56899665 0.33276491 63.60124534
-0.59641298 -0.80231671 -0.02407237 322.25238392
Axis -0.75211635 -0.22945489 0.61779564
Axis point 0.00000000 92.01912888 241.47241752
Rotation angle (degrees) 131.01028827
Shift along axis 1.84311598
> volume #7 level 0.3601
> volume #7 level 0.23
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.1965, steps = 48
shifted from previous position = 0.03
rotated from previous position = 0.0361 degrees
atoms outside contour = 560, contour level = 0.23001
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.28126895 -0.18022319 -0.94255366 242.72144095
0.75194556 -0.56884494 0.33315661 63.53100383
-0.59620942 -0.80245564 -0.02448039 322.30204666
Axis -0.75232377 -0.22944716 0.61754591
Axis point 0.00000000 92.02935354 241.39800605
Rotation angle (degrees) 130.99765869
Shift along axis 1.85419388
> view matrix models
> #5,-0.36946,0.87741,-0.30601,118.67,-0.34372,0.17692,0.92226,46.28,0.86334,0.44592,0.23622,-69.749
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.2195, steps = 328
shifted from previous position = 11.8
rotated from previous position = 81.7 degrees
atoms outside contour = 568, contour level = 0.23001
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.81230932 0.57386616 0.10407300 -29.29072289
-0.44770256 0.49918214 0.74187574 33.45650193
0.37378600 -0.64922633 0.66241165 94.24638394
Axis -0.79634527 -0.15439893 -0.58480354
Axis point 0.00000000 97.20694793 28.21550835
Rotation angle (degrees) 60.85958773
Shift along axis -36.95573903
> volume #7 level 0.5661
> volume #7 level 0.2625
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.81231,0.57387,0.10407,-42.319,-0.4477,0.49918,0.74188,40.929,0.37379,-0.64923,0.66241,93.692
> view matrix models
> #5,0.81231,0.57387,0.10407,-37.196,-0.4477,0.49918,0.74188,38.258,0.37379,-0.64923,0.66241,102.78
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.63584,0.39011,-0.66598,89.02,0.72247,-0.60442,0.33573,76.706,-0.27156,-0.69462,-0.66615,328.12
> view matrix models
> #5,0.60443,0.21395,-0.76739,127.73,0.76086,-0.44052,0.47648,34.811,-0.2361,-0.87188,-0.42905,324.08
> view matrix models
> #5,0.30867,0.78132,-0.54246,65.842,0.94422,-0.18291,0.27383,-4.6979,0.11473,-0.59673,-0.7942,276.32
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.30867,0.78132,-0.54246,70.633,0.94422,-0.18291,0.27383,-8.9517,0.11473,-0.59673,-0.7942,275.19
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.30867,0.78132,-0.54246,63.861,0.94422,-0.18291,0.27383,-8.3377,0.11473,-0.59673,-0.7942,274.7
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.29984,0.26478,-0.91651,174.05,0.94376,-0.22264,0.24443,0.17349,-0.13933,-0.93826,-0.31664,307.52
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.1967, steps = 112
shifted from previous position = 5.09
rotated from previous position = 32.3 degrees
atoms outside contour = 640, contour level = 0.26254
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.44864176 -0.08708017 -0.88945916 203.50881235
0.88679756 0.16693402 0.43095601 -63.21654100
0.11095327 -0.98211510 0.15211606 232.01096575
Axis -0.71135055 -0.50361509 0.49025732
Axis point -0.00000000 41.22039643 225.41746826
Rotation angle (degrees) 96.67019529
Shift along axis 0.81577319
> close #8
> volume #7 level 0.2137
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.1967, steps = 60
shifted from previous position = 0.00126
rotated from previous position = 0.0145 degrees
atoms outside contour = 525, contour level = 0.21375
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.44882672 -0.08716291 -0.88935774 203.48509373
0.88669818 0.16706035 0.43111152 -63.23655642
0.11099948 -0.98208628 0.15226834 231.98661051
Axis -0.71139493 -0.50357356 0.49023558
Axis point 0.00000000 41.23951085 225.40948751
Rotation angle (degrees) 96.65682456
Shift along axis 0.81408511
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.1967, steps = 40
shifted from previous position = 0.0104
rotated from previous position = 0.0213 degrees
atoms outside contour = 524, contour level = 0.21375
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.44892040 -0.08746795 -0.88928050 203.50396553
0.88664936 0.16723838 0.43114291 -63.26404265
0.11101064 -0.98202885 0.15263013 231.93461330
Axis -0.71135539 -0.50352159 0.49034633
Axis point 0.00000000 41.24285037 225.44007238
Rotation angle (degrees) 96.63855329
Shift along axis 0.81945617
Average map value = 0.1967 for 1026 atoms, 524 outside contour
> fitmap #5 inMap #7
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1365_004_volume_map.mrc (#7) using 1026 atoms
average map value = 0.1967, steps = 60
shifted from previous position = 0.0305
rotated from previous position = 0.0643 degrees
atoms outside contour = 526, contour level = 0.21375
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1365_004_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.44804251 -0.08727816 -0.88974177 203.63666449
0.88712756 0.16667644 0.43037615 -63.14713216
0.11073656 -0.98214127 0.15210499 232.03589538
Axis -0.71110822 -0.50367404 0.49054822
Axis point 0.00000000 41.17579832 225.49004987
Rotation angle (degrees) 96.69522882
Shift along axis 0.82266151
> volume #7 level 0.4414
> volume #7 level 0.2788
> view matrix models
> #5,0.74511,-0.17925,-0.6424,152.14,0.27912,-0.79099,0.54446,138.27,-0.60572,-0.58499,-0.53934,341.55
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.74511,-0.17925,-0.6424,146.69,0.27912,-0.79099,0.54446,130.83,-0.60572,-0.58499,-0.53934,343.95
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.59739,-0.46751,-0.65159,207.02,0.29624,-0.62639,0.72103,88.05,-0.74523,-0.62376,-0.2357,337.24
> view matrix models
> #5,0.22781,-0.53317,-0.81476,281.45,0.60695,-0.57655,0.547,57.522,-0.76139,-0.61913,0.19227,295.7
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.22781,-0.53317,-0.81476,280.85,0.60695,-0.57655,0.547,62.782,-0.76139,-0.61913,0.19227,295.69
> view matrix models
> #5,0.22781,-0.53317,-0.81476,279.86,0.60695,-0.57655,0.547,62.171,-0.76139,-0.61913,0.19227,297.59
> volume #7 level 0.165
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1376_004_volume_map.mrc
Opened cryosparc_P380_J1376_004_volume_map.mrc as #6, grid size 180,180,180,
pixel 1.45, shown at level 0.364, step 1, values float32
> volume #6 level 0.1725
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.47871,-0.67052,0.56678,126.68,0.14623,-0.57565,-0.80451,258.98,0.86571,0.46801,-0.17752,-30.949
> view matrix models
> #5,0.66894,-0.35317,0.65405,48.843,0.37358,-0.60097,-0.70659,222.53,0.64262,0.71701,-0.27008,-26.518
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.66894,-0.35317,0.65405,56.248,0.37358,-0.60097,-0.70659,225.09,0.64262,0.71701,-0.27008,-23.039
> fitmap #5 inMap #6
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1376_004_volume_map.mrc (#6) using 1026 atoms
average map value = 0.2105, steps = 132
shifted from previous position = 3.74
rotated from previous position = 23.6 degrees
atoms outside contour = 413, contour level = 0.17248
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1376_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.84962538 -0.43509852 0.29803686 81.22192174
0.10474081 -0.41465223 -0.90393189 253.62634347
0.51688108 0.79922011 -0.30672649 -12.96220050
Axis 0.94618883 -0.12157926 0.29990861
Axis point 0.00000000 140.50966765 66.35005406
Rotation angle (degrees) 115.84109100
Shift along axis 42.12809678
> volume #6 level 0.3799
> view matrix models
> #5,0.84963,-0.4351,0.29804,75.321,0.10474,-0.41465,-0.90393,224.56,0.51688,0.79922,-0.30673,-10.566
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.16766,-0.54285,0.82292,127.73,0.43595,-0.70786,-0.55577,186.22,0.88422,0.45193,0.11798,-53.915
> view matrix models
> #5,-0.48374,0.38021,0.78831,89.872,0.26081,-0.79716,0.54453,111.09,0.83545,0.46901,0.28646,-66.763
> volume #6 level 0.1459
> volume #6 level 0.0555
> volume #6 level 0.1991
> volume #6 level 0.3054
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.48374,0.38021,0.78831,104.61,0.26081,-0.79716,0.54453,133.23,0.83545,0.46901,0.28646,-63.235
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.65338,0.20098,0.72986,157.72,0.40458,-0.72217,0.56105,102.17,0.63985,0.66187,0.39054,-74.461
> view matrix models
> #5,0.37696,-0.019137,0.92603,31.989,0.12532,0.99165,-0.03052,-38.26,-0.91771,0.12755,0.37621,207.08
> view matrix models
> #5,-0.48745,0.38177,0.78527,105.19,0.75102,-0.27543,0.60009,-9.3875,0.44538,0.88227,-0.15246,-24.564
> volume #6 level 0.1831
> volume #6 level 0.2469
> volume #6 level 0.3533
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.48745,0.38177,0.78527,100.39,0.75102,-0.27543,0.60009,-2.0602,0.44538,0.88227,-0.15246,-25.098
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.34228,0.23029,0.91094,89.462,0.84275,-0.35346,0.40601,16.1,0.41548,0.90666,-0.073097,-32.493
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.34228,0.23029,0.91094,89.676,0.84275,-0.35346,0.40601,13.608,0.41548,0.90666,-0.073097,-31.526
> volume #6 level 0.2629
> volume #6 level 0.3373
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.5371,0.48854,-0.68765,240.55,0.82439,0.47666,-0.30525,-27.175,0.17865,-0.73084,-0.65876,285.09
> view matrix models
> #5,0.26117,0.8136,-0.51947,73.002,0.77857,-0.49567,-0.38488,121.31,-0.57062,-0.30393,-0.7629,335.77
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.26117,0.8136,-0.51947,70.397,0.77857,-0.49567,-0.38488,111.96,-0.57062,-0.30393,-0.7629,331.73
> fitmap #5 inMap #6
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1376_004_volume_map.mrc (#6) using 1026 atoms
average map value = 0.2172, steps = 204
shifted from previous position = 8.03
rotated from previous position = 54.5 degrees
atoms outside contour = 807, contour level = 0.33732
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1376_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
0.86933414 0.30836016 -0.38622814 48.24318165
0.11383675 -0.88540327 -0.45066866 266.59547986
-0.48093592 0.34781470 -0.80481400 236.66600837
Axis 0.96519654 0.11448156 -0.23513743
Axis point 0.00000000 103.32675049 153.83570317
Rotation angle (degrees) 155.56644484
Shift along axis 21.43538220
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.048473,0.48963,-0.87058,193.43,0.85652,0.46876,0.21595,-85.978,0.51383,-0.73521,-0.4421,218.17
> view matrix models
> #5,0.26832,-0.51309,-0.81531,284.53,0.72853,-0.44566,0.52023,26.769,-0.63028,-0.73357,0.25422,299.41
> fitmap #5 inMap #6
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1376_004_volume_map.mrc (#6) using 1026 atoms
average map value = 0.2328, steps = 212
shifted from previous position = 8.59
rotated from previous position = 65.6 degrees
atoms outside contour = 760, contour level = 0.33732
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1376_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
-0.50154260 -0.80745682 -0.31059380 372.63418075
0.86380806 -0.48725048 -0.12815074 83.52805580
-0.04786079 -0.33256649 0.94186457 96.71754158
Axis -0.11995559 -0.15417742 0.98073441
Axis point 166.77646800 156.89227582 0.00000000
Rotation angle (degrees) 121.56491474
Shift along axis 37.27652834
> view matrix models
> #5,-0.28123,0.93215,0.22806,48.821,0.93441,0.21186,0.28635,-64.146,0.2186,0.29364,-0.93059,163.19
> view matrix models
> #5,-0.4451,0.64554,0.62062,70.656,-0.89523,-0.30423,-0.3256,311.01,-0.021377,-0.70052,0.71332,167.06
> fitmap #5 inMap #6
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1376_004_volume_map.mrc (#6) using 1026 atoms
average map value = 0.2084, steps = 172
shifted from previous position = 15.1
rotated from previous position = 22.4 degrees
atoms outside contour = 827, contour level = 0.33732
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1376_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
-0.52236405 0.67157270 0.52547684 101.27803904
-0.77025215 -0.10721803 -0.62866200 293.40421616
-0.36585165 -0.73314011 0.57328716 229.61736958
Axis -0.06151903 0.52483406 -0.84897857
Axis point 146.44326425 185.48182069 0.00000000
Rotation angle (degrees) 121.88037121
Shift along axis -47.18222741
> volume #6 level 0.3054
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.52236,0.67157,0.52548,93.178,-0.77025,-0.10722,-0.62866,302.75,-0.36585,-0.73314,0.57329,230.29
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.52236,0.67157,0.52548,92.349,-0.77025,-0.10722,-0.62866,228.72,-0.36585,-0.73314,0.57329,231.64
> volume #6 level 0.231
> volume #7 level 0.4035
> volume #3 level 0.3062
> volume #3 level 0.1778
> view matrix models
> #5,-0.52236,0.67157,0.52548,92.982,-0.77025,-0.10722,-0.62866,227.32,-0.36585,-0.73314,0.57329,219.42
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.24903,0.04907,-0.96725,227.01,-0.95264,0.19238,-0.23551,170.52,0.17452,0.98009,0.094654,-40.816
> view matrix models
> #5,0.33154,-0.24992,-0.90974,251.63,-0.91802,-0.30779,-0.25001,236.53,-0.21753,0.91804,-0.33147,62.532
> view matrix models
> #5,-0.24965,0.095292,-0.96363,286.3,0.96642,0.086996,-0.24177,-68.401,0.060793,-0.99164,-0.11381,267.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.24965,0.095292,-0.96363,277.49,0.96642,0.086996,-0.24177,-88.889,0.060793,-0.99164,-0.11381,263.8
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.25762,-0.14743,-0.95493,243,0.96477,0.093954,0.24576,-138.67,0.053487,-0.9846,0.16644,235.6
> molmap #5 10
Opened dn82Rip1_1kb9.pdb map 10 as #8, grid size 27,32,32, pixel 3.33, shown
at level 0.0462, step 1, values float32
> volume #8 level 0.3007
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #8
1026 atoms, 1053 bonds, 4 pseudobonds, 135 residues, 4 models selected
> view matrix models
> #5,0.95463,-0.20779,-0.21332,84.445,-0.043556,-0.80605,0.59024,84.573,-0.29459,-0.55417,-0.77854,317.18,#8,0.95463,-0.20779,-0.21332,84.445,-0.043556,-0.80605,0.59024,84.573,-0.29459,-0.55417,-0.77854,317.18
> view matrix models
> #5,0.12074,0.25439,-0.95954,206.03,-0.44291,-0.85126,-0.28141,231.31,-0.8884,0.45896,0.0098922,176.48,#8,0.12074,0.25439,-0.95954,206.03,-0.44291,-0.85126,-0.28141,231.31,-0.8884,0.45896,0.0098922,176.48
> view matrix models
> #5,-0.31156,0.31248,-0.89738,248.99,-0.76145,-0.64705,0.039056,213.03,-0.56844,0.69547,0.43954,58.21,#8,-0.31156,0.31248,-0.89738,248.99,-0.76145,-0.64705,0.039056,213.03,-0.56844,0.69547,0.43954,58.21
> volume #8 level 0.3198
> view matrix models
> #5,0.58844,-0.07312,-0.80523,173.86,0.56334,-0.67732,0.47318,-1.869,-0.57999,-0.73205,-0.35737,337.21,#8,0.58844,-0.07312,-0.80523,173.86,0.56334,-0.67732,0.47318,-1.869,-0.57999,-0.73205,-0.35737,337.21
> view matrix models
> #5,-0.031384,0.61157,-0.79056,159.81,-0.98284,-0.16274,-0.086879,188.07,-0.18179,0.77427,0.60619,-20.644,#8,-0.031384,0.61157,-0.79056,159.81,-0.98284,-0.16274,-0.086879,188.07,-0.18179,0.77427,0.60619,-20.644
> volume #8 level 0.3485
> view matrix models
> #5,-0.027677,0.57791,-0.81563,166.49,-0.86726,-0.41963,-0.2679,226.48,-0.49709,0.69995,0.51281,40.77,#8,-0.027677,0.57791,-0.81563,166.49,-0.86726,-0.41963,-0.2679,226.48,-0.49709,0.69995,0.51281,40.77
> view matrix models
> #5,-0.016236,0.55444,-0.83207,169.87,-0.72008,-0.58384,-0.37499,240.46,-0.6937,0.59306,0.40872,92.049,#8,-0.016236,0.55444,-0.83207,169.87,-0.72008,-0.58384,-0.37499,240.46,-0.6937,0.59306,0.40872,92.049
> view matrix models
> #5,-0.030408,0.58865,-0.80782,164.58,-0.91577,-0.34027,-0.21348,216.46,-0.40054,0.73328,0.54942,19.697,#8,-0.030408,0.58865,-0.80782,164.58,-0.91577,-0.34027,-0.21348,216.46,-0.40054,0.73328,0.54942,19.697
> volume #8 level 0.3262
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.6185,0.27991,-0.73424,113.94,0.60004,-0.77155,0.21132,32.633,-0.50736,-0.57128,-0.64516,334.31,#8,0.6185,0.27991,-0.73424,113.94,0.60004,-0.77155,0.21132,32.633,-0.50736,-0.57128,-0.64516,334.31
> view matrix models
> #5,0.21063,-0.56236,-0.79962,290.94,0.20006,-0.77586,0.59835,47.268,-0.95688,-0.286,-0.050918,294.64,#8,0.21063,-0.56236,-0.79962,290.94,0.20006,-0.77586,0.59835,47.268,-0.95688,-0.286,-0.050918,294.64
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.21063,-0.56236,-0.79962,275.99,0.20006,-0.77586,0.59835,81.451,-0.95688,-0.286,-0.050918,289.99,#8,0.21063,-0.56236,-0.79962,275.99,0.20006,-0.77586,0.59835,81.451,-0.95688,-0.286,-0.050918,289.99
> view matrix models
> #5,0.21063,-0.56236,-0.79962,284.15,0.20006,-0.77586,0.59835,127.27,-0.95688,-0.286,-0.050918,302.77,#8,0.21063,-0.56236,-0.79962,284.15,0.20006,-0.77586,0.59835,127.27,-0.95688,-0.286,-0.050918,302.77
[deleted to fit within ticket size limits]
> view matrix models
> #5,0.49571,-0.71831,-0.48815,239.94,-0.42693,-0.69102,0.58329,208.61,-0.7563,-0.080736,-0.64922,317.22,#8,0.83451,-0.44151,-0.32964,141.7,0.16357,-0.37278,0.91339,46.894,-0.52615,-0.81615,-0.23887,340.32
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.49571,-0.71831,-0.48815,232.87,-0.42693,-0.69102,0.58329,215.8,-0.7563,-0.080736,-0.64922,313.68,#8,0.83451,-0.44151,-0.32964,134.62,0.16357,-0.37278,0.91339,54.09,-0.52615,-0.81615,-0.23887,336.78
> fitmap #8 inMap #1
Fit map dn82Rip1_1kb9.pdb map 8 in map cryosparc_P380_J1382_011_volume_map.mrc
using 445 points
correlation = 0.8638, correlation about mean = 0.09619, overlap = 18.47
steps = 164, shift = 6.14, angle = 25 degrees
Position of dn82Rip1_1kb9.pdb map 8 (#8) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.68373402 -0.48070674 -0.54902537 187.01708710
0.08710191 -0.69322648 0.71543712 125.76882024
-0.72451440 -0.53698987 -0.43211207 346.03699076
Axis -0.90344348 0.12658975 0.40959115
Axis point 0.00000000 154.15937775 187.05607395
Rotation angle (degrees) 136.12075618
Shift along axis -11.30463476
> view matrix models
> #5,0.49571,-0.71831,-0.48815,231.73,-0.42693,-0.69102,0.58329,222.23,-0.7563,-0.080736,-0.64922,311.89,#8,0.68373,-0.48071,-0.54903,185.88,0.087102,-0.69323,0.71544,132.2,-0.72451,-0.53699,-0.43211,344.24
> close #8
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 1026 atoms
average map value = 0.09645, steps = 160
shifted from previous position = 15.3
rotated from previous position = 35.9 degrees
atoms outside contour = 533, contour level = 0.10149
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.09141473 -0.98386232 -0.15381263 300.76531611
-0.74647576 -0.16993616 0.64334721 180.32438530
-0.65910345 0.05600597 -0.74996401 294.49200508
Axis -0.72481392 0.62355883 0.29294909
Axis point 0.00000000 263.36012967 179.94154891
Rotation angle (degrees) 156.09841228
Shift along axis -19.28485847
> volume #1 level 0.1072
> view matrix models
> #5,0.091415,-0.98386,-0.15381,286.45,-0.74648,-0.16994,0.64335,182.45,-0.6591,0.056006,-0.74996,290.74
> view matrix models
> #5,0.091415,-0.98386,-0.15381,285.62,-0.74648,-0.16994,0.64335,187.64,-0.6591,0.056006,-0.74996,290.36
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.30542,-0.81238,-0.49674,268.07,0.25531,-0.4327,0.86463,69.048,-0.91735,-0.3909,0.075259,303.33
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.30542,-0.81238,-0.49674,267.27,0.25531,-0.4327,0.86463,61.384,-0.91735,-0.3909,0.075259,302.93
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 1026 atoms
average map value = 0.1091, steps = 196
shifted from previous position = 15.5
rotated from previous position = 18.5 degrees
atoms outside contour = 523, contour level = 0.10718
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.00307829 -0.88796951 -0.45989207 317.56494112
0.29472218 -0.44027252 0.84811493 45.22265414
-0.95557806 -0.13292963 0.26305955 262.01747172
Axis -0.60761081 0.30700355 0.73250114
Axis point 253.15051122 80.46044704 0.00000000
Rotation angle (degrees) 126.16734284
Shift along axis 12.85572175
> view matrix models
> #5,-0.0030783,-0.88797,-0.45989,318.82,0.29472,-0.44027,0.84811,56.363,-0.95558,-0.13293,0.26306,252.6
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.38482,-0.8772,-0.2871,248.59,-0.21485,-0.38764,0.89642,111.71,-0.89764,-0.28328,-0.33764,326.13
> view matrix models
> #5,0.34787,-0.91698,-0.19528,249.75,-0.39624,-0.33257,0.8558,132.2,-0.8497,-0.22033,-0.47903,325.3
> view matrix models
> #5,0.2316,-0.55984,-0.79557,276.15,0.13622,-0.79109,0.59634,151.17,-0.96323,-0.24648,-0.10696,306.53
> view matrix models
> #5,-0.01599,-0.31519,-0.94889,290.53,0.56718,-0.78441,0.251,127.91,-0.82344,-0.53418,0.19131,297.79
> view matrix models
> #5,0.49189,-0.3791,-0.78379,215.51,-0.18803,-0.92524,0.32952,239.48,-0.85011,-0.014713,-0.5264,301.69
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.49189,-0.3791,-0.78379,216.1,-0.18803,-0.92524,0.32952,238.39,-0.85011,-0.014713,-0.5264,306.78
> view matrix models
> #5,0.49189,-0.3791,-0.78379,217.8,-0.18803,-0.92524,0.32952,237.04,-0.85011,-0.014713,-0.5264,304.37
> view matrix models
> #5,0.49189,-0.3791,-0.78379,217.57,-0.18803,-0.92524,0.32952,236.69,-0.85011,-0.014713,-0.5264,304.3
> view matrix models
> #5,0.49189,-0.3791,-0.78379,217.3,-0.18803,-0.92524,0.32952,237.88,-0.85011,-0.014713,-0.5264,304.44
> volume #1 level 0.08441
> view matrix models
> #5,0.49189,-0.3791,-0.78379,218.18,-0.18803,-0.92524,0.32952,236.85,-0.85011,-0.014713,-0.5264,305.09
> volume #1 level 0.07302
> select #5:start-94
89 atoms, 88 bonds, 13 residues, 1 model selected
> select #5:start-92
73 atoms, 72 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #5
953 atoms, 980 bonds, 4 pseudobonds, 124 residues, 2 models selected
> view matrix models
> #5,0.49189,-0.3791,-0.78379,217.8,-0.18803,-0.92524,0.32952,236.54,-0.85011,-0.014713,-0.5264,304.59
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 953 atoms
average map value = 0.09817, steps = 236
shifted from previous position = 9.41
rotated from previous position = 17.1 degrees
atoms outside contour = 316, contour level = 0.073024
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.47178708 -0.56919746 -0.67337303 244.25554908
-0.12242894 -0.79860243 0.58927522 183.49262914
-0.87317133 -0.19557210 -0.44645655 322.71377660
Axis -0.84854221 0.21601309 0.48302636
Axis point 0.00000000 170.26884623 204.00691899
Rotation angle (degrees) 152.45351869
Shift along axis -11.74507129
> volume #1 level 0.09769
> view matrix models
> #5,0.47179,-0.5692,-0.67337,241.11,-0.12243,-0.7986,0.58928,186.37,-0.87317,-0.19557,-0.44646,322.95
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 953 atoms
average map value = 0.09817, steps = 84
shifted from previous position = 4.27
rotated from previous position = 0.00298 degrees
atoms outside contour = 460, contour level = 0.097694
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.47177479 -0.56921685 -0.67336525 244.25972690
-0.12247928 -0.79859915 0.58926921 183.49680676
-0.87317091 -0.19552908 -0.44647622 322.71259129
Axis -0.84853962 0.21603388 0.48302160
Axis point 0.00000000 170.27136144 204.00811319
Rotation angle (degrees) 152.45529480
Shift along axis -11.74537564
> view matrix models
> #5,0.47177,-0.56922,-0.67337,237.67,-0.12248,-0.7986,0.58927,188.24,-0.87317,-0.19553,-0.44648,320.98
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 953 atoms
average map value = 0.1005, steps = 168
shifted from previous position = 8.27
rotated from previous position = 21.5 degrees
atoms outside contour = 422, contour level = 0.097694
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.27269656 -0.77343500 -0.57221931 284.26814591
-0.00589100 -0.59609183 0.80289463 117.26721685
-0.96208209 -0.21557566 -0.16710852 310.35872026
Axis -0.76371940 0.29234605 0.57555753
Axis point 0.00000000 191.27401390 232.65689288
Rotation angle (degrees) 138.18073895
Shift along axis -4.18918998
> view matrix models
> #5,0.2727,-0.77343,-0.57222,281.6,-0.005891,-0.59609,0.80289,118.8,-0.96208,-0.21558,-0.16711,305.5
> view matrix models
> #5,0.2727,-0.77343,-0.57222,281.23,-0.005891,-0.59609,0.80289,117.63,-0.96208,-0.21558,-0.16711,306.59
> view matrix models
> #5,0.2727,-0.77343,-0.57222,282.62,-0.005891,-0.59609,0.80289,119.18,-0.96208,-0.21558,-0.16711,306.07
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.31146,-0.80365,-0.50708,275.19,0.2756,-0.43429,0.85757,55.179,-0.90941,-0.40686,0.086223,299.94
> view matrix models
> #5,0.042878,-0.7318,-0.68016,317.98,0.44657,-0.59496,0.66828,72.138,-0.89372,-0.3324,0.30129,267.19
> view matrix models
> #5,0.69201,-0.29749,-0.65774,172.3,0.1416,-0.8375,0.52777,158.25,-0.70786,-0.45836,-0.53744,340.4
> view matrix models
> #5,0.7248,-0.5266,-0.44425,177.67,0.16326,-0.49517,0.85332,78.534,-0.66934,-0.69101,-0.27293,340.54
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.7248,-0.5266,-0.44425,177.46,0.16326,-0.49517,0.85332,76.941,-0.66934,-0.69101,-0.27293,342.33
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 953 atoms
average map value = 0.1013, steps = 120
shifted from previous position = 1.97
rotated from previous position = 20.5 degrees
atoms outside contour = 412, contour level = 0.097694
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.45052126 -0.74128276 -0.49752437 248.13107172
0.10439351 -0.50971941 0.85398365 85.22753113
-0.88664122 -0.43667610 -0.15225435 327.17471662
Axis -0.81104898 0.24452054 0.53142192
Axis point 0.00000000 181.02548179 218.35462966
Rotation angle (degrees) 127.28112016
Shift along axis -6.53875555
> view matrix models
> #5,0.45052,-0.74128,-0.49752,249.23,0.10439,-0.50972,0.85398,85.073,-0.88664,-0.43668,-0.15225,325.89
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.41132,-0.82482,0.38793,179.84,0.11977,-0.373,-0.92007,236.52,0.90359,0.4249,-0.054632,-34.765
> view matrix models
> #5,-0.50161,-0.56615,0.65411,240.71,0.33095,-0.82418,-0.45957,223.79,0.79929,-0.01405,0.60078,-26.187
> view matrix models
> #5,-0.65051,0.16782,0.74072,154.8,-0.44896,-0.87161,-0.19681,307.94,0.61259,-0.46058,0.64234,53.681
> view matrix models
> #5,-0.49122,-0.40463,-0.77135,355.81,0.66249,0.40139,-0.63245,34.226,0.56551,-0.82169,0.07089,163.04
> view matrix models
> #5,0.95297,-0.21992,0.2085,45.325,-0.12111,0.35432,0.92725,-6.64,-0.2778,-0.9089,0.31102,263.03
> view matrix models
> #5,0.18491,-0.51024,0.83992,124.42,-0.97924,-0.023447,0.20134,227.26,-0.083037,-0.85971,-0.50399,309.56
> view matrix models
> #5,0.33284,-0.51364,0.79081,110.03,0.12302,0.85511,0.50363,-64.348,-0.93492,-0.070345,0.34781,235.38
> view matrix models
> #5,0.33462,0.58596,0.73802,-30.794,0.94227,-0.2183,-0.25391,42.673,0.012331,0.78038,-0.62518,91.338
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 953 atoms
average map value = 0.1127, steps = 232
shifted from previous position = 11.8
rotated from previous position = 55.2 degrees
atoms outside contour = 383, contour level = 0.097694
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.82480691 0.10637095 0.55531868 -17.31714423
0.31720749 -0.90007611 -0.29873473 211.16554371
0.46805237 0.42254968 -0.77613058 97.11127733
Axis 0.95342732 0.11535267 0.27869356
Axis point 0.00000000 97.62911319 72.42408618
Rotation angle (degrees) 157.77413373
Shift along axis 34.91215878
> view matrix models
> #5,0.21087,-0.70945,0.67247,160.74,-0.53149,0.49416,0.68799,43.367,-0.8204,-0.50248,-0.27286,341.61
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.21087,-0.70945,0.67247,160.03,-0.53149,0.49416,0.68799,61.253,-0.8204,-0.50248,-0.27286,335.7
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1382_011_volume_map.mrc (#1) using 953 atoms
average map value = 0.1084, steps = 184
shifted from previous position = 11.1
rotated from previous position = 45.5 degrees
atoms outside contour = 373, contour level = 0.097694
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1382_011_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.43827435 -0.42484321 0.79210089 91.16741534
-0.88234449 -0.03528954 0.46927908 200.07909954
-0.17141716 -0.90457886 -0.39032458 314.19691158
Axis -0.78989187 0.55396927 -0.26303778
Axis point 0.00000000 243.55650515 59.23396064
Rotation angle (degrees) 119.58207968
Shift along axis -43.82038545
> view matrix models
> #5,0.43827,-0.42484,0.7921,87.678,-0.88234,-0.03529,0.46928,200.88,-0.17142,-0.90458,-0.39032,316.76
> volume #1 level 0.1262
> view matrix models
> #5,0.43827,-0.42484,0.7921,108.04,-0.88234,-0.03529,0.46928,242.64,-0.17142,-0.90458,-0.39032,311.53
> volume #1 step 1
> volume #1 step 2
> volume #1 level 0.1129
> view matrix models
> #5,0.43827,-0.42484,0.7921,96.584,-0.88234,-0.03529,0.46928,253.5,-0.17142,-0.90458,-0.39032,363.19
> view orient
> view matrix models
> #5,0.43827,-0.42484,0.7921,80.849,-0.88234,-0.03529,0.46928,119.72,-0.17142,-0.90458,-0.39032,349.81
> volume #1 level 0.1527
> volume #1 level 0.1489
> close #1
> volume #11 level 0.1265
> vop gaussian #11 sd 3
Opened cryosparc_P380_J1370_009_volume_map.mrc gaussian as #1, grid size
360,360,360, pixel 0.727, shown at step 1, values float32
> volume #1 level 0.06641
> volume #1 level 0.0315
> volume #1 level 0.03964
> volume #1 level 0.04372
> volume #1 level 0.02102
> view matrix models
> #5,0.43827,-0.42484,0.7921,84.241,-0.88234,-0.03529,0.46928,131.01,-0.17142,-0.90458,-0.39032,342.98
> view matrix models
> #5,0.43827,-0.42484,0.7921,118.75,-0.88234,-0.03529,0.46928,248.94,-0.17142,-0.90458,-0.39032,278.1
> view matrix models
> #5,0.43827,-0.42484,0.7921,126.96,-0.88234,-0.03529,0.46928,259.01,-0.17142,-0.90458,-0.39032,274.18
> volume #1 level 0.03964
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.35925,0.081902,-0.92964,331.96,0.39633,0.91524,-0.072523,16.153,0.84491,-0.39449,-0.36126,69.207
> view matrix models
> #5,0.78224,0.35964,-0.50869,103.29,-0.62161,0.50475,-0.59903,256.26,0.041328,0.78479,0.61839,-75.399
> view matrix models
> #5,0.19979,0.71449,-0.67052,149.05,0.93297,-0.34783,-0.092652,114.4,-0.29943,-0.60706,-0.73609,285.16
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.19979,0.71449,-0.67052,140.57,0.93297,-0.34783,-0.092652,62.482,-0.29943,-0.60706,-0.73609,327.03
> view matrix models
> #5,0.19979,0.71449,-0.67052,105.86,0.93297,-0.34783,-0.092652,49.799,-0.29943,-0.60706,-0.73609,333.89
> view matrix models
> #5,0.19979,0.71449,-0.67052,107.4,0.93297,-0.34783,-0.092652,51.506,-0.29943,-0.60706,-0.73609,331.75
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.07095, steps = 224
shifted from previous position = 12.8
rotated from previous position = 64.1 degrees
atoms outside contour = 115, contour level = 0.039643
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.95085049 0.09292588 -0.29537800 62.31460525
0.18425238 -0.93644929 0.29851938 194.40024789
-0.24886637 -0.33827143 -0.90754504 296.29936687
Axis -0.98729465 -0.07211266 0.14159464
Axis point 0.00000000 120.18352811 136.51079332
Rotation angle (degrees) 161.18625477
Shift along axis -33.58719415
> volume #1 level 0.07286
> view matrix models
> #5,0.95085,0.092926,-0.29538,52.179,0.18425,-0.93645,0.29852,193.79,-0.24887,-0.33827,-0.90755,305.82
> view matrix models
> #5,0.95085,0.092926,-0.29538,60.109,0.18425,-0.93645,0.29852,192.04,-0.24887,-0.33827,-0.90755,298.4
> view matrix models
> #5,0.95085,0.092926,-0.29538,59.169,0.18425,-0.93645,0.29852,191.79,-0.24887,-0.33827,-0.90755,296.34
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.056477,0.85821,-0.51018,96.973,0.3571,0.45983,0.81304,-65.875,0.93236,-0.2281,-0.2805,64.675
> view matrix models
> #5,0.81301,-0.55712,-0.16918,151.35,0.26961,0.61776,-0.73871,74.879,0.51606,0.55497,0.65245,-74.198
> view matrix models
> #5,-0.01071,0.37218,-0.9281,210.69,-0.86538,0.46159,0.19509,155.54,0.50101,0.80525,0.31713,-72.933
> view matrix models
> #5,-0.24009,0.36574,-0.89922,239.13,0.36519,-0.82423,-0.43275,223.69,-0.89944,-0.43229,0.064328,300.94
> view matrix models
> #5,0.3554,0.75335,-0.55332,75.459,0.89392,-0.44691,-0.034305,65.146,-0.27313,-0.48243,-0.83226,311.37
> view matrix models
> #5,0.90879,0.32452,-0.26225,30.847,0.40753,-0.8252,0.3911,138.53,-0.089494,-0.4623,-0.88219,289.22
> view matrix models
> #5,0.89003,0.42801,-0.15703,9.4423,0.45499,-0.85568,0.24658,150.26,-0.02883,-0.29091,-0.95632,265.64
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.07095, steps = 100
shifted from previous position = 3.64
rotated from previous position = 21.2 degrees
atoms outside contour = 469, contour level = 0.072856
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.95089827 0.09315135 -0.29515309 62.25814808
0.18431823 -0.93652200 0.29825049 194.42595062
-0.24863496 -0.33800800 -0.90770660 296.24916881
Axis -0.98730769 -0.07218405 0.14146728
Axis point 0.00000000 120.16873062 136.49031251
Rotation angle (degrees) 161.20282930
Shift along axis -33.59283691
> view matrix models
> #5,0.9076,-0.33108,0.25815,70.684,-0.36298,-0.9278,0.086255,286.25,0.21095,-0.17199,-0.96225,218.67
> view matrix models
> #5,0.26411,0.42367,-0.86646,164.67,0.11254,-0.90576,-0.40858,268.22,-0.95791,0.010399,-0.28689,283.96
> view matrix models
> #5,-0.51739,0.44405,-0.73153,252.4,0.50804,-0.52851,-0.68013,192.13,-0.68863,-0.72354,0.04785,313.17
> view matrix models
> #5,0.29973,0.37869,-0.87565,166.8,0.95259,-0.16911,0.25293,-4.6054,-0.052297,-0.90994,-0.41142,298.03
> view matrix models
> #5,0.071262,0.69593,-0.71456,139.43,0.93712,-0.2921,-0.19102,56.681,-0.34166,-0.65602,-0.67298,328
> view matrix models
> #5,-0.3353,0.22015,-0.91603,275.8,0.92005,-0.13265,-0.36865,54.996,-0.20268,-0.9664,-0.15807,300.92
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.07385, steps = 192
shifted from previous position = 4.98
rotated from previous position = 48.4 degrees
atoms outside contour = 453, contour level = 0.072856
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
-0.86021015 -0.19275251 -0.47210702 359.52374988
0.46996110 0.05968191 -0.88066713 136.07530466
0.19792706 -0.97943074 0.03924716 233.94306360
Axis -0.10422828 -0.70710760 0.69938209
Axis point 131.78663226 0.00000000 248.86678529
Rotation angle (degrees) 151.71972444
Shift along axis 29.92316343
> view matrix models
> #5,-0.72678,0.027992,-0.6863,333.32,0.68537,-0.036445,-0.72728,105.45,-0.045371,-0.99894,0.007302,271.83
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.07385, steps = 108
shifted from previous position = 0.706
rotated from previous position = 20.4 degrees
atoms outside contour = 451, contour level = 0.072856
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
-0.86005203 -0.19259686 -0.47245849 359.51539101
0.47029370 0.05978511 -0.88048256 136.00117551
0.19782417 -0.97945507 0.03915875 233.96849412
Axis -0.10441333 -0.70713015 0.69933168
Axis point 131.75095261 0.00000000 248.85797048
Rotation angle (degrees) 151.70927102
Shift along axis 29.91284958
> volume #1 level 0.04232
> view matrix models
> #5,-0.76983,0.52685,0.36025,171.7,-0.2268,0.30178,-0.92601,200.65,-0.59659,-0.79458,-0.11284,329.37
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.07287, steps = 152
shifted from previous position = 2.27
rotated from previous position = 38.9 degrees
atoms outside contour = 115, contour level = 0.042322
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
-0.77352667 0.63203809 0.04673761 187.75784508
0.37956211 0.52106241 -0.76447794 74.72486370
-0.50753242 -0.57360427 -0.64295338 336.74800320
Axis 0.29904717 0.86839052 -0.39556125
Axis point 112.32807895 -0.00000000 167.33622672
Rotation angle (degrees) 161.38929501
Shift along axis -12.16564469
> volume #1 level 0.07821
> view matrix models
> #5,-0.15351,-0.26167,-0.95287,320.76,0.80936,0.51991,-0.27316,-29.558,0.56689,-0.81315,0.13197,151.26
> view matrix models
> #5,0.55114,-0.62036,0.55803,128.84,-0.20005,0.55103,0.81015,-4.8031,-0.81008,-0.55814,0.17959,295.2
> view matrix models
> #5,0.27344,-0.58516,0.76342,141.08,-0.85119,0.22246,0.47539,157.33,-0.44801,-0.77981,-0.43725,336.29
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.06832, steps = 128
shifted from previous position = 4.85
rotated from previous position = 22 degrees
atoms outside contour = 567, contour level = 0.078212
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.50565493 -0.43221441 0.74666175 89.99936287
-0.85025356 -0.10297111 0.51620327 200.32744685
-0.14622592 -0.89587257 -0.41955971 312.67942367
Axis -0.81992690 0.51845843 -0.24273593
Axis point 0.00000000 233.59322343 65.00965182
Rotation angle (degrees) 120.55983858
Shift along axis -45.82997606
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.06832, steps = 64
shifted from previous position = 0.0108
rotated from previous position = 0.0591 degrees
atoms outside contour = 567, contour level = 0.078212
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.50653979 -0.43186473 0.74626422 89.87173274
-0.84974883 -0.10338884 0.51695034 200.25324457
-0.14609724 -0.89599309 -0.41934713 312.66284425
Axis -0.82023961 0.51803221 -0.24258940
Axis point 0.00000000 233.48644679 65.06044729
Rotation angle (degrees) 120.53722771
Shift along axis -45.82741435
> view matrix models
> #5,0.46666,-0.60555,0.64462,128,-0.81745,-0.57356,0.052989,303.15,0.33764,-0.55167,-0.76266,236.19
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.0719, steps = 204
shifted from previous position = 8.63
rotated from previous position = 43.8 degrees
atoms outside contour = 564, contour level = 0.078212
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.13691885 -0.17192832 0.97554796 89.30303656
-0.54402349 -0.83606140 -0.07099150 311.41369908
0.82782348 -0.52100096 -0.20800559 108.17991364
Axis -0.74713051 0.24526033 -0.61777291
Axis point 0.00000000 177.88122549 -16.40476316
Rotation angle (degrees) 162.47279906
Shift along axis -57.17421710
> view matrix models
> #5,0.16445,-0.11998,0.97906,78.435,-0.51226,-0.85861,-0.01918,305.18,0.84294,-0.49838,-0.20266,102.66
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.0719, steps = 52
shifted from previous position = 0.109
rotated from previous position = 3.71 degrees
atoms outside contour = 566, contour level = 0.078212
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.13739897 -0.17185073 0.97549413 89.23602782
-0.54404781 -0.83607367 -0.07065989 311.38823736
0.82772794 -0.52100686 -0.20837066 108.21895690
Axis -0.74728719 0.24519711 -0.61760848
Axis point 0.00000000 177.85857560 -16.34886378
Rotation angle (degrees) 162.46302396
Shift along axis -57.17038953
> view matrix models
> #5,0.27739,-0.12398,0.95273,66.558,-0.41244,-0.91098,0.001537,296.9,0.86773,-0.39337,-0.30383,95.244
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.27739,-0.12398,0.95273,59.026,-0.41244,-0.91098,0.001537,299.53,0.86773,-0.39337,-0.30383,96.421
> view matrix models
> #5,0.27739,-0.12398,0.95273,59.223,-0.41244,-0.91098,0.001537,299.12,0.86773,-0.39337,-0.30383,96.697
> volume #1 level 0.04982
> show #!11 models
> view matrix models
> #5,0.27739,-0.12398,0.95273,49.298,-0.41244,-0.91098,0.001537,299.6,0.86773,-0.39337,-0.30383,93.593
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.07286, steps = 152
shifted from previous position = 9.93
rotated from previous position = 39.1 degrees
atoms outside contour = 183, contour level = 0.049821
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.32640132 0.42733907 0.84311535 -11.62141863
0.11404650 -0.90325555 0.41366988 185.19090009
0.93832596 -0.03886806 -0.34356029 44.17526646
Axis -0.81016264 -0.17045218 -0.56087659
Axis point 0.00000000 95.38797194 10.52949309
Rotation angle (degrees) 163.78226510
Shift along axis -46.92782559
> view matrix models
> #5,0.3264,0.42734,0.84312,-27.09,0.11405,-0.90326,0.41367,186.09,0.93833,-0.038868,-0.34356,39.276
> volume #11 level 0.1091
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.18863,-0.81014,0.55506,182.98,-0.45345,-0.5732,-0.68252,323.53,0.87109,-0.12295,-0.47548,72.079
> view matrix models
> #5,0.45168,0.4453,0.7731,-39.287,0.2988,-0.89199,0.33921,167.33,0.84065,0.077793,-0.53596,55.361
> view matrix models
> #5,0.67941,-0.70246,0.21201,136.91,-0.66784,-0.47232,0.57524,216.89,-0.30395,-0.53241,-0.79004,312.35
> volume #11 level 0.04897
> view matrix models
> #5,0.99225,-0.081682,0.09363,24.681,-0.053856,0.39635,0.91652,-12.518,-0.11197,-0.91446,0.38888,223.52
> fitmap #5 inMap #1
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) using 953 atoms
average map value = 0.1012, steps = 324
shifted from previous position = 25
rotated from previous position = 97 degrees
atoms outside contour = 25, contour level = 0.049821
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1370_009_volume_map.mrc gaussian (#1) coordinates:
Matrix rotation and translation
0.62610617 -0.76786635 -0.13554460 180.80176857
0.69203961 0.62732108 -0.35714058 -42.98023941
0.35926626 0.12980572 0.92416351 -40.11877577
Axis 0.30122298 -0.30608797 0.90309184
Axis point 133.41123860 158.18613303 0.00000000
Rotation angle (degrees) 53.92842827
Shift along axis 31.38644338
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1383_004_volume_map.mrc
Opened cryosparc_P380_J1383_004_volume_map.mrc as #2, grid size 360,360,360,
pixel 0.727, shown at level 0.155, step 2, values float32
> volume #2 level 0.1247
> volume #2 level 0.1171
> volume #2 level 0.08284
> view matrix models
> #5,0.3808,-0.46019,-0.80201,236.98,-0.91805,-0.2917,-0.26852,283.42,-0.11038,0.83853,-0.53356,69.161
> volume #2 level 0.07524
> volume #2 level 0.08854
> volume #2 level 0.1057
> close #1
> view matrix models
> #5,0.0058339,0.75349,-0.65743,111.83,0.053627,-0.65673,-0.75221,249.91,-0.99854,-0.030868,-0.044239,254.64
> volume #2 level 0.08853
> volume #2 level 0.1228
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1384_004_volume_map.mrc
Opened cryosparc_P380_J1384_004_volume_map.mrc as #1, grid size 360,360,360,
pixel 0.727, shown at level 0.156, step 2, values float32
> volume #1 level 0.1061
> volume #1 level 0.08442
> volume #11 level 0.1524
> open /Users/cristianrosales/Downloads/cryosparc_P380_J1003__localfilter.mrc
Opened cryosparc_P380_J1003__localfilter.mrc as #3, grid size 360,360,360,
pixel 0.727, shown at level 0.165, step 2, values float32
> volume #3 level 0.1037
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1355_008_volume_map.mrc
Opened cryosparc_P380_J1355_008_volume_map.mrc as #4, grid size 180,180,180,
pixel 1.45, shown at level 0.373, step 1, values float32
> volume #4 level 0.1358
> volume #4 level 0.1616
> volume #4 level 0.239
> close #4
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.0058339,0.75349,-0.65743,123.02,0.053627,-0.65673,-0.75221,277.31,-0.99854,-0.030868,-0.044239,256.62
> view matrix models
> #5,0.0058339,0.75349,-0.65743,113.53,0.053627,-0.65673,-0.75221,270.69,-0.99854,-0.030868,-0.044239,242.54
> volume #11 level 0.1035
> volume #11 level 0.05649
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1387_class_00_00080_volume.mrc
Opened cryosparc_P380_J1387_class_00_00080_volume.mrc as #4, grid size
128,128,128, pixel 2.04, shown at level 0.555, step 1, values float32
> volume #4 level 0.2773
> open "/Users/cristianrosales/Downloads/cryosparc_P380_J1327_004_volume_map
> (1).mrc"
Opened cryosparc_P380_J1327_004_volume_map (1).mrc as #6, grid size
180,180,180, pixel 1.45, shown at level 0.368, step 1, values float32
> volume #6 level 0.2196
> volume #6 level 0.1538
> volume #6 level 0.2196
> open "/Users/cristianrosales/Downloads/cryosparc_P380_J1328_004_volume_map
> (1).mrc"
Opened cryosparc_P380_J1328_004_volume_map (1).mrc as #7, grid size
180,180,180, pixel 1.45, shown at level 0.368, step 1, values float32
> volume #7 level 0.2448
> volume #7 level 0.1107
> open "/Users/cristianrosales/Downloads/cryosparc_P380_J1328_004_volume_map
> (1).mrc"
Opened cryosparc_P380_J1328_004_volume_map (1).mrc as #8, grid size
180,180,180, pixel 1.45, shown at level 0.368, step 1, values float32
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1385_008_volume_map.mrc
Opened cryosparc_P380_J1385_008_volume_map.mrc as #9, grid size 360,360,360,
pixel 0.727, shown at level 0.155, step 2, values float32
> volume #9 level 0.08887
> volume #9 level 0.1243
> view matrix models
> #5,0.0058339,0.75349,-0.65743,122.41,0.053627,-0.65673,-0.75221,284.5,-0.99854,-0.030868,-0.044239,253.08
> view matrix models
> #5,0.0058339,0.75349,-0.65743,123.86,0.053627,-0.65673,-0.75221,266.18,-0.99854,-0.030868,-0.044239,270.71
> view matrix models
> #5,0.0058339,0.75349,-0.65743,117.62,0.053627,-0.65673,-0.75221,269.77,-0.99854,-0.030868,-0.044239,273.21
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.67872,0.71641,-0.16154,-14.534,0.69638,-0.55798,0.45134,55.163,0.23321,-0.41883,-0.87761,242.12
> view matrix models
> #5,0.7969,-0.15389,0.58418,13.002,-0.43421,-0.81824,0.37677,246.57,0.42002,-0.5539,-0.71887,219.93
> view matrix models
> #5,0.441,-0.084173,0.89355,20.968,-0.49287,-0.85475,0.16273,279.88,0.75006,-0.51217,-0.41843,141.63
> view matrix models
> #5,-0.79344,-0.60282,-0.084026,347.71,0.54306,-0.76349,0.34952,112.55,-0.27485,0.23169,0.93315,48.054
> view matrix models
> #5,-0.34531,-0.7292,-0.59079,354.13,0.79908,-0.55859,0.22239,63.791,-0.49217,-0.39529,0.77557,175.15
> view matrix models
> #5,0.19651,-0.32231,-0.92601,260.89,0.60653,-0.70209,0.37309,93.727,-0.7704,-0.63497,0.057518,313.2
> view matrix models
> #5,0.63844,-0.37355,-0.67294,184.69,0.067241,-0.84391,0.53225,168.53,-0.76673,-0.38506,-0.51367,334.85
> view matrix models
> #5,0.70015,-0.2737,-0.65945,161.98,0.026263,-0.91311,0.40686,195.26,-0.71351,-0.30219,-0.63213,328.28
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.70015,-0.2737,-0.65945,165.51,0.026263,-0.91311,0.40686,199.62,-0.71351,-0.30219,-0.63213,331.79
> view matrix models
> #5,0.70015,-0.2737,-0.65945,164.97,0.026263,-0.91311,0.40686,198.48,-0.71351,-0.30219,-0.63213,332.14
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.56536,-0.035193,-0.82409,167.14,0.55866,-0.7187,0.41396,101.54,-0.60684,-0.69443,-0.38667,346.25
> view matrix models
> #5,0.49702,-0.050399,-0.86627,182.29,0.61722,-0.68118,0.39376,90.765,-0.60993,-0.73038,-0.30745,343.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.49702,-0.050399,-0.86627,185.37,0.61722,-0.68118,0.39376,91.516,-0.60993,-0.73038,-0.30745,341.18
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.92923,-0.052189,-0.36581,79.968,0.14292,-0.86217,0.48605,169.38,-0.34075,-0.50393,-0.79369,322.56
> view matrix models
> #5,0.8051,0.51067,-0.30171,15.625,0.57087,-0.8052,0.16049,136.65,-0.16098,-0.30145,-0.93979,286.06
> view matrix models
> #5,0.7553,0.61937,-0.21426,-0.64228,0.65418,-0.69272,0.30363,96.868,0.039641,-0.3695,-0.92839,267.41
> view matrix models
> #5,0.70923,0.61505,-0.34453,18.631,0.7028,-0.57846,0.41408,64.608,0.055382,-0.53581,-0.84252,279.05
> view matrix models
> #5,0.45219,0.69667,-0.55693,62.398,0.88277,-0.26034,0.39108,0.85088,0.12746,-0.66849,-0.73272,276.47
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.45219,0.69667,-0.55693,61.173,0.88277,-0.26034,0.39108,-1.7717,0.12746,-0.66849,-0.73272,272.05
> volume #9 level 0.08222
> fitmap #5 inMap #9
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1385_008_volume_map.mrc (#9) using 953 atoms
average map value = 0.1048, steps = 160
shifted from previous position = 11.5
rotated from previous position = 45.3 degrees
atoms outside contour = 320, contour level = 0.082225
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1385_008_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.88899338 0.45736860 0.02246613 -10.95620672
0.38190533 -0.76759785 0.51472499 122.83944894
0.25266399 -0.44900723 -0.85706089 242.90734608
Axis -0.96982953 -0.23165427 -0.07594071
Axis point 0.00000000 95.66299671 106.18879049
Rotation angle (degrees) 150.20775392
Shift along axis -36.27718638
> view matrix models
> #5,0.88899,0.45737,0.022466,-18.826,0.38191,-0.7676,0.51472,123.54,0.25266,-0.44901,-0.85706,239.82
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.25428,0.92955,-0.26698,30.652,0.9176,-0.14467,0.37025,-15.953,0.30554,-0.33913,-0.88974,221.42
> view matrix models
> #5,-0.69785,-0.65005,0.30075,311.11,-0.16989,-0.25769,-0.95118,270.84,0.69581,-0.71487,0.069386,126.76
> view matrix models
> #5,-0.85476,-0.51876,-0.01651,345.18,0.26163,-0.40318,-0.87692,225.79,0.44825,-0.75388,0.48035,124.96
> view matrix models
> #5,-0.71778,-0.69158,-0.080636,356.15,0.53844,-0.47792,-0.69402,181.35,0.44144,-0.54158,0.71542,74.99
> fitmap #5 inMap #9
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1385_008_volume_map.mrc (#9) using 953 atoms
average map value = 0.105, steps = 208
shifted from previous position = 11
rotated from previous position = 43.4 degrees
atoms outside contour = 323, contour level = 0.082225
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1385_008_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
-0.42710458 -0.69096257 -0.58322588 375.37784380
0.61892679 0.24681843 -0.74566092 74.63697015
0.65917473 -0.67944933 0.32223794 104.44434071
Axis 0.03665012 -0.68770628 0.72506334
Axis point 141.07664695 249.86624732 0.00000000
Rotation angle (degrees) 115.40564307
Shift along axis 38.15809185
> view matrix models
> #5,0.077443,0.96819,-0.23794,55.33,0.96662,-0.13138,-0.21999,27.863,-0.24425,-0.21296,-0.94604,284.94
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.077443,0.96819,-0.23794,41.69,0.96662,-0.13138,-0.21999,-19.968,-0.24425,-0.21296,-0.94604,257.12
> volume #9 level 0.1323
> volume #9 level 0.09476
> volume #9 level 0.1177
> volume #9 level 0.09684
> view matrix models
> #5,0.077443,0.96819,-0.23794,34.733,0.96662,-0.13138,-0.21999,-40.975,-0.24425,-0.21296,-0.94604,259.53
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.61146,-0.29554,0.73401,37.453,0.5515,-0.50602,-0.66317,106.5,0.56742,0.81031,-0.14643,-60.871
> view matrix models
> #5,0.66194,-0.21159,0.71908,21.091,-0.051974,-0.96998,-0.23758,206.72,0.74776,0.11989,-0.65306,55.735
> view matrix models
> #5,0.56464,-0.70667,0.42638,127.88,-0.75817,-0.64825,-0.070381,241.43,0.32614,-0.28353,-0.9018,189.08
> view matrix models
> #5,0.57361,-0.73685,0.3578,137.33,-0.64139,-0.13233,0.75572,77.701,-0.50951,-0.66297,-0.54851,315.83
> view matrix models
> #5,0.29047,-0.77977,0.5546,161.47,-0.71488,0.20842,0.66746,50.819,-0.63606,-0.59035,-0.4969,317.98
> volume #9 level 0.06761
> volume #9 level 0.1156
> volume #8 level 0.3045
> open "/Users/cristianrosales/Library/CloudStorage/OneDrive-
> Personal/LMU/PhD/Lab/Data/CryoEM
> Data/Coot/Bcs1_ms/Bcs1-dn82Rip1-ATPgS_P280_J261.mrc"
Opened Bcs1-dn82Rip1-ATPgS_P280_J261.mrc as #12, grid size 360,360,360, pixel
0.727, shown at level 0.392, step 2, values float32
> fitmap #12 inMap #8
Fit map Bcs1-dn82Rip1-ATPgS_P280_J261.mrc in map
cryosparc_P380_J1328_004_volume_map (1).mrc using 58307 points
correlation = 0.9475, correlation about mean = 0.7308, overlap = 1.881e+04
steps = 128, shift = 2.03, angle = 22 degrees
Position of Bcs1-dn82Rip1-ATPgS_P280_J261.mrc (#12) relative to
cryosparc_P380_J1328_004_volume_map (1).mrc (#8) coordinates:
Matrix rotation and translation
0.95838413 0.28353079 -0.03331906 -27.61162129
-0.28282893 0.92711526 -0.24589649 74.26273023
-0.03882862 0.24508689 0.96872326 -22.57817836
Axis 0.65501820 0.00735027 -0.75557735
Axis point 229.10800662 129.90223044 0.00000000
Rotation angle (degrees) 22.01109094
Shift along axis -0.48070350
> volume #12 level 0.3099
> volume #8 level 0.1821
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.40996,0.79627,0.44484,-52.561,-0.86882,0.19247,0.45618,93.754,0.27763,-0.5735,0.77073,72.146
> view matrix models
> #5,0.092962,0.18903,0.97756,18.347,-0.94661,-0.28762,0.14564,197.7,0.30869,-0.9389,0.1522,176.28
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1402_008_volume_map.mrc
Opened cryosparc_P380_J1402_008_volume_map.mrc as #14, grid size 180,180,180,
pixel 1.45, shown at level 0.368, step 1, values float32
> volume #14 level 0.1832
> volume #14 level 0.1967
> volume #14 level 0.05223
> volume #14 level 0.3277
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1400_008_volume_map.mrc
Opened cryosparc_P380_J1400_008_volume_map.mrc as #15, grid size 180,180,180,
pixel 1.45, shown at level 0.369, step 1, values float32
> volume #15 level 0.2319
> volume #15 level 0.1158
> volume #15 level 0.1034
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1398_008_volume_map.mrc
Opened cryosparc_P380_J1398_008_volume_map.mrc as #16, grid size 180,180,180,
pixel 1.45, shown at level 0.377, step 1, values float32
> volume #16 level 0.1201
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1398_008_volume_map.mrc
Opened cryosparc_P380_J1398_008_volume_map.mrc as #17, grid size 180,180,180,
pixel 1.45, shown at level 0.377, step 1, values float32
> volume #17 level 0.1549
> volume #17 level 0.1854
> vop gaussian #17 sd 3
Opened cryosparc_P380_J1398_008_volume_map.mrc gaussian as #18, grid size
180,180,180, pixel 1.45, shown at step 1, values float32
> volume #18 level 0.08123
> volume #18 level 0.09955
> volume #18 level 0.07338
> volume #18 level 0.08777
> volume #18 level 0.08515
> view matrix models
> #5,-0.48402,0.80377,0.34594,74.389,-0.66664,-0.082615,-0.74078,219.21,-0.56684,-0.58917,0.57582,204.9
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.48402,0.80377,0.34594,63.912,-0.66664,-0.082615,-0.74078,241.62,-0.56684,-0.58917,0.57582,288.13
> view matrix models
> #5,-0.48402,0.80377,0.34594,140.33,-0.66664,-0.082615,-0.74078,215.09,-0.56684,-0.58917,0.57582,209.28
> hide #!5 models
> show #!5 models
> view orient
> view matrix models
> #5,-0.48402,0.80377,0.34594,116,-0.66664,-0.082615,-0.74078,286.89,-0.56684,-0.58917,0.57582,234.49
> view matrix models
> #5,-0.48402,0.80377,0.34594,116.08,-0.66664,-0.082615,-0.74078,292.6,-0.56684,-0.58917,0.57582,236.43
> volume #17 level 0.268
> view matrix models
> #5,-0.48402,0.80377,0.34594,98.747,-0.66664,-0.082615,-0.74078,302.55,-0.56684,-0.58917,0.57582,241.39
> volume #17 level 0.4159
> view matrix models
> #5,-0.48402,0.80377,0.34594,100.31,-0.66664,-0.082615,-0.74078,303.37,-0.56684,-0.58917,0.57582,234.05
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.43494,-0.82677,-0.35677,377.83,0.86267,-0.269,-0.4283,95.336,0.25813,-0.49406,0.83023,87.595
> volume #17 level 0.3159
> view matrix models
> #5,-0.12106,-0.94219,0.31245,286.83,0.94483,-0.20588,-0.25476,59.307,0.30436,0.26437,0.91513,-27.233
> view matrix models
> #5,0.4718,-0.39568,-0.78793,242.34,-0.62862,-0.77758,0.01407,317.41,-0.61825,0.48867,-0.6156,213.28
> view matrix models
> #5,-0.28875,-0.21409,-0.93316,333.04,0.61965,-0.78479,-0.01169,155.56,-0.72983,-0.58161,0.35926,275.57
> volume #18 level 0.1558
> view matrix models
> #5,0.10352,-0.64992,0.75292,175.76,0.89869,-0.26324,-0.35079,82.305,0.42619,0.71295,0.55683,-68.144
> view matrix models
> #5,0.23616,-0.64419,0.7275,159.89,0.94466,-0.023239,-0.32723,42.139,0.2277,0.76452,0.60305,-53.164
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.23616,-0.64419,0.7275,155.8,0.94466,-0.023239,-0.32723,43.637,0.2277,0.76452,0.60305,-55.941
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.68551,-0.35707,0.63449,67.256,0.70755,0.12129,-0.69618,91.571,0.17163,0.92617,0.33579,-44.084
> view matrix models
> #5,0.65645,-0.66129,0.363,137.67,0.48017,-0.0048343,-0.87716,155.9,0.58181,0.75012,0.31436,-72.999
> view matrix models
> #5,-0.028146,0.20758,-0.97781,242.89,0.72225,-0.67204,-0.16346,143.21,-0.69106,-0.71082,-0.13101,332.2
> view matrix models
> #5,0.094771,-0.12964,-0.98702,272.19,0.47209,-0.86705,0.15921,170.97,-0.87644,-0.48105,-0.020971,315.66
> volume #18 level 0.1977
> view matrix models
> #5,-0.43735,-0.067495,-0.89675,325.68,0.50503,-0.84352,-0.18282,196.57,-0.74409,-0.53284,0.403,263.99
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.43735,-0.067495,-0.89675,325.88,0.50503,-0.84352,-0.18282,195.01,-0.74409,-0.53284,0.403,266.41
> view matrix models
> #5,-0.43735,-0.067495,-0.89675,325.27,0.50503,-0.84352,-0.18282,195.85,-0.74409,-0.53284,0.403,265.3
> volume #18 level 0.1741
> volume #18 level 0.1166
> view matrix models
> #5,-0.43735,-0.067495,-0.89675,326.08,0.50503,-0.84352,-0.18282,196.02,-0.74409,-0.53284,0.403,260.53
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.51231,0.48759,-0.70696,244.1,-0.66678,-0.74463,-0.030389,323.34,-0.54125,0.45582,0.7066,73.302
> volume #18 level 0.1493
> view matrix models
> #5,0.50872,-0.80057,0.31669,180.57,-0.85993,-0.45472,0.23184,285.14,-0.041599,-0.39027,-0.91976,276.56
> view matrix models
> #5,0.63073,-0.76285,-0.14224,203.8,-0.71279,-0.642,0.28241,285.58,-0.30676,-0.076742,-0.94869,272.93
> view matrix models
> #5,-0.71362,-0.26577,0.64816,239.5,-0.5852,0.73477,-0.34301,146.75,-0.38508,-0.62408,-0.67988,329.82
> view matrix models
> #5,0.26101,-0.43482,0.86186,112.17,-0.75614,0.46292,0.46255,127.49,-0.6001,-0.77242,-0.20796,332.3
> volume #18 level 0.1781
> volume #17 level 0.1375
> view matrix models
> #5,0.27445,-0.76122,0.58756,180.17,-0.58012,-0.61838,-0.53017,343.48,0.7669,-0.19535,-0.61131,113.84
> view matrix models
> #5,0.87719,-0.47101,0.093238,109.72,-0.46405,-0.8815,-0.08727,320.13,0.12329,0.033285,-0.99181,205.57
> view matrix models
> #5,-0.26729,-0.32629,0.90669,163.41,-0.93081,-0.15601,-0.33055,309.34,0.24931,-0.93231,-0.26201,246.24
> view matrix models
> #5,-0.22551,-0.58489,0.77913,204.48,-0.65852,-0.49786,-0.56434,341.2,0.71798,-0.64034,-0.2729,146.54
> volume #17 level 0.2637
> view matrix models
> #5,0.2165,-0.11594,-0.96937,252.94,-0.57313,-0.81892,-0.030053,320.75,-0.79035,0.56208,-0.24374,184.13
> view matrix models
> #5,0.75021,-0.61472,0.24352,131.04,-0.54044,-0.35791,0.76146,178.78,-0.38093,-0.70287,-0.60072,332.05
> view matrix models
> #5,0.71,-0.70291,0.042645,167.48,-0.44707,-0.40314,0.7985,168.82,-0.54409,-0.586,-0.60048,338.15
> volume #4 level 0.2519
> volume #17 level 0.1636
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.2045, steps = 108
shifted from previous position = 3.43
rotated from previous position = 16 degrees
atoms outside contour = 332, contour level = 0.16361
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.52199747 -0.82818054 0.20404811 196.21669817
-0.61675640 -0.20124327 0.76099448 165.76010137
-0.58917756 -0.52308520 -0.61583414 336.81658458
Axis -0.84253719 0.52046780 0.13872402
Axis point 0.00000000 237.16707564 134.44567452
Rotation angle (degrees) 130.35638327
Shift along axis -32.32251890
> view matrix models
> #5,0.40571,-0.91332,-0.035261,246.04,-0.59984,-0.29517,0.74369,177.64,-0.68963,-0.28057,-0.6676,322.99
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.2045, steps = 104
shifted from previous position = 0.204
rotated from previous position = 16.1 degrees
atoms outside contour = 330, contour level = 0.16361
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.52177085 -0.82861047 0.20287891 196.42043728
-0.61616707 -0.20157767 0.76138328 165.66011586
-0.58999435 -0.52227494 -0.61573986 336.80238449
Axis -0.84247996 0.52037203 0.13942910
Axis point 0.00000000 237.14376242 134.58468726
Rotation angle (degrees) 130.37393191
Shift along axis -32.31533713
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.2045, steps = 120
shifted from previous position = 0.0254
rotated from previous position = 0.0544 degrees
atoms outside contour = 333, contour level = 0.16361
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.52181286 -0.82837860 0.20371604 196.30073756
-0.61668681 -0.20130936 0.76103339 165.75194728
-0.58941387 -0.52274604 -0.61589599 336.80933780
Axis -0.84248703 0.52049569 0.13892385
Axis point 0.00000000 237.17574592 134.48652298
Rotation angle (degrees) 130.36813402
Shift along axis -32.31680081
> view matrix models
> #5,0.31684,-0.94816,0.024481,256.65,-0.44435,-0.12558,0.88701,120.71,-0.83796,-0.29192,-0.4611,324.16
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.2037, steps = 80
shifted from previous position = 2.09
rotated from previous position = 15.2 degrees
atoms outside contour = 340, contour level = 0.16361
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.50004091 -0.85511961 0.13685586 210.78024780
-0.35176107 -0.05615146 0.93440412 94.18493077
-0.79134269 -0.51538088 -0.32887585 335.77929574
Axis -0.80833549 0.51752213 0.28065029
Axis point 0.00000000 246.64591825 162.80906947
Rotation angle (degrees) 116.26306624
Shift along axis -27.40181268
> volume #17 level 0.2389
> view matrix models
> #5,0.61523,-0.73816,0.27678,166.5,-0.22995,0.16779,0.95863,46.04,-0.75406,-0.65342,-0.066515,323.76
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.61523,-0.73816,0.27678,163.74,-0.22995,0.16779,0.95863,44.687,-0.75406,-0.65342,-0.066515,322.3
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.2029, steps = 76
shifted from previous position = 3.49
rotated from previous position = 6.66 degrees
atoms outside contour = 618, contour level = 0.23892
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.54494038 -0.75465557 0.36542434 169.59647192
-0.27108966 0.25383982 0.92848030 41.86126180
-0.79344211 -0.60502918 -0.06625180 323.21123072
Axis -0.77370493 0.58468546 0.24397457
Axis point 0.00000000 271.43438478 155.48779562
Rotation angle (degrees) 97.68552401
Shift along axis -27.88663346
> volume #17 level 0.1475
> close #18
> vop gaussian #17 sd 1
Opened cryosparc_P380_J1398_008_volume_map.mrc gaussian as #18, grid size
180,180,180, pixel 1.45, shown at step 1, values float32
> volume #18 level 0.1642
> view matrix models
> #5,0.54494,-0.75466,0.36542,165.78,-0.27109,0.25384,0.92848,37.383,-0.79344,-0.60503,-0.066252,321.77
> view matrix models
> #5,0.54494,-0.75466,0.36542,149.22,-0.27109,0.25384,0.92848,49.94,-0.79344,-0.60503,-0.066252,326.12
> show sel surfaces
> volume #18 level 0.2167
> view matrix models
> #5,0.54494,-0.75466,0.36542,156.55,-0.27109,0.25384,0.92848,39.801,-0.79344,-0.60503,-0.066252,324.1
> view matrix models
> #5,0.54494,-0.75466,0.36542,164.63,-0.27109,0.25384,0.92848,39.38,-0.79344,-0.60503,-0.066252,324.06
> hide sel surfaces
> view matrix models
> #5,0.54494,-0.75466,0.36542,164.72,-0.27109,0.25384,0.92848,42.196,-0.79344,-0.60503,-0.066252,324
> view matrix models
> #5,0.54494,-0.75466,0.36542,166.65,-0.27109,0.25384,0.92848,40.553,-0.79344,-0.60503,-0.066252,324.34
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.5155,-0.78966,0.33271,178.35,0.063543,0.42244,0.90416,-23.746,-0.85453,-0.44495,0.26795,278.89
> view matrix models
> #5,0.53166,-0.73755,0.41636,161.21,-0.022162,0.47932,0.87736,-17.341,-0.84667,-0.47569,0.23849,284.77
> view matrix models
> #5,0.57506,-0.71735,-0.39334,231.11,0.7784,0.33179,0.53292,-70.485,-0.25179,-0.61264,0.74918,174.75
> view matrix models
> #5,-0.78627,-0.32553,0.52517,270.61,-0.15376,-0.72014,-0.67658,309.32,0.59844,-0.61273,0.51617,84.717
> view matrix models
> #5,-0.5079,-0.35907,0.78301,213.26,-0.48636,-0.6307,-0.60471,334.56,0.71097,-0.68796,0.1457,115.62
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.2106, steps = 116
shifted from previous position = 9.38
rotated from previous position = 35.6 degrees
atoms outside contour = 265, contour level = 0.14748
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
-0.55221300 -0.75589738 0.35168153 317.98193819
-0.31779420 -0.19913199 -0.92701309 292.21950079
0.77075785 -0.62367106 -0.13025652 120.83689903
Axis 0.44745982 -0.61817946 0.64624598
Axis point 74.35202017 244.46968779 0.00000000
Rotation angle (degrees) 160.18647071
Shift along axis 39.73040758
> view matrix models
> #5,0.30686,-0.5895,0.74721,143.92,-0.41737,-0.78892,-0.451,337.51,0.85536,-0.17347,-0.48813,84.597
> volume #18 level 0.1712
> view matrix models
> #5,-0.095126,-0.69697,0.71077,214.92,-0.90448,-0.2377,-0.35414,319.6,0.41577,-0.67656,-0.60778,221.04
> view matrix models
> #5,0.88868,-0.44078,-0.12631,131.67,-0.45511,-0.81436,-0.36013,337.09,0.055875,0.37752,-0.92431,159.65
> view matrix models
> #5,0.8229,0.47135,-0.31728,37.989,0.27347,-0.81804,-0.50599,255.21,-0.49805,0.32962,-0.80206,227.52
> view matrix models
> #5,-0.67324,0.68487,-0.27876,204.08,0.66747,0.40065,-0.62767,53.329,-0.31819,-0.60863,-0.72686,320.74
> view matrix models
> #5,-0.80949,0.33306,-0.48353,288.55,0.57325,0.62637,-0.52824,26.278,0.12694,-0.70479,-0.69797,271.75
> volume #18 level 0.1291
> view matrix models
> #5,0.023777,0.19143,-0.98122,245.12,-0.80144,-0.58306,-0.13317,330.35,-0.5976,0.78955,0.13955,88.679
> view matrix models
> #5,-0.074463,0.81536,-0.57415,136.08,-0.99308,-0.0081714,0.11719,255.33,0.090861,0.5789,0.81032,-39.454
> view matrix models
> #5,-0.26311,0.72475,-0.6368,179.12,-0.96123,-0.25339,0.10876,284.42,-0.082536,0.64073,0.76332,-20.139
> volume #18 level 0.2237
> volume #18 level 0.1607
> view matrix models
> #5,-0.39518,-0.42543,0.81415,208.67,-0.49915,-0.64458,-0.5791,341.61,0.77116,-0.63523,0.042369,105.62
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.39518,-0.42543,0.81415,200.24,-0.49915,-0.64458,-0.5791,344.08,0.77116,-0.63523,0.042369,102.75
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.61888,-0.65693,-0.43062,217.04,0.37895,0.72991,-0.56889,44.691,0.68803,0.18889,0.70067,-59.117
> view matrix models
> #5,0.93664,-0.32856,0.12143,78.059,0.16007,0.70983,0.68594,-45.04,-0.31157,-0.62305,0.71745,179.2
> view matrix models
> #5,0.87268,-0.4847,0.059162,113.24,-0.48588,-0.84991,0.20388,293.79,-0.048537,-0.20666,-0.97721,253.12
> view matrix models
> #5,0.37389,0.54665,-0.74926,120.83,0.90632,-0.3869,0.16999,51.368,-0.19696,-0.74262,-0.64009,311.18
> volume #18 level 0.1116
> view matrix models
> #5,0.4975,-0.25515,-0.82909,218.42,0.67594,-0.48501,0.55486,57.648,-0.54369,-0.83646,-0.06883,314.27
> view matrix models
> #5,0.31702,-0.60525,-0.73018,279.14,0.37041,-0.62974,0.68281,104.91,-0.8731,-0.48693,0.024554,302.55
> view matrix models
> #5,0.20373,-0.60019,-0.77348,297.66,0.13065,-0.76631,0.62904,159.95,-0.97027,-0.22921,-0.077701,291.16
> fitmap #5 inMap #17
Fit molecule dn82Rip1_1kb9.pdb (#5) to map
cryosparc_P380_J1398_008_volume_map.mrc (#17) using 953 atoms
average map value = 0.223, steps = 92
shifted from previous position = 11.1
rotated from previous position = 28.4 degrees
atoms outside contour = 238, contour level = 0.14748
Position of dn82Rip1_1kb9.pdb (#5) relative to
cryosparc_P380_J1398_008_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.42518933 -0.43944233 -0.79126760 254.64993284
0.50771649 -0.60793069 0.61044591 84.03180734
-0.74929167 -0.66129471 -0.03537357 321.91332045
Axis -0.80172663 -0.02646233 0.59710481
Axis point 0.00000000 139.37235468 230.06817553
Rotation angle (degrees) 127.52138280
Shift along axis -14.16731692
> volume #18 level 0.2237
> volume #18 level 0.1186
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.42519,-0.43944,-0.79127,238.72,0.50772,-0.60793,0.61045,81.365,-0.74929,-0.66129,-0.035374,328.87
> view matrix models
> #5,0.42519,-0.43944,-0.79127,243.56,0.50772,-0.60793,0.61045,81.448,-0.74929,-0.66129,-0.035374,324.21
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.51685,0.38652,-0.76385,256.21,0.8545,0.28699,-0.43297,17.874,0.051871,-0.87649,-0.47861,289.51
> view matrix models
> #5,0.004847,-0.95694,-0.29026,319.33,0.99999,0.0047609,0.0010029,-5.9699,0.00042225,-0.29026,0.95695,79.789
> view matrix models
> #5,-0.56391,-0.58227,-0.58564,373.57,0.083333,-0.74564,0.66111,150.99,-0.82162,0.32401,0.469,154.45
> view matrix models
> #5,-0.65045,0.051995,-0.75777,317.64,-0.2588,-0.95313,0.15675,272.57,-0.7141,0.29807,0.63342,127.74
> view matrix models
> #5,-0.28731,-0.094836,-0.95313,307.9,-0.35147,-0.91523,0.19701,275.93,-0.89102,0.3916,0.22962,177.83
> view matrix models
> #5,-0.09071,-0.050342,-0.9946,279.99,-0.20231,-0.97696,0.0679,276.84,-0.97511,0.20738,0.078436,228
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.09071,-0.050342,-0.9946,280.18,-0.20231,-0.97696,0.0679,276.22,-0.97511,0.20738,0.078436,228.17
> open
> /Users/cristianrosales/Downloads/cryosparc_P380_J1403_004_volume_map.mrc
Opened cryosparc_P380_J1403_004_volume_map.mrc as #19, grid size 180,180,180,
pixel 1.45, shown at level 0.364, step 1, values float32
> volume #19 level 0.1198
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.72608,0.41285,0.54988,153.55,-0.61199,-0.023417,-0.79052,287.15,-0.31349,-0.9105,0.26966,270.19
> view matrix models
> #5,-0.52212,0.15846,0.83802,132.38,-0.79681,0.25974,-0.54556,250.41,-0.30411,-0.95259,-0.009354,301.51
> view matrix models
> #5,-0.81993,0.33148,0.46674,184.8,-0.48709,0.024388,-0.87301,272.26,-0.30077,-0.94315,0.14147,285.23
> view matrix models
> #5,-0.47242,0.29929,-0.829,268.39,-0.38637,-0.91571,-0.11041,309.72,-0.79217,0.26814,0.54824,150.46
> view matrix models
> #5,-0.48766,-0.27571,-0.82836,346.53,-0.41311,-0.76301,0.49716,234.26,-0.76911,0.58464,0.25819,133.52
> view matrix models
> #5,-0.21137,-0.7764,0.59374,238.73,0.71157,0.29421,0.63805,-68.373,-0.67007,0.55735,0.49028,101.57
> view matrix models
> #5,-0.04264,-0.72078,0.69185,199.53,0.84877,0.33917,0.40566,-70.018,-0.52704,0.60452,0.59731,66.033
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.04264,-0.72078,0.69185,204.11,0.84877,0.33917,0.40566,-61.752,-0.52704,0.60452,0.59731,63.865
> view matrix models
> #5,-0.04264,-0.72078,0.69185,204.45,0.84877,0.33917,0.40566,-64.994,-0.52704,0.60452,0.59731,64.159
> open "/Users/cristianrosales/Downloads/cryosparc_P380_J1403_004_volume_map
> (1).mrc"
Opened cryosparc_P380_J1403_004_volume_map (1).mrc as #20, grid size
180,180,180, pixel 1.45, shown at level 0.364, step 1, values float32
> volume #20 level 0.2013
> volume #20 level 0.09651
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2,6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 10 days, 19 hours, 9 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Radeon Pro 555X:
Chipset Model: Radeon Pro 555X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00e3
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501P-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP Z27:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: CN49080HD4
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash setting volume level(?) |
comment:2 by , 15 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash setting volume level(?) → Crash in event loop, setting volume level, probable Apple AMD graphics crash |
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Very likely an Apple AMD graphics crash. The stack trace is missing symbols so little info about exactly where it crashed, except it was in the Qt event loop.