![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 51 minutes ago
Last modified 49 minutes ago
#20850 assigned defect
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f029dd80 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imaging, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._webp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.dssp._dssp (total: 114)
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{
"uptime" : 330000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 49738,
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"build" : "25F84",
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"captureTime" : "2026-08-13 19:05:20.0114 +0200",
"codeSigningMonitor" : 2,
"incident" : "EF39D985-6229-43A9-9F21-F84598E884E5",
"pid" : 59746,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-08-11 11:17:57.9316 +0200",
"procStartAbsTime" : 5639605513864,
"procExitAbsTime" : 7965033464002,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"01C7356A-D39E-5EF8-9986-FCAB10057ABE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BB58D8D2-8D93-1262-608A-0AAABD742ED8",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "84F1A8A8-C1B3-4D57-90DD-93DA253C7BB9",
"sip" : "enabled",
"vmRegionInfo" : "0x100000171 is not in any region. Bytes before following region: 5783183\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100584000-100588000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
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"ktriageinfo" : "CL - (arg = 0x0) cluster_pagein past EOF\nAPFS - (arg = 0x3be2001600200040) cluster_pagein() failed\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/reconstruction_only/cryosparc_P429_J648_volume_map.mrc
Opened cryosparc_P429_J648_volume_map.mrc as #1, grid size 512,512,512, pixel
0.82, shown at level 0.0352, step 2, values float32
> volume #1 step 1
> volume #1 level 0.08317
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/Homo_refine/cryosparc_P436_J104_010_volume_map_sharp.mrc
Opened cryosparc_P436_J104_010_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 0.82, shown at level 0.141, step 2, values float32
> volume #2 step 1
> volume #2 level 0.4384
> volume #2 level 0.4597
> close #2
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/Homo_refine/cryosparc_P436_J104_010_volume_map.mrc
Opened cryosparc_P436_J104_010_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.82, shown at level 0.0398, step 2, values float32
> volume #2 level 0.1343
> volume #2 step 1
> volume #2 level 0.2293
> ui tool show "Fit in Map"
> select add #2
2 models selected
> ui mousemode right rotate
> select subtract #2
Nothing selected
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.74984,-0.44906,0.48589,41.595,0.094901,-0.65379,-0.7507,478.8,0.65478,0.60901,-0.44762,44.691
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.74984,-0.44906,0.48589,55.33,0.094901,-0.65379,-0.7507,477.07,0.65478,0.60901,-0.44762,59.2
> fitmap #2 inMap #1
Fit map cryosparc_P436_J104_010_volume_map.mrc in map
cryosparc_P429_J648_volume_map.mrc using 228558 points
correlation = 0.6116, correlation about mean = 0.07121, overlap = 5602
steps = 112, shift = 2.59, angle = 5.52 degrees
Position of cryosparc_P436_J104_010_volume_map.mrc (#2) relative to
cryosparc_P429_J648_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.80738923 -0.41477804 0.41962104 49.49492866
0.08097445 -0.62657358 -0.77514430 481.73377094
0.58443629 0.65982174 -0.47230233 68.29547870
Axis 0.93966179 -0.10792631 0.32463463
Axis point 0.00000000 228.18630486 144.97044127
Rotation angle (degrees) 130.22143165
Shift along axis 16.68782256
> view matrix models
> #2,0.80739,-0.41478,0.41962,47.87,0.080974,-0.62657,-0.77514,482.65,0.58444,0.65982,-0.4723,70.517
> fitmap #2 inMap #1
Fit map cryosparc_P436_J104_010_volume_map.mrc in map
cryosparc_P429_J648_volume_map.mrc using 228558 points
correlation = 0.9848, correlation about mean = 0.8849, overlap = 1.508e+04
steps = 72, shift = 4.02, angle = 0.265 degrees
Position of cryosparc_P436_J104_010_volume_map.mrc (#2) relative to
cryosparc_P429_J648_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.80829847 -0.41612856 0.41652204 48.38426100
0.08005470 -0.62319431 -0.77795893 486.01912434
0.58330509 0.66216756 -0.47041396 67.62263804
Axis 0.93983921 -0.10884409 0.32381356
Axis point 0.00000000 230.19444972 146.46506372
Rotation angle (degrees) 129.99007461
Shift along axis 14.47024473
> volume #2 level 0.2018
> select subtract #2
Nothing selected
> volume #2 level 0.2093
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/Homo_refine/cryosparc_P436_J58_009_volume_map.mrc
Opened cryosparc_P436_J58_009_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.82, shown at level 0.0468, step 2, values float32
> volume #3 level 0.2038
> volume #3 step 1
> close #3
> volume #1 level 0.07369
> volume #1 level 0.0779
> open 7o3h fromDatabase pdb format mmcif
7o3h title:
Murine CIII2 focus-refined from supercomplex CICIII2 [more info...]
Chain information for 7o3h #3
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE 1-446
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE 1-439
C N | Cytochrome b | CYB_MOUSE 1-381
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE 1-241
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE 1-196
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE 1-110
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE 1-81
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE 1-76
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE 1-63
K V | Cytochrome b-c1 complex subunit 10 | QCR10_MOUSE 1-56
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE 1-78
Non-standard residues in 7o3h #3
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
FES — FE2/S2 (inorganic) cluster
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
> select add #3
33700 atoms, 34505 bonds, 43 pseudobonds, 4185 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.85215,0.20176,0.48284,-43.076,0.19118,0.73886,-0.64616,57.485,-0.48712,0.64294,0.59105,21.591
> view matrix models
> #3,0.41304,0.78512,0.46151,-52.012,0.77487,-0.036699,-0.63106,70.446,-0.47852,0.61826,-0.62352,121.11
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.41304,0.78512,0.46151,-68.521,0.77487,-0.036699,-0.63106,93.901,-0.47852,0.61826,-0.62352,259.97
> view matrix models
> #3,0.41304,0.78512,0.46151,114.38,0.77487,-0.036699,-0.63106,167.96,-0.47852,0.61826,-0.62352,316.02
> view matrix models
> #3,0.41304,0.78512,0.46151,108.82,0.77487,-0.036699,-0.63106,211.37,-0.47852,0.61826,-0.62352,276.21
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.92312,-0.35146,0.15594,285.5,-0.37146,0.71046,-0.59772,229.95,0.099285,-0.60969,-0.7864,332.6
> view matrix models
> #3,-0.71331,-0.37904,0.58951,239.54,-0.6455,0.68293,-0.34195,227.35,-0.27298,-0.62445,-0.73181,351.38
> view matrix models
> #3,-0.88093,-0.3902,0.26779,276.36,-0.47239,0.69105,-0.54707,233.11,0.028411,-0.60843,-0.7931,337.3
> view matrix models
> #3,-0.78775,-0.48959,0.37383,268.48,-0.61423,0.57847,-0.53674,247.88,0.046538,-0.65244,-0.75641,336.03
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.78775,-0.48959,0.37383,268.05,-0.61423,0.57847,-0.53674,247.25,0.046538,-0.65244,-0.75641,329.82
> fitmap #3 inMap #1
Fit molecule 7o3h (#3) to map cryosparc_P429_J648_volume_map.mrc (#1) using
33700 atoms
average map value = 0.07725, steps = 160
shifted from previous position = 3.08
rotated from previous position = 15.5 degrees
atoms outside contour = 20942, contour level = 0.077905
Position of 7o3h (#3) relative to cryosparc_P429_J648_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.63384653 -0.63273240 0.44484635 261.28374934
-0.74747886 0.35329263 -0.56254747 274.69690126
0.19878107 -0.68908201 -0.69688741 318.09865427
Axis -0.42242564 0.82146964 -0.38307207
Axis point 215.73664803 0.00000000 211.24870885
Rotation angle (degrees) 171.38632196
Shift along axis -6.57250250
> view matrix models
> #3,-0.63385,-0.63273,0.44485,259.02,-0.74748,0.35329,-0.56255,274.04,0.19878,-0.68908,-0.69689,318.24
> fitmap #3 inMap #1
Fit molecule 7o3h (#3) to map cryosparc_P429_J648_volume_map.mrc (#1) using
33700 atoms
average map value = 0.07725, steps = 60
shifted from previous position = 2.36
rotated from previous position = 0.00482 degrees
atoms outside contour = 20944, contour level = 0.077905
Position of 7o3h (#3) relative to cryosparc_P429_J648_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.63388656 -0.63273981 0.44477876 261.28494817
-0.74743170 0.35331404 -0.56259668 274.69391238
0.19883074 -0.68906423 -0.69689082 318.08939191
Axis -0.42240720 0.82147729 -0.38307600
Axis point 215.72517920 0.00000000 211.24919355
Rotation angle (degrees) 171.39053898
Shift along axis -6.56624745
> hide sel atoms
> show sel cartoons
> view matrix models
> #3,-0.63389,-0.63274,0.44478,255.58,-0.74743,0.35331,-0.5626,276.15,0.19883,-0.68906,-0.69689,317.03
> fitmap #3 inMap #1
Fit molecule 7o3h (#3) to map cryosparc_P429_J648_volume_map.mrc (#1) using
33700 atoms
average map value = 0.07725, steps = 124
shifted from previous position = 5.99
rotated from previous position = 0.0113 degrees
atoms outside contour = 20950, contour level = 0.077905
Position of 7o3h (#3) relative to cryosparc_P429_J648_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.63381860 -0.63268498 0.44495357 261.27293587
-0.74750813 0.35321171 -0.56255939 274.69651972
0.19876007 -0.68916702 -0.69680933 318.08920068
Axis -0.42243613 0.82144362 -0.38311629
Axis point 215.74294986 0.00000000 211.24712529
Rotation angle (degrees) 171.38152441
Shift along axis -6.58857817
> volume #1 level 0.06725
> close #3
> open 7o3e fromDatabase pdb format mmcif
7o3e title:
Murine supercomplex CIII2CIV in the intermediate locked conformation [more
info...]
Chain information for 7o3e #3
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_MOUSE 1-446
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_MOUSE 1-439
C N | Cytochrome b | CYB_MOUSE 1-381
D O | Cytochrome c1, heme protein, mitochondrial | CY1_MOUSE 1-241
F Q | Cytochrome b-c1 complex subunit 7 | Q9CQB4_MOUSE 1-110
G R | Cytochrome b-c1 complex subunit 8 | QCR8_MOUSE 1-81
H S | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_MOUSE 1-76
I | Cox7a2l protein | Q99KD6_MOUSE 1-113
J U | Cytochrome b-c1 complex subunit 9 | QCR9_MOUSE 1-63
P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_MOUSE 1-196
T | Cytochrome b-c1 complex subunit 9 | UCRI_MOUSE 1-78
a | Cytochrome c oxidase subunit 1 | COX1_MOUSE 1-514
b | Cytochrome c oxidase subunit 2 | COX2_MOUSE 1-227
c | Cytochrome c oxidase subunit 3 | COX3_MOUSE 1-261
d | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | COX41_MOUSE 1-147
e | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_MOUSE 1-109
f | Cytochrome c oxidase subunit 5B, mitochondrial | COX5B_MOUSE 1-99
g | Cytochrome c oxidase subunit 6A2, mitochondrial | CX6A2_MOUSE 1-85
h | Cytochrome c oxidase subunit 6B1 | CX6B1_MOUSE 1-85
i | Cytochrome c oxidase subunit 6C | COX6C_MOUSE 1-75
k | Cytochrome c oxidase subunit 7B, mitochondrial | COX7B_MOUSE 1-56
l | Cytochrome c oxidase subunit 7C, mitochondrial | COX7C_MOUSE 1-47
m | Cytochrome c oxidase subunit 8B, mitochondrial | COX8B_MOUSE 1-46
Non-standard residues in 7o3e #3
---
3PE — 1,2-Distearoyl-sn-glycerophosphoethanolamine (3-Sn-
phosphatidylethanolamine; 1,2-diacyl-Sn-glycero-3-phosphoethanolamine)
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
NA — sodium ion
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)
TGL — tristearoylglycerol (triacylglycerol)
ZN — zinc ion
> hide atoms
> show cartoons
> select add #3
44039 atoms, 45184 bonds, 70 pseudobonds, 5451 residues, 3 models selected
> view matrix models #3,1,0,0,109.52,0,1,0,72.576,0,0,1,151.08
> view matrix models #3,1,0,0,103.3,0,1,0,74.93,0,0,1,145.27
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.24772,0.5458,-0.80046,220.26,-0.78302,0.37376,0.49717,157.63,0.57054,0.74994,0.33478,82.189
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.24772,0.5458,-0.80046,230.63,-0.78302,0.37376,0.49717,192.37,0.57054,0.74994,0.33478,62.313
> view matrix models
> #3,-0.24772,0.5458,-0.80046,231.09,-0.78302,0.37376,0.49717,186.32,0.57054,0.74994,0.33478,56.249
> fitmap #3 inMap #1
Fit molecule 7o3e (#3) to map cryosparc_P429_J648_volume_map.mrc (#1) using
44039 atoms
average map value = 0.07085, steps = 272
shifted from previous position = 18.5
rotated from previous position = 23.5 degrees
atoms outside contour = 28553, contour level = 0.067246
Position of 7o3e (#3) relative to cryosparc_P429_J648_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.22101657 0.17522918 -0.95939898 299.47123313
-0.86238255 0.42429979 0.27616304 212.35887244
0.45546461 0.88840555 0.05733730 65.98271541
Axis 0.32946190 -0.76137092 -0.55836294
Axis point 191.12726593 0.00000000 103.19203855
Rotation angle (degrees) 111.69648396
Shift along axis -99.86181173
> select #3/a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u
14047 atoms, 14472 bonds, 33 pseudobonds, 1723 residues, 2 models selected
> hide sel cartoons
> select #3/I
834 atoms, 856 bonds, 111 residues, 1 model selected
> hide sel cartoons
> select #3/A,B,C,D,E,F,G,H,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
29158 atoms, 29856 bonds, 37 pseudobonds, 3617 residues, 3 models selected
> select clear
> color #3 #4f8f00ff
> color #3 #ff9300ff
> set bgColor white
> volume #1 level 0.06325
> volume #1 level 0.07391
> volume #1 color black
> volume #1 color #00000052
> volume #1 color #00000080
> volume #1 style mesh
> volume #1 style image
> volume #1 level -0.005934,0 level 0.03518,0.8 level 0.5327,1
> volume #1 level -0.005934,0 level 0.02319,0.9853 level 0.5327,1
> volume #1 level -0.005934,0 level 0.06582,1 level 0.5327,1
> volume #1 level 0.05002,0 level 0.06582,1 level 0.5327,1
> volume #1 level 0.05002,0 level 0.08181,1 level 0.5327,1
> volume #1 level 0.07267,0.2206 level 0.08181,1 level 0.5327,1
> volume #1 style surface
> color #1 #ffffffdb models
> color #1 white models
> color #1 #fffffffb models
> color #1 silver models
> color #1 #c0c0c0a8 models
> color #1 #919191ff models
> color #1 #9191919c models
> hide #!3 models
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/Maps_models/emd_12705.map
Opened emd_12705.map as #4, grid size 152,202,170, pixel 1.06,1.06,1.06, shown
at level 0.105, step 1, values float32
> select add #4
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-36.205,0,1,0,40.439,0,0,1,77.056
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.70122,0.05636,-0.71071,48.666,0.33263,0.85586,0.39605,-8.1626,0.6306,-0.51412,0.5814,120.7
> view matrix models
> #4,0.98074,0.051862,0.18833,-57.922,-0.026781,0.99071,-0.13335,56.134,-0.1935,0.12574,0.97301,81.711
> view matrix models
> #4,0.52764,0.27697,-0.80305,47.79,-0.81238,-0.11174,-0.57232,277.65,-0.24825,0.95436,0.16604,73.963
> view matrix models
> #4,-0.085811,0.059015,-0.99456,138.12,-0.87797,0.4674,0.10349,157.63,0.47097,0.88207,0.011705,38.621
> view matrix models
> #4,-0.27178,0.11381,-0.95561,143.51,-0.84252,0.45173,0.29342,138.56,0.46507,0.88486,-0.026885,42.431
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.27178,0.11381,-0.95561,321.97,-0.84252,0.45173,0.29342,175.56,0.46507,0.88486,-0.026885,93.268
> view matrix models
> #4,-0.27178,0.11381,-0.95561,310.06,-0.84252,0.45173,0.29342,196.66,0.46507,0.88486,-0.026885,70.722
> select subtract #4
Nothing selected
> fitmap #4 inMap #1
Fit map emd_12705.map in map cryosparc_P429_J648_volume_map.mrc using 52181
points
correlation = 0.6811, correlation about mean = -0.1275, overlap = 571.5
steps = 156, shift = 10.3, angle = 5 degrees
Position of emd_12705.map (#4) relative to cryosparc_P429_J648_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.22008743 0.17588221 -0.95949309 299.27049391
-0.86195828 0.42545840 0.27570469 212.24749644
0.45671594 0.88772214 0.05796508 65.92016077
Axis 0.32914982 -0.76165303 -0.55816221
Axis point 190.97731432 -0.00000000 103.34564041
Rotation angle (degrees) 111.61278237
Shift along axis -99.94826170
> volume #4 level 0.08533
> volume #1 level 0.08762
> volume #4 level 0.07416
> volume #1 level 0.09311
> volume #1 level 0.07802
> volume #1 level 0.06979
> volume #1 level 0.089
> volume #1 level 0.07116
> open 9etz fromDatabase pdb format mmcif
Summary of feedback from opening 9etz fetched from pdb
---
note | Fetching compressed mmCIF 9etz from http://files.rcsb.org/download/9etz.cif
9etz title:
III2IV respiratory supercomplex from Saccharomyces cerevisiae [more info...]
Chain information for 9etz #5
---
Chain | Description | UniProt
A L | Cytochrome b-c1 complex subunit 1, mitochondrial | QCR1_YEAST 27-457
B M | Cytochrome b-c1 complex subunit 2, mitochondrial | QCR2_YEAST 17-368
C N | Cytochrome b | CYB_YEAST 1-385
D O | Cytochrome c1, heme protein, mitochondrial | CY1_YEAST 62-308
E P | Cytochrome b-c1 complex subunit Rieske, mitochondrial | UCRI_YEAST 31-215
F Q | Cytochrome b-c1 complex subunit 6, mitochondrial | QCR6_YEAST 73-147
G R | Cytochrome b-c1 complex subunit 7, mitochondrial | QCR7_YEAST 2-127
H S | Cytochrome b-c1 complex subunit 8, mitochondrial | QCR8_YEAST 2-94
I T | Cytochrome b-c1 complex subunit 9, mitochondrial | QCR9_YEAST 2-58
J U | Cytochrome b-c1 complex subunit 10, mitochondrial | QCR10_YEAST 2-77
a | Cytochrome c oxidase subunit 1 | COX1_YEAST 1-534
b | Cytochrome c oxidase subunit 2 | COX2_YEAST 16-251
c | Cytochrome c oxidase subunit 3 | COX3_YEAST 1-269
d | Cytochrome c oxidase subunit 4, mitochondrial | COX4_YEAST 30-149
e | Cytochrome c oxidase subunit 5A, mitochondrial | COX5A_YEAST 21-153
f | Cytochrome c oxidase subunit 6, mitochondrial | COX6_YEAST 45-146
g | Cytochrome c oxidase subunit 7, mitochondrial | COX7_YEAST 2-60
h | Cytochrome c oxidase subunit 8, mitochondrial | COX8_YEAST 28-78
i | Cytochrome c oxidase subunit 9, mitochondrial | COX9_YEAST 2-56
j | Cytochrome c oxidase subunit 12, mitochondrial | COX12_YEAST 7-81
k | Cytochrome c oxidase subunit 13, mitochondrial | COX13_YEAST 13-125
l | Cytochrome c oxidase subunit 26, mitochondrial | COX26_YEAST 22-66
Non-standard residues in 9etz #5
---
CA — calcium ion
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)
CU — copper (II) ion
CUA — dinuclear copper ion
FES — FE2/S2 (inorganic) cluster
HEA — heme-A
HEC — heme C
HEM — protoporphyrin IX containing Fe (HEME)
MG — magnesium ion
PCF — 1,2-diacyl-Sn-glycero-3-phoshocholine
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)
UQ6 — 5-(3,7,11,15,19,23-hexamethyl-
tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol
ZN — zinc ion
> hide #!5 atoms
> show #!5 cartoons
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> view matrix models #5,1,0,0,-5.7786,0,1,0,5.7017,0,0,1,-27.378
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.34269,-0.90087,0.26643,550.05,-0.88773,0.21774,-0.40561,562.39,0.30739,-0.37552,-0.87435,435.11
> view matrix models
> #5,-0.37696,-0.74508,0.55023,451.28,-0.8962,0.14337,-0.41985,587.25,0.23394,-0.65138,-0.72179,489.54
> view matrix models
> #5,-0.92347,0.37593,0.076629,440.84,0.34947,0.90665,-0.23632,-14.897,-0.15831,-0.19145,-0.96865,547.07
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.92347,0.37593,0.076629,333.08,0.34947,0.90665,-0.23632,-54.872,-0.15831,-0.19145,-0.96865,547.74
> view matrix models
> #5,-0.92347,0.37593,0.076629,334.42,0.34947,0.90665,-0.23632,-54.949,-0.15831,-0.19145,-0.96865,551.39
> view matrix models
> #5,-0.92347,0.37593,0.076629,334.24,0.34947,0.90665,-0.23632,-54.999,-0.15831,-0.19145,-0.96865,551.23
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.98179,0.058799,0.18062,406.59,-0.15768,0.27795,-0.94757,426.1,-0.10592,-0.95879,-0.26362,559.41
> view matrix models
> #5,-0.94796,0.025012,0.3174,372,-0.25471,0.53855,-0.80317,352.93,-0.19102,-0.84222,-0.50415,613.17
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.94796,0.025012,0.3174,386.09,-0.25471,0.53855,-0.80317,343.56,-0.19102,-0.84222,-0.50415,611.2
> view matrix models
> #5,-0.94796,0.025012,0.3174,373.65,-0.25471,0.53855,-0.80317,337.89,-0.19102,-0.84222,-0.50415,621.54
> view matrix models
> #5,-0.94796,0.025012,0.3174,378.72,-0.25471,0.53855,-0.80317,327.17,-0.19102,-0.84222,-0.50415,628.3
> view matrix models
> #5,-0.94796,0.025012,0.3174,374.44,-0.25471,0.53855,-0.80317,335.16,-0.19102,-0.84222,-0.50415,627.15
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.52931,0.61118,-0.58846,15.197,0.032377,-0.70764,-0.70583,544.75,-0.84781,0.35455,-0.39435,487.49
> view matrix models
> #5,0.78696,0.11576,-0.60605,70.379,-0.61352,0.042413,-0.78854,562.45,-0.065577,0.99237,0.1044,-24.383
> view matrix models
> #5,-0.89214,0.37657,0.24958,285.25,-0.075285,0.4208,-0.90402,337.36,-0.44545,-0.8253,-0.34706,658.78
> view matrix models
> #5,-0.62389,0.3745,0.68594,101.25,0.16138,0.92053,-0.35579,7.6655,-0.76467,-0.11127,-0.63474,640.3
> view matrix models
> #5,-0.89042,-0.1048,0.44291,360.11,-0.28586,0.88602,-0.36503,149.12,-0.35418,-0.45164,-0.81889,652.04
> view matrix models
> #5,-0.91347,0.052049,0.40356,336.52,-0.1762,0.84338,-0.50761,162.72,-0.36677,-0.53479,-0.76123,662.82
> view matrix models
> #5,-0.90083,0.14575,0.40897,307.68,-0.089332,0.8596,-0.50311,132.17,-0.42487,-0.48975,-0.76133,668.33
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.90083,0.14575,0.40897,311.33,-0.089332,0.8596,-0.50311,125.16,-0.42487,-0.48975,-0.76133,649.67
> fitmap #5 inMap #1
Fit molecule 9etz (#5) to map cryosparc_P429_J648_volume_map.mrc (#1) using
48795 atoms
average map value = 0.07776, steps = 248
shifted from previous position = 8.81
rotated from previous position = 6.49 degrees
atoms outside contour = 30289, contour level = 0.071164
Position of 9etz (#5) relative to cryosparc_P429_J648_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.87125915 0.19293606 0.45131273 282.27352321
-0.11742572 0.81086323 -0.57333414 168.35438886
-0.47656973 -0.55251833 -0.68381635 654.23382247
Axis 0.02127027 0.94814088 -0.31713790
Axis point 227.59453988 0.00000000 316.24319837
Rotation angle (degrees) 150.70431555
Shift along axis -41.85462967
> volume #1 level 0.07254
> select clear
> select #5/a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> ui tool show "Color Actions"
> color sel light slate gray
> color sel cadet blue
> color sel steel blue
> color sel turquoise
> color sel light sea green
> color sel deep sky blue
> color sel royal blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> color sel powder blue
> color sel gainsboro
> color sel light cyan
> color sel powder blue
> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
33775 atoms, 34573 bonds, 43 pseudobonds, 4094 residues, 2 models selected
> ui tool show "Color Actions"
> color sel peach puff
> color sel wheat
> color sel moccasin
> color sel navajo white
> color sel tan
> volume #1 level 0.07254
> select clear
> select #5/E,P,U,J
4345 atoms, 4445 bonds, 7 pseudobonds, 532 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!5 & sel) #ff7e79ff
> color (#!5 & sel) #ff7e79fe
> color (#!5 & sel) #ff7e79e8
> color (#!5 & sel) #ff7e79d3
> color (#!5 & sel) #ff7e79be
> color (#!5 & sel) #ff7e79a8
> color (#!5 & sel) #ff7e79a1
> color (#!5 & sel) #ff7e799b
> color (#!5 & sel) #ff7e7996
> color (#!5 & sel) #ff7e7991
> color (#!5 & sel) #ff7e798a
> color (#!5 & sel) #ff7e7983
> color (#!5 & sel) #ff7e797e
> color (#!5 & sel) #ff7e797b
> color (#!5 & sel) #ff7e797a
> color (#!5 & sel) #ff7e7979
> color (#!5 & sel) #ff7e7976
> color (#!5 & sel) #ff7e7979
> color (#!5 & sel) #ff7e7978
> color (#!5 & sel) #ff7e7977
> color (#!5 & sel) #ff7e7976
> color (#!5 & sel) #ff7e7975
> color (#!5 & sel) #ff7e7973
> color (#!5 & sel) #ff7e7972
> color (#!5 & sel) #ff7e7971
> color (#!5 & sel) #ff7e7970
> color (#!5 & sel) #ff7e796f
> color (#!5 & sel) #ff7e796e
> color (#!5 & sel) #ff7e796d
> color (#!5 & sel) #ff7e796a
> color (#!5 & sel) #ff7e7969
> color (#!5 & sel) #ff7e7968
> color (#!5 & sel) #ff7e7967
> color (#!5 & sel) #ff7e7966
> color (#!5 & sel) #ff7e7965
> color (#!5 & sel) #ff7e7964
> color (#!5 & sel) #ff7e7963
> color (#!5 & sel) #ff7e7962
> color (#!5 & sel) #ff7e7961
> color (#!5 & sel) #ff7e7960
> color (#!5 & sel) #ff7e795f
> color (#!5 & sel) #ff7e7960
> color (#!5 & sel) #ff7e7962
> color (#!5 & sel) #ff7e7964
> color (#!5 & sel) #ff7e7968
> color (#!5 & sel) #ff7e796a
> color (#!5 & sel) #ff7e796c
> color (#!5 & sel) #ff7e796e
> color (#!5 & sel) #ff7e796f
> color (#!5 & sel) #ff7e7971
> color (#!5 & sel) #ff7e7972
> color (#!5 & sel) #ff7e7973
> color (#!5 & sel) #ff7e7974
> color (#!5 & sel) #ff7e7975
> color (#!5 & sel) #ff7e7974
> color (#!5 & sel) #ff7e7973
> color (#!5 & sel) #ff7e796f
> color (#!5 & sel) #ff7e7969
> color (#!5 & sel) #ff7e7965
> color (#!5 & sel) #ff7e795e
> color (#!5 & sel) #ff7e795a
> color (#!5 & sel) #ff7e7957
> color (#!5 & sel) #ff7e7955
> color (#!5 & sel) #ff7e7953
> color (#!5 & sel) #ff7e7951
> color (#!5 & sel) #ff7e7950
> color (#!5 & sel) #ff7e794f
> color (#!5 & sel) #ff7e794b
> color (#!5 & sel) #ff7e794a
> color (#!5 & sel) #ff7e7949
> color (#!5 & sel) #ff7e7945
> color (#!5 & sel) #ff7e7943
> color (#!5 & sel) #ff7e7941
> color (#!5 & sel) #ff7e793f
> color (#!5 & sel) #ff7e793e
> color (#!5 & sel) #ff7e793d
> color (#!5 & sel) #ff7e793c
> color (#!5 & sel) #ff7e793a
> color (#!5 & sel) #ff7e7939
> color (#!5 & sel) #ff7e7937
> color (#!5 & sel) #ff7e7936
> color (#!5 & sel) #ff7e7935
> color (#!5 & sel) #ff7e7934
> color (#!5 & sel) #ff7e7933
> color (#!5 & sel) #ff7e7932
> color (#!5 & sel) #ff7e7931
> color (#!5 & sel) #ff7e7930
> color (#!5 & sel) #ff7e792f
> color (#!5 & sel) #ff7e7930
> color (#!5 & sel) #ff7e7931
> color (#!5 & sel) #ff7e7933
> color (#!5 & sel) #ff7e7934
> color (#!5 & sel) #ff7e7933
> select #5/E,P,U,J,T,I
5352 atoms, 5478 bonds, 7 pseudobonds, 648 residues, 2 models selected
> color (#!5 & sel) #ff7e7934
> select clear
> select #5/E,P,U,J,T,I
5352 atoms, 5478 bonds, 7 pseudobonds, 648 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light coral
> color sel crimson
> color (#!5 & sel) #ff7e7933
> color (#!5 & sel) #ff7e7965
> color (#!5 & sel) #ff7e79a9
> color (#!5 & sel) #ff7e79db
> color (#!5 & sel) #ff7e79ff
> color sel coral
> color sel crimson
> color sel indian red
> select clear
> volume #1 color #919191f4
> volume #1 color #919191
> volume #1 color #919191cb
> volume #1 color #919191
> volume #1 color #91919100
> volume #1 color #9191913b
> volume #1 color black
> volume #1 color #000000ef
> volume #1 color #00000052
> volume #1 color #ebebeb
> volume #1 color #d6d6d6
> volume #1 color silver
> volume #1 color darkgrey
> select #5/E,P,U,J,T,I
5352 atoms, 5478 bonds, 7 pseudobonds, 648 residues, 2 models selected
> ui tool show "Color Actions"
> color sel crimson
> color sel tomato
> color sel brown
> color sel coral
> color sel maroon
> color sel fire brick
> color sel salmon
> color sel indian red
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!1 models
> volume #1 level 0.0547
> volume #1 level 0.06842
> select #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> cartoon style (#!5 & sel) modeHelix tube sides 20
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> select clear
> volume #1 level 0.05059
> turn x 90
> turn x -90
> turn y -90
> turn y 90
> turn y -90
> turn y 90
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.tif
> width 9360 height 6840 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.tif
> width 93600 height 68400 supersample 4 transparentBackground true
Image size 93600 x 68400 too large, exceeds maximum OpenGL render buffer size
16384
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.tif
> width 16384 height 11973 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.jpg
> width 9360 height 6840 supersample 4
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.png
> width 9360 height 6840 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.png
> width 16000 height 11692 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A.png
> width 9360 height 6840 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1A_small.png
> width 936 height 684 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1B.png
> width 9360 height 6840 supersample 4 transparentBackground true
> volume #1 level 0.08214
> volume #1 level 0.07939
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1D.png
> width 9360 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1C.png
> width 9360 height 6840 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1E.png
> width 9360 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1F.png
> width 9360 height 6840 supersample 4 transparentBackground true
> volume #1 color silver
> volume #1 color darkgrey
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.88371,0.18643,0.4293,283.54,0.023789,0.93395,-0.35662,90.392,-0.46743,-0.30494,-0.82977,565.71
> fitmap #2 inMap #1
Fit map cryosparc_P436_J104_010_volume_map.mrc in map
cryosparc_P429_J648_volume_map.mrc using 257609 points
correlation = 0.9877, correlation about mean = 0.9129, overlap = 1.576e+04
steps = 144, shift = 13.2, angle = 2.7 degrees
Position of cryosparc_P436_J104_010_volume_map.mrc (#2) relative to
cryosparc_P429_J648_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.88074256 0.15847480 0.44629394 275.90865632
0.01148920 0.94922520 -0.31438752 72.14204859
-0.47345596 -0.27176691 -0.83784378 563.26233274
Axis 0.04571088 0.98643763 -0.15764299
Axis point 206.80618238 0.00000000 252.77314383
Rotation angle (degrees) 152.21223764
Shift along axis -5.01870310
> fitmap #4 inMap #1
Fit map emd_12705.map in map cryosparc_P429_J648_volume_map.mrc using 127446
points
correlation = 0.6971, correlation about mean = 0.02079, overlap = 1061
steps = 44, shift = 0.0645, angle = 0.133 degrees
Position of emd_12705.map (#4) relative to cryosparc_P429_J648_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.22187739 0.17497216 -0.95924719 299.54010037
-0.86220422 0.42423776 0.27681438 212.31743862
0.45538369 0.88848583 0.05673297 66.04467753
Axis 0.32926239 -0.76149498 -0.55831145
Axis point 191.10801173 0.00000000 103.13404741
Rotation angle (degrees) 111.74357809
Shift along axis -99.92487577
> select clear
> volume #2 color darkgrey
> volume #2 level 0.1033
> volume #1 level 0.0506
> volume #2 level 0.1386
> volume #2 level 0.2093
> select #5/a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> hide sel cartoons
> turn y 180
> volume #2 level 0.139
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1G.png
> width 9440 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1H.png
> width 9440 height 6840 supersample 4 transparentBackground true
> volume #2 level 0.209
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1J.png
> width 9440 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1I.png
> width 9440 height 6840 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1K.png
> width 9440 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1L.png
> width 9440 height 6840 supersample 4 transparentBackground true
> volume #1 level 0.0794
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1C_zoom.png
> width 9440 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1C_zoom.png
> width 9440 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1D_zoom.png
> width 9440 height 6840 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1J_zoom.png
> width 9440 height 6840 supersample 4 transparentBackground true
> turn y 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig_1I_zoom.png
> width 9440 height 6840 supersample 4 transparentBackground true
> close #3
> close #4
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig1.cxs
> includeMaps true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> lighting simple
> show sel surfaces
> hide sel surfaces
> select clear
> show surfaces
> hide surfaces
> close #1
> close #2
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J107_003_volume_map.mrc
Opened cryosparc_P436_J107_003_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.82, shown at level 0.0239, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J108_003_volume_map.mrc
Opened cryosparc_P436_J108_003_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.82, shown at level 0.0233, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J109_005_volume_map.mrc
Opened cryosparc_P436_J109_005_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.82, shown at level 0.0238, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J110_005_volume_map.mrc
Opened cryosparc_P436_J110_005_volume_map.mrc as #4, grid size 512,512,512,
pixel 0.82, shown at level 0.0258, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J111_005_volume_map.mrc
Opened cryosparc_P436_J111_005_volume_map.mrc as #6, grid size 512,512,512,
pixel 0.82, shown at level 0.0246, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J112_005_volume_map.mrc
Opened cryosparc_P436_J112_005_volume_map.mrc as #7, grid size 512,512,512,
pixel 0.82, shown at level 0.0245, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J113_004_volume_map.mrc
Opened cryosparc_P436_J113_004_volume_map.mrc as #8, grid size 512,512,512,
pixel 0.82, shown at level 0.0244, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J114_003_volume_map.mrc
Opened cryosparc_P436_J114_003_volume_map.mrc as #9, grid size 512,512,512,
pixel 0.82, shown at level 0.0249, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J115_005_volume_map.mrc
Opened cryosparc_P436_J115_005_volume_map.mrc as #10, grid size 512,512,512,
pixel 0.82, shown at level 0.0236, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J116_003_volume_map.mrc
Opened cryosparc_P436_J116_003_volume_map.mrc as #11, grid size 512,512,512,
pixel 0.82, shown at level 0.0246, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J117_003_volume_map.mrc
Opened cryosparc_P436_J117_003_volume_map.mrc as #12, grid size 512,512,512,
pixel 0.82, shown at level 0.0255, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J118_003_volume_map.mrc
Opened cryosparc_P436_J118_003_volume_map.mrc as #13, grid size 512,512,512,
pixel 0.82, shown at level 0.0249, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J119_004_volume_map.mrc
Opened cryosparc_P436_J119_004_volume_map.mrc as #14, grid size 512,512,512,
pixel 0.82, shown at level 0.0252, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J120_004_volume_map.mrc
Opened cryosparc_P436_J120_004_volume_map.mrc as #15, grid size 512,512,512,
pixel 0.82, shown at level 0.0259, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J121_003_volume_map.mrc
Opened cryosparc_P436_J121_003_volume_map.mrc as #16, grid size 512,512,512,
pixel 0.82, shown at level 0.0253, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J122_004_volume_map.mrc
Opened cryosparc_P436_J122_004_volume_map.mrc as #17, grid size 512,512,512,
pixel 0.82, shown at level 0.0246, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J123_006_volume_map.mrc
Opened cryosparc_P436_J123_006_volume_map.mrc as #18, grid size 512,512,512,
pixel 0.82, shown at level 0.0329, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J124_004_volume_map.mrc
Opened cryosparc_P436_J124_004_volume_map.mrc as #19, grid size 512,512,512,
pixel 0.82, shown at level 0.0253, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J125_004_volume_map.mrc
Opened cryosparc_P436_J125_004_volume_map.mrc as #20, grid size 512,512,512,
pixel 0.82, shown at level 0.0261, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J126_004_volume_map.mrc
Opened cryosparc_P436_J126_004_volume_map.mrc as #21, grid size 512,512,512,
pixel 0.82, shown at level 0.0243, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J127_004_volume_map.mrc
Opened cryosparc_P436_J127_004_volume_map.mrc as #22, grid size 512,512,512,
pixel 0.82, shown at level 0.0236, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J128_003_volume_map.mrc
Opened cryosparc_P436_J128_003_volume_map.mrc as #23, grid size 512,512,512,
pixel 0.82, shown at level 0.0248, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J129_003_volume_map.mrc
Opened cryosparc_P436_J129_003_volume_map.mrc as #24, grid size 512,512,512,
pixel 0.82, shown at level 0.0253, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J131_004_volume_map.mrc
Opened cryosparc_P436_J131_004_volume_map.mrc as #25, grid size 512,512,512,
pixel 0.82, shown at level 0.0269, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J132_003_volume_map.mrc
Opened cryosparc_P436_J132_003_volume_map.mrc as #26, grid size 512,512,512,
pixel 0.82, shown at level 0.0251, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J133_004_volume_map.mrc
Opened cryosparc_P436_J133_004_volume_map.mrc as #27, grid size 512,512,512,
pixel 0.82, shown at level 0.0251, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J134_004_volume_map.mrc
Opened cryosparc_P436_J134_004_volume_map.mrc as #28, grid size 512,512,512,
pixel 0.82, shown at level 0.0261, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J135_004_volume_map.mrc
Opened cryosparc_P436_J135_004_volume_map.mrc as #29, grid size 512,512,512,
pixel 0.82, shown at level 0.0257, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J136_004_volume_map.mrc
Opened cryosparc_P436_J136_004_volume_map.mrc as #30, grid size 512,512,512,
pixel 0.82, shown at level 0.0252, step 2, values float32
> volume #1 level 0.05289
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!4 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!10 models
> hide #!9 models
> hide #!11 models
> hide #!12 models
> hide #!15 models
> hide #!14 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!13 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!24 models
> hide #!23 models
> hide #!25 models
> hide #!26 models
> hide #!27 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!5 models
> volume #1 step 1
> volume #1 level 0.09063
> volume #2 step 1
> volume #2 level 0.0451
> volume #2 level 0.0857
> vop subtract #1 #2 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J108_003_volume_map.mrc #2" above
level 0.085698 is 0.99714
> volume #31 level 0.07769
> close #31
> volume #3 level 0.05075
> volume #3 step 1
> volume #3 level 0.06234
> volume #3 level 0.06775
> vop subtract #2 #3 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J109_005_volume_map.mrc #3" above
level 0.067749 is 1.0572
> volume #31 level 0.0817
> volume #31 level 0.07038
> volume #31 level 0.07238
> close #31
> vop subtract #1 #2 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J108_003_volume_map.mrc #2" above
level 0.085698 is 0.99714
> volume #31 level 0.07985
> close #31
> vop subtract #2 #3 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J109_005_volume_map.mrc #3" above
level 0.067749 is 1.0572
> close #31
> volume #4 step 1
> volume #4 level 0.07168
> vop subtract #3 #4 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J110_005_volume_map.mrc #4" above
level 0.071682 is 0.79986
> volume #31 level 0.07634
> volume #31 level 0.08016
> close #31
> volume #3 level 0.07779
> vop subtract #2 #4 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J110_005_volume_map.mrc #4" above
level 0.071682 is 0.94181
> close #31
> volume #3 level 0.07779
> volume #6 level 0.06057
> volume #6 step 1
> volume #6 level 0.06853
> volume #6 level 0.07967
> vop subtract #3 #6 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J111_005_volume_map.mrc #6" above
level 0.079673 is 0.93513
> volume #31 level 0.0567
> close #31
> volume #7 step 1
> volume #7 level 0.08229
> vop subtract #6 #7 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J112_005_volume_map.mrc #7" above
level 0.08229 is 0.91313
> volume #31 level 0.05907
> close #31
> volume #6 level 0.07729
> volume #7 level 0.08932
> vop subtract #6 #7 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J112_005_volume_map.mrc #7" above
level 0.089315 is 0.91721
> volume #31 level 0.06786
> close #31
> volume #8 step 1
> volume #8 level 0.07765
> vop subtract #7 #8 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J113_004_volume_map.mrc #8" above
level 0.077651 is 0.83478
> close #31
> volume #8 level 0.08564
> volume #9 level 0.09538
> volume #9 step 1
> volume #10 level 0.03734
> volume #10 step 1
> volume #10 level 0.07913
> vop subtract #8 #10 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J115_005_volume_map.mrc #10"
above level 0.079126 is 1.0442
> volume #31 level 0.07771
> close #31
> volume #11 level 0.07193
> volume #11 step 1
> volume #11 level 0.09
> volume #11 level 0.06892
> volume #11 level 0.08398
> volume #11 level 0.09301
> volume #11 level 0.08097
> vop subtract #4 #11 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J116_003_volume_map.mrc #11"
above level 0.080965 is 0.88407
> volume #31 level 0.07027
> close #31
> volume #12 level 0.08555
> volume #12 step 1
> volume #12 level 0.08877
> select add #12
2 models selected
> view matrix models
> #12,-0.98933,0.13774,-0.04754,405.66,-0.11744,-0.94685,-0.29948,496.64,-0.086265,-0.2907,0.95292,89.323
> ui tool show "Fit in Map"
> fitmap #12 inMap #1
Fit map cryosparc_P436_J117_003_volume_map.mrc in map
cryosparc_P436_J107_003_volume_map.mrc using 209123 points
correlation = 0.9752, correlation about mean = 0.7955, overlap = 3859
steps = 212, shift = 6.84, angle = 18.4 degrees
Position of cryosparc_P436_J117_003_volume_map.mrc (#12) relative to
cryosparc_P436_J107_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.98712498 0.04682961 -0.15294200 439.60071639
0.04477312 -0.83705908 -0.54527742 491.49898101
-0.15355662 -0.54510466 0.82418522 183.83744522
Axis 0.08023228 0.28542979 -0.95503540
Axis point 227.66095006 273.09718540 0.00000000
Rotation angle (degrees) 179.93831225
Shift along axis -0.01264931
> select clear
> volume #12 level 0.07286
> volume #13 level 0.07578
> volume #13 step 1
> volume #13 level 0.08255
> vop subtract #12 #13 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J118_003_volume_map.mrc #13"
above level 0.082549 is 1.0178
> close #31
> volume #14 level 0.06362
> volume #14 step 1
> volume #14 level 0.07421
> vop subtract #11 #14 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J119_004_volume_map.mrc #14"
above level 0.074209 is 1.0067
> volume #31 level 0.08557
> close #31
> volume #15 step 1
> volume #15 level 0.08087
> volume #15 level 0.06898
> volume #15 level 0.09499
> volume #15 level 0.07938
> volume #15 level 0.08904
> show #!16 models
> hide #!15 models
> volume #16 level 0.08908
> volume #16 step 1
> volume #16 level 0.08812
> volume #17 level 0.06175
> volume #17 step 1
> volume #17 level 0.08188
> volume #17 level 0.07368
> vop subtract #13 #17 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J122_004_volume_map.mrc #17"
above level 0.073679 is 1.045
> close #15
> close #31
> vop subtract #12 #17 minrms True
Opened volume difference as #15, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J122_004_volume_map.mrc #17"
above level 0.073679 is 1.1327
> close #15
> volume #18 level 0.08755
> volume #18 step 1
> vop subtract #2 #18 minrms True
Opened volume difference as #15, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J123_006_volume_map.mrc #18"
above level 0.08755 is 1.1088
> volume #15 level 0.07738
> close #15
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> volume #18 level 0.08354
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J120_004_volume_map.mrc
Opened cryosparc_P436_J120_004_volume_map.mrc as #15, grid size 512,512,512,
pixel 0.82, shown at level 0.0259, step 2, values float32
> volume #15 level 0.07817
> volume #15 step 1
> volume #15 color #ff9300
> select add #15
2 models selected
> view matrix models
> #15,-0.92254,-0.37212,-0.10217,510.74,0.34121,-0.66296,-0.66638,422.73,0.18023,-0.64963,0.73858,155.36
> view matrix models
> #15,-0.75852,-0.65146,0.015626,509.46,0.56728,-0.67193,-0.47614,335.39,0.32069,-0.3523,0.87923,32.183
> view matrix models
> #15,-0.99612,-0.028571,-0.083238,449.67,0.071335,-0.81604,-0.57358,492.65,-0.051537,-0.57729,0.81491,173.03
> select clear
> ui tool show "Fit in Map"
> fitmap #15 inMap #1
Fit map cryosparc_P436_J120_004_volume_map.mrc in map
cryosparc_P436_J107_003_volume_map.mrc using 240747 points
correlation = 0.9706, correlation about mean = 0.799, overlap = 3702
steps = 116, shift = 8.4, angle = 6.25 degrees
Position of cryosparc_P436_J120_004_volume_map.mrc (#15) relative to
cryosparc_P436_J107_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.98733193 0.04513560 -0.15211326 439.85089232
0.04532494 -0.83850912 -0.54299918 491.44947814
-0.15205695 -0.54301495 0.82584105 182.83924894
Axis -0.07958723 -0.28415963 0.95546804
Axis point 227.52764822 272.92466681 0.00000000
Rotation angle (degrees) 179.99432310
Shift along axis 0.04044435
> volume #15 level 0.09705
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> vop subtract #18 #15 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J120_004_volume_map.mrc #15"
above level 0.097055 is 0.78446
> volume #31 level 0.08036
> close #31
> close #15
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J120_004_volume_map.mrc
Opened cryosparc_P436_J120_004_volume_map.mrc as #15, grid size 512,512,512,
pixel 0.82, shown at level 0.0259, step 2, values float32
> volume #15 level 0.07077
> volume #15 step 1
> volume #19 level 0.07612
> volume #19 step 1
> vop subtract #3 #19 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J124_004_volume_map.mrc #19"
above level 0.076122 is 0.8206
> volume #31 level 0.07741
> volume #31 level 0.08389
> volume #31 level 0.06979
> close #31
> show #!19 models
> volume #20 level 0.06537
> volume #20 step 1
> volume #20 level 0.083
> show #!14 models
> hide #!20 models
> show #!11 models
> hide #!14 models
> show #!14 models
> hide #!11 models
> hide #!14 models
> vop subtract #19 #20 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J125_004_volume_map.mrc #20"
above level 0.083003 is 0.84783
> close #31
> volume #21 level 0.06973
> volume #21 step 1
> volume #21 level 0.0846
> show #!14 models
> vop subtract #14 #21 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J126_004_volume_map.mrc #21"
above level 0.084603 is 0.99719
> close #31
> show #!14 models
> show #!11 models
> hide #!11 models
> hide #!14 models
> volume #22 level 0.05638
> volume #22 step 1
> volume #22 level 0.08122
> vop subtract #19 #22 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J127_004_volume_map.mrc #22"
above level 0.08122 is 1.0255
> close #31
> show #!22 models
> volume #23 level 0.08962
> volume #23 step 1
> show #!20 models
> hide #!20 models
> volume #24 step 1
> volume #24 level 0.1106
> show #!9 models
> hide #!9 models
> show #!9 models
> vop subtract #9 #24 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J129_003_volume_map.mrc #24"
above level 0.11058 is 1.0126
> close #31
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> volume #25 level 0.0688
> volume #25 step 1
> volume #25 level 0.0933
> show #!22 models
> hide #!22 models
> select add #25
2 models selected
> view matrix models
> #25,-0.94338,0.28056,0.17696,316.89,-0.33158,-0.78294,-0.52636,561.55,-0.00913,-0.55523,0.83164,155.76
> show #!22 models
> view matrix models
> #25,-0.97998,0.19907,0.0040942,378.97,-0.16824,-0.81687,-0.55174,539.35,-0.10649,-0.54138,0.83401,173.07
> select clear
> ui tool show "Fit in Map"
> fitmap #25 inMap #1
Fit map cryosparc_P436_J131_004_volume_map.mrc in map
cryosparc_P436_J107_003_volume_map.mrc using 190942 points
correlation = 0.9829, correlation about mean = 0.8232, overlap = 3924
steps = 140, shift = 7.45, angle = 12.6 degrees
Position of cryosparc_P436_J131_004_volume_map.mrc (#25) relative to
cryosparc_P436_J107_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.98728773 0.04518015 -0.15238665 439.87644158
0.04559711 -0.83794146 -0.54385202 491.39813454
-0.15226240 -0.54388682 0.82522924 183.09798223
Axis -0.07972514 -0.28465663 0.95530859
Axis point 227.55036473 273.00336137 0.00000000
Rotation angle (degrees) 179.98749599
Shift along axis -0.03387455
> hide #!22 models
> show #!22 models
> vop subtract #22 #25 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J131_004_volume_map.mrc #25"
above level 0.093302 is 0.79243
> close #31
> show #!25 models
> volume #26 level 0.06567
> volume #26 step 1
> volume #26 level 0.0992
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> vop subtract #16 #26 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J132_003_volume_map.mrc #26"
above level 0.099204 is 0.97406
> close #31
> show #!16 models
> hide #!16 models
> show #!16 models
> volume #16 level 0.06997
> volume #16 level 0.09132
> hide #!16 models
> volume #27 level 0.067
> volume #27 step 1
> volume #28 level 0.07325
> volume #28 step 1
> select add #28
2 models selected
> view matrix models
> #28,-0.95412,-0.0055359,-0.29938,481.84,0.1702,-0.83263,-0.52703,465.83,-0.24636,-0.55381,0.79537,213.97
> view matrix models
> #28,-0.94192,-0.0456,-0.33274,494.94,0.234,-0.79978,-0.5528,450.86,-0.24091,-0.59855,0.764,229.06
> select subtract #28
Nothing selected
> ui tool show "Fit in Map"
> fitmap #28 inMap #1
Fit map cryosparc_P436_J134_004_volume_map.mrc in map
cryosparc_P436_J107_003_volume_map.mrc using 262440 points
correlation = 0.9698, correlation about mean = 0.8035, overlap = 3703
steps = 168, shift = 10.8, angle = 12.5 degrees
Position of cryosparc_P436_J134_004_volume_map.mrc (#28) relative to
cryosparc_P436_J107_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.98723709 0.04628661 -0.15238265 439.55778003
0.04451236 -0.83850165 -0.54307792 491.67911358
-0.15291034 -0.54292958 0.82573961 182.95598565
Axis 0.07988269 0.28416357 -0.95544221
Axis point 227.54664103 272.93976307 0.00000000
Rotation angle (degrees) 179.94680090
Shift along axis 0.02647686
> hide #!26 models
> hide #!28 models
> volume #28 level 0.1162
> volume #28 level 0.08003
> volume #29 level 0.06175
> volume #29 step 1
> volume #29 level 0.0895
> show #!8 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!8 models
> vop subtract #8 #29 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J135_004_volume_map.mrc #29"
above level 0.089499 is 0.90898
> hide #!31 models
> show #!31 models
> close #31
> show #!10 models
> vop subtract #10 #29 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J135_004_volume_map.mrc #29"
above level 0.089499 is 0.80387
> close #31
> volume #30 level 0.07879
> volume #30 step 1
> show #!17 models
> hide #!17 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #30 level 0.1032
> volume #30 level 0.08947
> show #!11 models
> volume #11 level 0.08432
> vop subtract #11 #30 minrms True
Opened volume difference as #31, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J136_004_volume_map.mrc #30"
above level 0.08947 is 1.0508
> close #31
> close #15
> show #!21 models
> hide #!21 models
> show #!14 models
> hide #!14 models
> show #!11 models
> hide #!11 models
> volume #30 level 0.08337
> volume #1 level 0.08826
> close #28
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J134_004_volume_map.mrc
Opened cryosparc_P436_J134_004_volume_map.mrc as #15, grid size 512,512,512,
pixel 0.82, shown at level 0.0261, step 2, values float32
> volume #15 level 0.07594
> show #!4 models
> hide #!15 models
> show #!20 models
> show #!23 models
> hide #!23 models
> vop subtract #4 #20 minrms True
Opened volume difference as #28, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J125_004_volume_map.mrc #20"
above level 0.083003 is 0.87162
> volume #28 level 0.07281
> close #28
> show #!4 models
> show #!23 models
> vop subtract #4 #23 minrms True
Opened volume difference as #28, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P436_J128_003_volume_map.mrc #23"
above level 0.089623 is 0.78518
> volume #28 level 0.08532
> close #28
> hide #!12 models
> show #!4 models
> show #!20 models
> hide #!4 models
> show #!23 models
> hide #!20 models
> show #!20 models
> hide #!23 models
> show #!4 models
> hide #!20 models
> hide #!4 models
> show #!8 models
> show #!10 models
> hide #!8 models
> show #!29 models
> hide #!29 models
> hide #!10 models
> show #!8 models
> select add #1
2 models selected
> select subtract #1
Nothing selected
> close #1-4
> close #6-27,29-30
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J587_004_volume_map.mrc
Opened cryosparc_P429_J587_004_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.82, shown at level 0.04, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/reconstruction_only/cryosparc_P429_J593_volume_map.mrc
Opened cryosparc_P429_J593_volume_map.mrc as #2, grid size 512,512,512, pixel
0.82, shown at level 0.0403, step 2, values float32
> volume #2 level 0.0781
> volume #1 level 0.06605
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.08679
> volume #2 level 0.08174
> vop subtract #1 #2 minrms True
Opened volume difference as #3, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J593_volume_map.mrc #2" above
level 0.081744 is 0.96172
> volume #3 level 0.04435
> volume #3 level 0.06162
> close #3
> close #1-2
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J587_004_volume_map.mrc
Opened cryosparc_P429_J587_004_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.82, shown at level 0.04, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J588_005_volume_map.mrc
Opened cryosparc_P429_J588_005_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.82, shown at level 0.0389, step 2, values float32
> volume #1 level 0.08557
> volume #2 level 0.06608
> volume #2 step 1
> volume #1 step 1
> volume #2 level 0.07635
> volume #1 level 0.09122
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J594_004_volume_map.mrc
Opened cryosparc_P429_J594_004_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.82, shown at level 0.0403, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J595_006_volume_map.mrc
Opened cryosparc_P429_J595_006_volume_map.mrc as #4, grid size 512,512,512,
pixel 0.82, shown at level 0.038, step 2, values float32
> volume #3 level 0.07744
> hide #!1 models
> hide #!2 models
> hide #!4 models
> volume #3 level 0.08893
> volume #3 step 1
> volume #4 level 0.06886
> volume #4 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J600_008_volume_map.mrc
Opened cryosparc_P429_J600_008_volume_map.mrc as #6, grid size 512,512,512,
pixel 0.82, shown at level 0.0366, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J599_004_volume_map.mrc
Opened cryosparc_P429_J599_004_volume_map.mrc as #7, grid size 512,512,512,
pixel 0.82, shown at level 0.04, step 2, values float32
> volume #6 step 1
> volume #6 level 0.06381
> volume #7 level 0.07581
> volume #7 step 1
> volume #7 level 0.08834
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J604_004_volume_map.mrc
Opened cryosparc_P429_J604_004_volume_map.mrc as #8, grid size 512,512,512,
pixel 0.82, shown at level 0.0401, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J605_008_volume_map.mrc
Opened cryosparc_P429_J605_008_volume_map.mrc as #9, grid size 512,512,512,
pixel 0.82, shown at level 0.0384, step 2, values float32
> volume #8 level 0.07036
> volume #9 level 0.06937
> volume #8 level 0.08159
> volume #9 level 0.07341
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J609_005_volume_map.mrc
Opened cryosparc_P429_J609_005_volume_map.mrc as #10, grid size 512,512,512,
pixel 0.82, shown at level 0.0404, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J610_008_volume_map.mrc
Opened cryosparc_P429_J610_008_volume_map.mrc as #11, grid size 512,512,512,
pixel 0.82, shown at level 0.0372, step 2, values float32
> volume #10 step 1
> volume #10 level 0.08679
> volume #11 level 0.06587
> volume #11 step 1
> volume #11 level 0.07255
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J614_004_volume_map.mrc
Opened cryosparc_P429_J614_004_volume_map.mrc as #12, grid size 512,512,512,
pixel 0.82, shown at level 0.0404, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J615_006_volume_map.mrc
Opened cryosparc_P429_J615_006_volume_map.mrc as #13, grid size 512,512,512,
pixel 0.82, shown at level 0.0388, step 2, values float32
> volume #12 level 0.08414
> volume #12 step 1
> volume #13 level 0.07135
> volume #13 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J619_004_volume_map.mrc
Opened cryosparc_P429_J619_004_volume_map.mrc as #14, grid size 512,512,512,
pixel 0.82, shown at level 0.0405, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J620_008_volume_map.mrc
Opened cryosparc_P429_J620_008_volume_map.mrc as #15, grid size 512,512,512,
pixel 0.82, shown at level 0.0392, step 2, values float32
> volume #14 level 0.08188
> volume #14 step 1
> volume #14 level 0.09673
> volume #15 level 0.06887
> volume #15 step 1
> volume #15 level 0.07959
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J624_004_volume_map.mrc
Opened cryosparc_P429_J624_004_volume_map.mrc as #16, grid size 512,512,512,
pixel 0.82, shown at level 0.04, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J625_006_volume_map.mrc
Opened cryosparc_P429_J625_006_volume_map.mrc as #17, grid size 512,512,512,
pixel 0.82, shown at level 0.0391, step 2, values float32
> volume #16 level 0.08299
> volume #16 step 1
> volume #16 level 0.0944
> volume #17 level 0.08312
> volume #17 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J629_003_volume_map.mrc
Opened cryosparc_P429_J629_003_volume_map.mrc as #18, grid size 512,512,512,
pixel 0.82, shown at level 0.0399, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J630_008_volume_map.mrc
Opened cryosparc_P429_J630_008_volume_map.mrc as #19, grid size 512,512,512,
pixel 0.82, shown at level 0.0382, step 2, values float32
> volume #18 level 0.08554
> volume #18 step 1
> volume #19 level 0.06829
> volume #19 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J634_004_volume_map.mrc
Opened cryosparc_P429_J634_004_volume_map.mrc as #20, grid size 512,512,512,
pixel 0.82, shown at level 0.0373, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J635_007_volume_map.mrc
Opened cryosparc_P429_J635_007_volume_map.mrc as #21, grid size 512,512,512,
pixel 0.82, shown at level 0.0341, step 2, values float32
> volume #20 level 0.09471
> volume #20 step 1
> volume #21 level 0.05737
> volume #21 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J639_004_volume_map.mrc
Opened cryosparc_P429_J639_004_volume_map.mrc as #22, grid size 512,512,512,
pixel 0.82, shown at level 0.0406, step 2, values float32
> volume #22 level 0.07825
> volume #22 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J640_006_volume_map.mrc
Opened cryosparc_P429_J640_006_volume_map.mrc as #23, grid size 512,512,512,
pixel 0.82, shown at level 0.0361, step 2, values float32
> volume #23 level 0.06507
> volume #23 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J644_004_volume_map.mrc
Opened cryosparc_P429_J644_004_volume_map.mrc as #24, grid size 512,512,512,
pixel 0.82, shown at level 0.039, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J645_007_volume_map.mrc
Opened cryosparc_P429_J645_007_volume_map.mrc as #25, grid size 512,512,512,
pixel 0.82, shown at level 0.0359, step 2, values float32
> volume #24 level 0.08573
> volume #24 step 1
> volume #25 level 0.06261
> volume #25 step 1
> volume #25 level 0.07172
> show #!4 models
> show #!6 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!25 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!4 models
> hide #!6 models
> hide #!9 models
> hide #!13 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> show #!5 models
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> show sel cartoons
> select subtract #5
32 models selected
> show #!1 models
> volume #1 level 0.07286
> hide #!1 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!20 models
> hide #!20 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> show #!24 models
> show #!3 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> hide #!4 models
> vop subtract #3 #24 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J644_004_volume_map.mrc #24"
above level 0.085732 is 0.94254
> volume #26 level 0.07473
> volume #26 level 0.0905
> close #26
> show #!4 models
> show #!25 models
> vop subtract #4 #25 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J645_007_volume_map.mrc #25"
above level 0.071724 is 0.46187
> close #26
> hide #!25 models
> show #!25 models
> color #25 #00fa92ff models
> show #!24 models
> hide #!25 models
> show #!3 models
> hide #!4 models
> color #3 #945200ff models
> hide #!3 models
> show #!3 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!4 models
> show #!25 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!24 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!24 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!6 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!6 models
> hide #!24 models
> hide #!7 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!25 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!9 models
> vop subtract #3 #8 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J604_004_volume_map.mrc #8" above
level 0.081594 is 0.92037
> close #26
> show #!8 models
> show #!9 models
> show #!3 models
> show #!4 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!4 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!11 models
> hide #!9 models
> show #!25 models
> hide #!25 models
> show #!10 models
> show #!9 models
> hide #!9 models
> hide #!11 models
> show #!8 models
> vop subtract #8 #10 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J609_005_volume_map.mrc #10"
above level 0.086787 is 0.95515
> volume #26 level 0.09571
> close #26
> show #!10 models
> show #!8 models
> hide #!8 models
> show #!11 models
> hide #!11 models
> show #!8 models
> show #!11 models
> hide #!10 models
> hide #!8 models
> show #!9 models
> show #!4 models
> hide #!4 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!12 models
> show #!13 models
> hide #!11 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> show #!15 models
> hide #!15 models
> show #!16 models
> hide #!14 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!16 models
> show #!19 models
> hide #!19 models
> show #!10 models
> vop subtract #10 #18 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J629_003_volume_map.mrc #18"
above level 0.085539 is 0.86731
> volume #26 level 0.09056
> close #26
> show #!18 models
> show #!10 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!19 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!19 models
> hide #!11 models
> hide #!10 models
> show #!10 models
> hide #!18 models
> show #!18 models
> hide #!10 models
> show #!10 models
> hide #!18 models
> show #!18 models
> hide #!10 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!20 models
> hide #!20 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!20 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!19 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!20 models
> hide #!18 models
> show #!20 models
> show #!18 models
> hide #!19 models
> hide #!21 models
> vop subtract #18 #20 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J634_004_volume_map.mrc #20"
above level 0.094707 is 0.94953
> close #26
> show #!20 models
> show #!22 models
> hide #!22 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!21 models
> hide #!21 models
> hide #!18 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!20 models
> hide #!22 models
> show #!24 models
> show #!25 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!24 models
> show #!24 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!12 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!25 models
> hide #!13 models
> hide #!6 models
> vop subtract #12 #24 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J644_004_volume_map.mrc #24"
above level 0.085732 is 0.96002
> close #26
> show #!12 models
> show #!13 models
> show #!25 models
> hide #!12 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!24 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!14 models
> show #!15 models
> show #!6 models
> hide #!6 models
> hide #!13 models
> show #!17 models
> hide #!17 models
> show #!17 models
> show #!13 models
> show #!14 models
> hide #!15 models
> hide #!17 models
> hide #!13 models
> show #!12 models
> hide #!25 models
> vop subtract #12 #14 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J619_004_volume_map.mrc #14"
above level 0.096729 is 0.90492
> close #26
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> vop subtract #14 #16 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J624_004_volume_map.mrc #16"
above level 0.0944 is 0.92766
> close #26
> show #!22 models
> show #!16 models
> vop subtract #16 #22 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J639_004_volume_map.mrc #22"
above level 0.078247 is 0.99668
> close #26
> show #!6 models
> show #!13 models
> show #!15 models
> show #!17 models
> show #!23 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> color #13 #011993ff models
> hide #!13 models
> show #!1 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!8 models
> show #!10 models
> show #!18 models
> show #!20 models
> hide #!20 models
> hide #!18 models
> hide #!8 models
> hide #!10 models
> hide #!3 models
> show #!7 models
> show #!12 models
> show #!14 models
> show #!16 models
> show #!22 models
> show #!24 models
> hide #!24 models
> hide #!22 models
> hide #!16 models
> hide #!14 models
> hide #!12 models
> show #!12 models
> hide #!7 models
> show #!7 models
> hide #!12 models
> show #!12 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!14 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!14 models
> show #!14 models
> hide #!12 models
> show #!16 models
> hide #!14 models
> show #!22 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!24 models
> hide #!22 models
> hide #!24 models
> show #!6 models
> show #!13 models
> show #!15 models
> show #!17 models
> show #!23 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!6 models
> show #!6 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!6 models
> hide #!6 models
> hide #!13 models
> show #!13 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!6 models
> show #!15 models
> hide #!6 models
> hide #!15 models
> hide #!13 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> hide #!17 models
> show #!4 models
> show #!9 models
> show #!11 models
> show #!19 models
> color #19 #942193ff models
> show #!21 models
> color #21 #76d6ffff models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> color #11 #4f8f00ff models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!19 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!4 models
> hide #!21 models
> vop subtract #4 #11 minrms True
Opened volume difference as #26, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J610_008_volume_map.mrc #11"
above level 0.072553 is 0.51662
> show #!4 models
> hide #!26 models
> show #!21 models
> vop subtract #4 #21 minrms True
Opened volume difference as #27, grid size 512,512,512, pixel 0.82, shown at
step 1, values float32
Minimum RMS scale factor for "cryosparc_P429_J635_007_volume_map.mrc #21"
above level 0.057373 is 0.60886
> show #!26 models
> hide #!27 models
> show #!27 models
> hide #!26 models
> close #26-27
> show #!4 models
> show #!21 models
> show #!11 models
> hide #!21 models
> hide #!4 models
> show #!9 models
> show #!19 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> close #1-4
> close #6-25
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J113_004_volume_map.mrc
Opened cryosparc_P436_J113_004_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.82, shown at level 0.0244, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J115_005_volume_map.mrc
Opened cryosparc_P436_J115_005_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.82, shown at level 0.0236, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J135_004_volume_map.mrc
Opened cryosparc_P436_J135_004_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.82, shown at level 0.0257, step 2, values float32
> volume #1 level 0.04867
> volume #2 level 0.04444
> volume #3 level 0.05735
> volume #3 level 0.07002
> volume #3 step 1
> volume #2 level 0.0664
> volume #2 step 1
> volume #1 level 0.07425
> volume #1 step 1
> volume #2 level 0.07554
> volume #3 level 0.0798
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J302_006_volume_map.mrc
Opened cryosparc_P436_J302_006_volume_map.mrc as #4, grid size 512,512,512,
pixel 0.82, shown at level 0.0229, step 2, values float32
> volume #4 level 0.07037
> volume #4 step 1
> volume #4 level 0.08121
> volume #4 level 0.08446
> volume #3 level 0.09633
> volume #4 level 0.09909
> volume #2 level 0.08955
> volume #1 level 0.09888
> volume #4 level 0.06413
> volume #4 level 0.07795
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> view matrix models
> #5,0.89503,-0.44527,-0.025622,45.642,0.40883,0.84203,-0.3519,-47.005,0.17827,0.30449,0.93569,-149.28
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.89503,-0.44527,-0.025622,97.783,0.40883,0.84203,-0.3519,-5.5808,0.17827,0.30449,0.93569,-131.61
> view matrix models
> #5,0.89503,-0.44527,-0.025622,106.55,0.40883,0.84203,-0.3519,-12.849,0.17827,0.30449,0.93569,-138.1
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.76117,0.63682,-0.12279,-106,-0.62116,0.77028,0.14432,184.93,0.18648,-0.033582,0.98188,-65.752
> view matrix models
> #5,0.91845,-0.15833,-0.36246,108.78,-0.1933,0.61983,-0.76055,318.84,0.34508,0.7686,0.53868,-208.1
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.91845,-0.15833,-0.36246,117.84,-0.1933,0.61983,-0.76055,311.24,0.34508,0.7686,0.53868,-215.43
> view matrix models
> #5,0.91845,-0.15833,-0.36246,107.71,-0.1933,0.61983,-0.76055,290.75,0.34508,0.7686,0.53868,-193.6
> view matrix models
> #5,0.91845,-0.15833,-0.36246,110.59,-0.1933,0.61983,-0.76055,281.66,0.34508,0.7686,0.53868,-213.98
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.98896,-0.10507,-0.10449,13.634,0.020008,0.79339,-0.60838,138.23,0.14682,0.59958,0.78673,-173.58
> select subtract #5
32 models selected
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit molecule 9etz (#5) to map cryosparc_P436_J302_006_volume_map.mrc (#4)
using 48795 atoms
average map value = 0.05366, steps = 508
shifted from previous position = 12.2
rotated from previous position = 23.4 degrees
atoms outside contour = 34672, contour level = 0.077953
Position of 9etz (#5) relative to cryosparc_P436_J302_006_volume_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99237872 0.09796052 -0.07475440 -48.12592510
-0.11524409 0.95259177 -0.28158076 64.56703658
0.04362663 0.28804975 0.95662117 -101.22790904
Axis 0.91929810 -0.19104920 -0.34408022
Axis point 0.00000000 399.58064878 147.27168481
Rotation angle (degrees) 18.04827266
Shift along axis -21.74703074
> volume #4 level 0.07712
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J124_004_volume_map.mrc
Opened cryosparc_P436_J124_004_volume_map.mrc as #6, grid size 512,512,512,
pixel 0.82, shown at level 0.0253, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J131_004_volume_map.mrc
Opened cryosparc_P436_J131_004_volume_map.mrc as #7, grid size 512,512,512,
pixel 0.82, shown at level 0.0269, step 2, values float32
> close #1
> close #2
> close #3
> volume #7 level 0.09784
> volume #6 level 0.08491
> hide #!5 models
> volume #6 level 0.07271
> volume #7 level 0.08588
> volume #7 step 1
> volume #6 step 1
> ui tool show "Map Coordinates"
> turn y 180 #7
Expected 'forever' or an integer >= 1 or a keyword
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #7 level 0.08588
> volume #7 level -0.00799
> volume #7 color #ffb2b254
> close #6
> close #4
> close #7
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J594_004_volume_map.mrc
Opened cryosparc_P429_J594_004_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.82, shown at level 0.0403, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J595_006_volume_map.mrc
Opened cryosparc_P429_J595_006_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.82, shown at level 0.038, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J649_004_volume_map.mrc
Opened cryosparc_P429_J649_004_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.82, shown at level 0.0366, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J650_005_volume_map.mrc
Opened cryosparc_P429_J650_005_volume_map.mrc as #4, grid size 512,512,512,
pixel 0.82, shown at level 0.0339, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J651_004_volume_map.mrc
Opened cryosparc_P429_J651_004_volume_map.mrc as #6, grid size 512,512,512,
pixel 0.82, shown at level 0.0385, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J652_005_volume_map.mrc
Opened cryosparc_P429_J652_005_volume_map.mrc as #7, grid size 512,512,512,
pixel 0.82, shown at level 0.037, step 2, values float32
> volume #1 level 0.08362
> volume #2 level 0.05404
> volume #3 level 0.08023
> volume #4 level 0.06552
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> volume #4 step 1
> volume #6 level 0.09955
> volume #6 step 1
> volume #7 level 0.08935
> volume #7 step 1
> hide #!7 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> volume #2 level 0.06564
> volume #1 level 0.08545
> volume #3 level 0.08125
> volume #6 level 0.09372
> volume #7 level 0.07659
> volume #4 level 0.05909
> volume #3 level 0.09041
> volume #4 level 0.06552
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J644_004_volume_map.mrc
Opened cryosparc_P429_J644_004_volume_map.mrc as #8, grid size 512,512,512,
pixel 0.82, shown at level 0.039, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J645_007_volume_map.mrc
Opened cryosparc_P429_J645_007_volume_map.mrc as #9, grid size 512,512,512,
pixel 0.82, shown at level 0.0359, step 2, values float32
> hide #!3 models
> hide #!4 models
> volume #8 level 0.09439
> volume #9 level 0.05921
> volume #9 level 0.06318
> volume #8 level 0.09439
> volume #8 step 1
> volume #9 step 1
> volume #8 level 0.08017
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J599_004_volume_map.mrc
Opened cryosparc_P429_J599_004_volume_map.mrc as #10, grid size 512,512,512,
pixel 0.82, shown at level 0.04, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J600_008_volume_map.mrc
Opened cryosparc_P429_J600_008_volume_map.mrc as #11, grid size 512,512,512,
pixel 0.82, shown at level 0.0366, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J614_004_volume_map.mrc
Opened cryosparc_P429_J614_004_volume_map.mrc as #12, grid size 512,512,512,
pixel 0.82, shown at level 0.0404, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J615_006_volume_map.mrc
Opened cryosparc_P429_J615_006_volume_map.mrc as #13, grid size 512,512,512,
pixel 0.82, shown at level 0.0388, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J653_004_volume_map.mrc
Opened cryosparc_P429_J653_004_volume_map.mrc as #14, grid size 512,512,512,
pixel 0.82, shown at level 0.0385, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J654_004_volume_map.mrc
Opened cryosparc_P429_J654_004_volume_map.mrc as #15, grid size 512,512,512,
pixel 0.82, shown at level 0.0368, step 2, values float32
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!8 models
> hide #!9 models
> volume #10 level 0.07232
> volume #10 step 1
> volume #10 level 0.0858
> volume #11 level 0.05989
> volume #11 step 1
> volume #11 level 0.06461
> volume #12 level 0.077
> volume #12 step 1
> volume #12 level 0.08426
> volume #13 level 0.07073
> volume #13 step 1
> volume #14 level 0.07947
> volume #14 step 1
> volume #15 level 0.07353
> volume #15 step 1
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J619_004_volume_map.mrc
Opened cryosparc_P429_J619_004_volume_map.mrc as #16, grid size 512,512,512,
pixel 0.82, shown at level 0.0405, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J620_008_volume_map.mrc
Opened cryosparc_P429_J620_008_volume_map.mrc as #17, grid size 512,512,512,
pixel 0.82, shown at level 0.0392, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J587_004_volume_map.mrc
Opened cryosparc_P429_J587_004_volume_map.mrc as #18, grid size 512,512,512,
pixel 0.82, shown at level 0.04, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_SC_krios_data_collection/loc_ref/cryosparc_P429_J588_005_volume_map.mrc
Opened cryosparc_P429_J588_005_volume_map.mrc as #19, grid size 512,512,512,
pixel 0.82, shown at level 0.0389, step 2, values float32
> volume #16 level 0.08278
> volume #16 step 1
> volume #17 level 0.07577
> volume #17 step 1
> volume #18 level 0.08862
> volume #18 step 1
> volume #19 level 0.07859
> volume #19 step 1
> hide #!19 models
> show #!1 models
> show #!2 models
> show #!5 models
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> view matrix models
> #5,-0.81165,0.020956,0.58377,337.21,-0.15526,0.95567,-0.25017,67.803,-0.56313,-0.29369,-0.77242,644.92
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.81165,0.020956,0.58377,289.81,-0.15526,0.95567,-0.25017,87.41,-0.56313,-0.29369,-0.77242,624.37
> view matrix models
> #5,-0.81165,0.020956,0.58377,279.93,-0.15526,0.95567,-0.25017,68.182,-0.56313,-0.29369,-0.77242,633.28
> fitmap #5 inMap #1
Fit molecule 9etz (#5) to map cryosparc_P429_J594_004_volume_map.mrc (#1)
using 48795 atoms
average map value = 0.03808, steps = 164
shifted from previous position = 4.47
rotated from previous position = 12.8 degrees
atoms outside contour = 42983, contour level = 0.085448
Position of 9etz (#5) relative to cryosparc_P429_J594_004_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.78205397 0.23689059 0.57643251 221.32424246
-0.01825617 0.91583493 -0.40113975 80.26440909
-0.62294325 -0.32423638 -0.71190763 641.94820679
Axis 0.06259310 0.97619455 -0.20766876
Axis point 219.48830396 0.00000000 290.13429451
Rotation angle (degrees) 142.09806472
Shift along axis -41.10554052
> view matrix models
> #5,-0.78205,0.23689,0.57643,212.25,-0.018256,0.91583,-0.40114,71.557,-0.62294,-0.32424,-0.71191,649.97
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.82271,0.047447,0.56648,274.72,-0.22479,0.88813,-0.40086,138.77,-0.52213,-0.45713,-0.72001,656.35
> fitmap #5 inMap #18
Fit molecule 9etz (#5) to map cryosparc_P429_J587_004_volume_map.mrc (#18)
using 48795 atoms
average map value = 0.08005, steps = 244
shifted from previous position = 6.47
rotated from previous position = 12.6 degrees
atoms outside contour = 32029, contour level = 0.088618
Position of 9etz (#5) relative to cryosparc_P429_J587_004_volume_map.mrc (#18)
coordinates:
Matrix rotation and translation
-0.87025327 0.19495003 0.45238672 281.32963039
-0.11541919 0.81209715 -0.57199357 167.29635121
-0.47889212 -0.54999338 -0.68422922 654.33184400
Axis 0.02240613 0.94846256 -0.31609608
Axis point 227.36104206 0.00000000 316.00246296
Rotation angle (degrees) 150.59753236
Shift along axis -41.85389624
> select subtract #5
32 models selected
> select add #19
2 models selected
> select subtract #19
Nothing selected
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
33775 atoms, 34573 bonds, 43 pseudobonds, 4094 residues, 2 models selected
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
> displayedOnly true relModel #1
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
> select clear
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
> hide #!2 models
> hide #!1 models
> select #5/A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z
33775 atoms, 34573 bonds, 43 pseudobonds, 4094 residues, 2 models selected
> select clear
> hide #!5 models
> show #!5 models
> volume #18 level 0.07494
> volume #18 level 0.08613
> select #5/a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> show sel atoms
> hide sel atoms
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J588_SC.pdb
> selectedOnly true relModel #19
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J588_SC.pdb
Summary of feedback from opening
/Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J588_SC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 58 GLU A 62 1 5
Start residue of secondary structure not found: HELIX 2 2 GLY A 68 LEU A 78 1
11
Start residue of secondary structure not found: HELIX 3 3 SER A 79 GLU A 89 1
11
Start residue of secondary structure not found: HELIX 4 4 SER A 112 PHE A 124
1 13
Start residue of secondary structure not found: HELIX 5 5 ASN A 136 ASN A 154
1 19
270 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (101 )
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (101 )
Cannot find LINK/SSBOND residue CYS (178 )
18 messages similar to the above omitted
Chain information for 9etz_CIV_rel_J588_SC.pdb #20
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> hide sel atoms
> select clear
> hide atoms
> hide #!5 models
> hide #!20 models
> show #!20 models
> show #!20 cartoons
> show #!19 models
> fitmap #20 inMap #19
Fit molecule 9etz_CIV_rel_J588_SC.pdb (#20) to map
cryosparc_P429_J588_005_volume_map.mrc (#19) using 15020 atoms
average map value = 0.1025, steps = 84
shifted from previous position = 3.28
rotated from previous position = 3.69 degrees
atoms outside contour = 5362, contour level = 0.078594
Position of 9etz_CIV_rel_J588_SC.pdb (#20) relative to
cryosparc_P429_J588_005_volume_map.mrc (#19) coordinates:
Matrix rotation and translation
0.99945811 0.00777967 -0.03198371 5.90432355
-0.00953601 0.99843349 -0.05513290 13.33087987
0.03150469 0.05540802 0.99796664 -16.45455216
Axis 0.85926145 -0.49351077 -0.13459897
Axis point 0.00000000 304.03712890 239.50480190
Rotation angle (degrees) 3.68799517
Shift along axis 0.70919062
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J588_SC.pdb
> models #20 relModel #19
> select add #20
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> ui tool show "Color Actions"
> color sel powder blue
> select subtract #20
Nothing selected
> hide #!19 models
> hide #!20 models
> show #!5 models
> select #5/A,B,C,D,F,G,H,I:25:58,J,K,L,M,N,O,Q,R,S,T:25-58,V,W,X,Y,Z
1586 atoms, 1623 bonds, 202 residues, 1 model selected
> select #5/A,B,C,D,F,G,H,I:25-58,J,K,L,M,N,O,Q,R,S,T:25-58,V,W,X,Y,Z
1586 atoms, 1623 bonds, 202 residues, 1 model selected
> select #5/A-H,I:25-58,J,K,L,M,N,O,Q,R,S,T:25-58,V,W,X,Y,Z
1820 atoms, 1862 bonds, 230 residues, 1 model selected
> select #5/A-H,J-S,V-Z,I:25-58,T:25-58
3633 atoms, 3719 bonds, 460 residues, 1 model selected
> select #5/A,B,C,D,F,G,H,,J,K,L,M,N,O,Q,R,S,V,W,X,Y,Z
Expected an objects specifier or a keyword
> select #5/A,B,C,D,F,G,H,J,K,L,M,N,O,Q,R,S,V,W,X,Y,Z
29077 atoms, 29767 bonds, 36 pseudobonds, 3524 residues, 2 models selected
> select add #5/I:25-58
29358 atoms, 30056 bonds, 36 pseudobonds, 3558 residues, 17 models selected
> select add #5/T:25-58
29639 atoms, 30345 bonds, 36 pseudobonds, 3592 residues, 18 models selected
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J587_SC.pdb
> models #5 selectedOnly true relModel #18
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 19 models selected
> select subtract #5
32 models selected
> hide #!5 models
> show #!20 models
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J587_SC.pdb
Summary of feedback from opening
/Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J587_SC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 71 71 ASP E 48 SER E 81 1 34
Start residue of secondary structure not found: HELIX 72 72 THR E 85 ALA E 90
1 6
Start residue of secondary structure not found: HELIX 73 73 THR E 122 SER E
131 1 10
Start residue of secondary structure not found: HELIX 90 90 PHE I 3 PHE I 11 1
9
Start residue of secondary structure not found: HELIX 91 91 ARG I 13 ASN I 44
1 32
122 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (27 )
Cannot find LINK/SSBOND residue CYS (37 )
Cannot find LINK/SSBOND residue CYS (111 )
25 messages similar to the above omitted
Chain information for 9etz_CIII_rel_J587_SC.pdb #21
---
Chain | Description
A L | No description available
B M | No description available
C N | No description available
D O | No description available
F Q | No description available
G R | No description available
H S | No description available
I T | No description available
J | No description available
> hide #!20-21 atoms
> show #!20-21 cartoons
> show #!18 models
> hide #!18 models
> select #20/T:25-58
Nothing selected
> select #20/I,T
Nothing selected
> select #21/I,T
562 atoms, 578 bonds, 68 residues, 1 model selected
> select #21
29639 atoms, 30345 bonds, 36 pseudobonds, 3592 residues, 2 models selected
> color sel tan
> select #21/I,T
562 atoms, 578 bonds, 68 residues, 1 model selected
> color sel indian red
> select #21/I:21-25
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #21/I:25-45
179 atoms, 185 bonds, 21 residues, 1 model selected
> select #21/I:25-44
170 atoms, 176 bonds, 20 residues, 1 model selected
> dssp #21/I:25-44
> dssp #21/T:25-44
> select clear
> dssp #21/F
> select #21/F
633 atoms, 648 bonds, 75 residues, 1 model selected
> color sel indian red
> ui tool show "Color Actions"
> color sel light coral
> color sel rosy brown
> color sel saddle brown
> color sel sienna
> color sel goldenrod
> color sel dark goldenrod
> color sel sienna
> select clear
> select #21/F
633 atoms, 648 bonds, 75 residues, 1 model selected
> select clear
> show #!20-21 surfaces
> hide #!20-21 surfaces
> show #!20-21 surfaces
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> hide #!20-21 surfaces
> show #!18 models
> hide #!18 models
> show #!20-21 surfaces
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
Summary of feedback from opening
/Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 71 71 ASP E 48 SER E 81 1 34
Start residue of secondary structure not found: HELIX 72 72 THR E 85 ALA E 90
1 6
Start residue of secondary structure not found: HELIX 73 73 THR E 122 SER E
131 1 10
Start residue of secondary structure not found: HELIX 90 90 PHE I 3 PHE I 11 1
9
Start residue of secondary structure not found: HELIX 91 91 ARG I 13 ASN I 44
1 32
122 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (27 )
Cannot find LINK/SSBOND residue CYS (37 )
Cannot find LINK/SSBOND residue CYS (111 )
25 messages similar to the above omitted
Chain information for 9etz_CIII_rel_J594_SC.pdb #22
---
Chain | Description
A L | No description available
B M | No description available
C N | No description available
D O | No description available
F Q | No description available
G R | No description available
H S | No description available
I T | No description available
J | No description available
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J595_SC.pdb
Chain information for 9etz_CIV_rel_J595_SC.pdb #23
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> fitmap #22 inMap #1
Fit molecule 9etz_CIII_rel_J594_SC.pdb (#22) to map
cryosparc_P429_J594_004_volume_map.mrc (#1) using 29639 atoms
average map value = 0.09734, steps = 64
shifted from previous position = 0.158
rotated from previous position = 0.348 degrees
atoms outside contour = 14463, contour level = 0.085448
Position of 9etz_CIII_rel_J594_SC.pdb (#22) relative to
cryosparc_P429_J594_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999628 -0.00150518 0.00227521 -0.31986524
0.00149280 0.99998412 0.00543355 -1.68011123
-0.00228336 -0.00543013 0.99998265 1.61253624
Axis -0.89362928 0.37498099 0.24660893
Axis point 0.00000000 293.52878768 313.76035549
Rotation angle (degrees) 0.34826897
Shift along axis 0.05349701
> hide #!20 models
> hide #!21 models
> show #!2 models
> select add #23
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #23,1,0,0,22.137,0,1,0,13.257,0,0,1,-12.803
> ui mousemode right "rotate selected models"
> view matrix models
> #23,0.61698,0.34263,-0.70847,127.62,-0.47775,0.87845,0.0087788,109.95,0.62537,0.33306,0.70568,-128.31
> fitmap #23 inMap #2
Fit molecule 9etz_CIV_rel_J595_SC.pdb (#23) to map
cryosparc_P429_J595_006_volume_map.mrc (#2) using 15020 atoms
average map value = 0.08554, steps = 236
shifted from previous position = 18
rotated from previous position = 25.5 degrees
atoms outside contour = 5336, contour level = 0.065638
Position of 9etz_CIV_rel_J595_SC.pdb (#23) relative to
cryosparc_P429_J595_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.79316965 0.30709020 -0.52590637 75.60132065
-0.53502413 0.76388722 -0.36086771 220.69193630
0.29091422 0.56760191 0.77019282 -131.68988034
Axis 0.62058039 -0.54595523 -0.56286132
Axis point 0.00000000 379.00537801 364.41400171
Rotation angle (degrees) 48.42308632
Shift along axis 0.55192157
> select subtract #23
Nothing selected
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
> models #22 relModel #1
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J595_SC.pdb
> models #23 relModel #2
> close #22
> close #23
> hide #!2 models
> show #!20 models
> show #!21 models
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
Chain information for 9etz_CIII_rel_J594_SC.pdb #22
---
Chain | Description
A L | No description available
B M | No description available
C N | No description available
D O | No description available
F Q | No description available
G R | No description available
H S | No description available
I T | No description available
J | No description available
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J595_SC.pdb
Chain information for 9etz_CIV_rel_J595_SC.pdb #23
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> hide #!20 models
> hide #!21 models
> select #22/F
633 atoms, 648 bonds, 75 residues, 1 model selected
> select ~sel & ##selected
29006 atoms, 29697 bonds, 36 pseudobonds, 3517 residues, 2 models selected
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
> models #22 selectedOnly true relModel #1
> close #22
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
Summary of feedback from opening
/Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J594_SC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 71 71 ASP F 76 LYS F 86 1 11
Start residue of secondary structure not found: HELIX 72 72 THR F 88 ILE F 107
1 20
Start residue of secondary structure not found: HELIX 73 73 CYS F 123 ALA F
139 1 17
Start residue of secondary structure not found: HELIX 74 74 PRO F 140 LEU F
142 1 3
Cannot find LINK/SSBOND residue CYS (101 )
Chain information for 9etz_CIII_rel_J594_SC.pdb #22
---
Chain | Description
A L | No description available
B M | No description available
C N | No description available
D O | No description available
G R | No description available
H S | No description available
I T | No description available
J | No description available
Q | No description available
> select add #23
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> select add #22
44026 atoms, 45117 bonds, 64 pseudobonds, 5340 residues, 4 models selected
> show sel surfaces
> hide sel atoms
> select #22
29006 atoms, 29697 bonds, 36 pseudobonds, 3517 residues, 2 models selected
> color sel tan
> select 23
Expected an objects specifier or a keyword
> select #23
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> color sel powder blue
> select clear
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!20 models
> hide #!20,22-23 surfaces
> show #!20,22-23 atoms
> hide #!20,22-23 atoms
> show #!20,22-23 cartoons
> show #!20,22-23 surfaces
> select #23
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light steel blue
> select clear
> hide #!20,22-23 surfaces
> show #!20,22-23 surfaces
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> show #!21 models
> lighting flat
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> color #23 #b0c4de49
> color #23 lightsteelblue
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!20,22-23 atoms
> hide #!20,22-23 surfaces
> select #22/I,T
562 atoms, 578 bonds, 68 residues, 1 model selected
> color sel indian red
> dssp sel
> select add #22
29006 atoms, 29697 bonds, 36 pseudobonds, 3517 residues, 4 models selected
> select subtract #22
16 models selected
> select #23
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> color sel powder blue
> select subtract #23
12 models selected
> hide #!23 models
> hide #!22 models
> hide #!20 models
> show #!19 models
> show #!17 models
> show #!15 models
> show #!13 models
> show #!11 models
> show #!9 models
> hide #!11 models
> hide #!13 models
> hide #!15 models
> hide #!17 models
> hide #!19 models
> show #!23 models
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J645_SC.pdb
Chain information for 9etz_CIV_rel_J645_SC.pdb #24
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> fitmap #24 inMap #9
Fit molecule 9etz_CIV_rel_J645_SC.pdb (#24) to map
cryosparc_P429_J645_007_volume_map.mrc (#9) using 15020 atoms
average map value = 0.07198, steps = 100
shifted from previous position = 7.65
rotated from previous position = 7.76 degrees
atoms outside contour = 6476, contour level = 0.063182
Position of 9etz_CIV_rel_J645_SC.pdb (#24) relative to
cryosparc_P429_J645_007_volume_map.mrc (#9) coordinates:
Matrix rotation and translation
0.99331629 0.00419571 0.11534796 -23.84537381
0.00394301 0.99752237 -0.07023946 14.34745120
-0.11535688 0.07022482 0.99083867 7.52441430
Axis 0.52004193 0.85414022 -0.00093557
Axis point 48.63936344 0.00000000 208.85459467
Rotation angle (degrees) 7.76156407
Shift along axis -0.15289885
> hide #!23-24 atoms
> show #!23-24 cartoons
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J645_SC.pdb
> models #24 relModel #9
> close #24
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIV_rel_J645_SC.pdb
Chain information for 9etz_CIV_rel_J645_SC.pdb #24
---
Chain | Description
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
> hide #!23-24 atoms
> show #!23-24 cartoons
> show #!8 models
> hide #!9 models
> show #!20 models
> hide #!20 models
> show #!21 models
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J644_SC.pdb
Summary of feedback from opening
/Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J644_SC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 71 71 ASP E 48 SER E 81 1 34
Start residue of secondary structure not found: HELIX 72 72 THR E 85 ALA E 90
1 6
Start residue of secondary structure not found: HELIX 73 73 THR E 122 SER E
131 1 10
Start residue of secondary structure not found: HELIX 90 90 PHE I 3 PHE I 11 1
9
Start residue of secondary structure not found: HELIX 91 91 ARG I 13 ASN I 44
1 32
122 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (164 )
Cannot find LINK/SSBOND residue CYS (27 )
Cannot find LINK/SSBOND residue CYS (37 )
Cannot find LINK/SSBOND residue CYS (111 )
25 messages similar to the above omitted
Chain information for 9etz_CIII_rel_J644_SC.pdb #25
---
Chain | Description
A L | No description available
B M | No description available
C N | No description available
D O | No description available
F Q | No description available
G R | No description available
H S | No description available
I T | No description available
J | No description available
> hide #!21 models
> fitmap #25 inMap #8
Fit molecule 9etz_CIII_rel_J644_SC.pdb (#25) to map
cryosparc_P429_J644_004_volume_map.mrc (#8) using 29639 atoms
average map value = 0.09643, steps = 48
shifted from previous position = 0.183
rotated from previous position = 0.367 degrees
atoms outside contour = 13580, contour level = 0.080169
Position of 9etz_CIII_rel_J644_SC.pdb (#25) relative to
cryosparc_P429_J644_004_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99999373 -0.00139836 0.00325311 -0.59099704
0.00138098 0.99998480 0.00533792 -1.64338561
-0.00326052 -0.00533340 0.99998046 1.82889484
Axis -0.83321587 0.50858408 0.21701047
Axis point 0.00000000 339.58612898 313.93598818
Rotation angle (degrees) 0.36690709
Shift along axis 0.05351768
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J644_SC.pdb
> models #25 relModel #8
> close #25
> open
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/9etz_CIII_rel_J644_SC.pdb
Chain information for 9etz_CIII_rel_J644_SC.pdb #25
---
Chain | Description
A L | No description available
B M | No description available
C N | No description available
D O | No description available
F Q | No description available
G R | No description available
H S | No description available
I T | No description available
J | No description available
> hide #!23-25 atoms
> show #!23-25 cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #24
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> color sel powder blue
> select subtract #24
Nothing selected
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> select add #25
29639 atoms, 30345 bonds, 36 pseudobonds, 3592 residues, 2 models selected
> color sel tan
> select #22/I,T
562 atoms, 578 bonds, 68 residues, 1 model selected
> select #25/I,T
562 atoms, 578 bonds, 68 residues, 1 model selected
> color sel indian red
> dssp sel
> select #25/F
633 atoms, 648 bonds, 75 residues, 1 model selected
> color sel sierra
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ui tool show "Color Actions"
> color sel sienna
> select clear
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!23 models
> show #!22 models
> show #!21 models
> hide #!21-22,25 surfaces
> show #!24 models
> show #!23 models
> show #!20 models
> hide #!20 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!22 models
> show #!22 models
> hide #!21 models
> show #!25 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!25 models
> show #!5 models
> hide #!5 models
> show #!23 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4A.png
> width 9430 height 6840 supersample 4 transparentBackground true
> show #!24 models
> show #!25 models
> hide #!23 models
> hide #!22 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4B.png
> width 9430 height 6840 supersample 4 transparentBackground true
> show #!20 models
> show #!21 models
> hide #!24 models
> hide #!25 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4C.png
> width 9430 height 6840 supersample 4 transparentBackground true
> show #!5 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4D.png
> width 9439 height 6847 supersample 4 transparentBackground true
> select #5/F
633 atoms, 648 bonds, 75 residues, 1 model selected
> color sel sienna
> select clear
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4D.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!20 models
> show #!21 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4C.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!24 models
> show #!25 models
> hide #!21 models
> hide #!20 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4B.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!23 models
> show #!22 models
> hide #!24 models
> hide #!25 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4A.png
> width 9439 height 6847 supersample 4 transparentBackground true
> turn x 90
> show #!24 models
> show #!25 models
> show #!21 models
> show #!20 models
> show #!19 models
> hide #!19 models
> show #!5 models
> hide #!5 models
> hide #!25 models
> hide #!24 models
> hide #!21 models
> hide #!20 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4E.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!25 models
> show #!24 models
> hide #!23 models
> hide #!22 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4F.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!21 models
> hide #!21 models
> show #!21 models
> show #!20 models
> hide #!24 models
> hide #!25 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4G.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!5 models
> hide #!21 models
> hide #!20 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4H.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!21 models
> show #!20 models
> hide #!20 models
> show #!20 models
> select add #20
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select subtract #20
12 models selected
> select add #20
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> cartoon style (#!20 & sel) modeHelix tube sides 20
> select subtract #20
12 models selected
> show #!24 models
> select add #24
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> cartoon style (#!24 & sel) modeHelix tube sides 20
> select clear
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!21 models
> select add #21
29639 atoms, 30345 bonds, 36 pseudobonds, 3592 residues, 2 models selected
> cartoon style (#!21 & sel) modeHelix tube sides 20
> select clear
> hide #!24 models
> turn x -90
> turn x 90
> turn x 180
> select add #21
29639 atoms, 30345 bonds, 36 pseudobonds, 3592 residues, 2 models selected
> select add #20
44659 atoms, 45765 bonds, 64 pseudobonds, 5415 residues, 21 models selected
> cartoon style (#!20-21 & sel & coil) xsection oval
> cartoon style (#!20-21 & sel) xsection barbell modeHelix default
> select subtract #21
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 31 models selected
> select subtract #20
12 models selected
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> cartoon style (#!5 & sel) modeHelix tube sides 20
> select clear
> turn x 180
> turn x -180
> turn x -90
> turn x -180
> hide #!21 models
> show #!21 models
> hide #!20 models
> hide #!5 models
> show #!20 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!24 models
> hide #!24 models
> show #!24 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!20 models
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> select add #24
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> cartoon style (#!24 & sel & coil) xsection oval
> cartoon style (#!24 & sel) xsection barbell modeHelix default
> select clear
> hide #!5 models
> hide #!20 models
> hide #!23 models
> hide #!24 models
> show #!24 models
> show #!23 models
> show #!25 models
> show #!22 models
> hide #!24 models
> hide #!25 models
> hide #!21 models
> show #!5 models
> hide #!5 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> hide #!24 models
> show #!24 models
> show #!25 models
> show #!21 models
> show #!20 models
> show #!19 models
> hide #!19 models
> show #!5 models
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> cartoon style (#!5 & sel) modeHelix tube sides 20
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> select subtract #5
32 models selected
> hide #!5 models
> hide #!21 models
> hide #!20 models
> hide #!24 models
> hide #!25 models
> show #!24 models
> show #!25 models
> hide #!25 models
> show #!20 models
> hide #!24 models
> hide #!20 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4I.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!25 models
> show #!24 models
> hide #!23 models
> hide #!22 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4J.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!20 models
> show #!21 models
> hide #!24 models
> hide #!25 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4K.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!5 models
> hide #!20 models
> hide #!21 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4L.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!22 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!5 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!25 models
> show #!25 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> select add #22
29006 atoms, 29697 bonds, 36 pseudobonds, 3517 residues, 2 models selected
> show sel surfaces
> select add #23
44026 atoms, 45117 bonds, 64 pseudobonds, 5340 residues, 20 models selected
> show sel surfaces
> select clear
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4M.png
> width 9439 height 6847 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4N.png
> width 9439 height 6847 supersample 4 transparentBackground true
> hide #!22-23,25 surfaces
> select #25/F
633 atoms, 648 bonds, 75 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> select add #24
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> select add #23
30040 atoms, 30840 bonds, 56 pseudobonds, 3646 residues, 4 models selected
> cartoon style (#!23-24 & sel) xsection oval modeHelix default
> select subtract #24
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 14 models selected
> select subtract #23
12 models selected
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> hide #!25 models
> show #!25 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4M.png
> width 9439 height 6847 supersample 4 transparentBackground true
> ui tool show "Side View"
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4M.png
> width 9439 height 6847 supersample 4 transparentBackground true
> select add #23
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> select add #25
44659 atoms, 45765 bonds, 64 pseudobonds, 5415 residues, 16 models selected
> cartoon style (#!23,25 & sel) modeHelix tube sides 20
> show #!24 models
> select add #24
59679 atoms, 61185 bonds, 92 pseudobonds, 7238 residues, 19 models selected
> cartoon style (#!23-25 & sel) modeHelix tube sides 20
> select subtract #23
44659 atoms, 45765 bonds, 64 pseudobonds, 5415 residues, 17 models selected
> select subtract #24
29639 atoms, 30345 bonds, 36 pseudobonds, 3592 residues, 3 models selected
> select subtract #25
1 model selected
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4M.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!24 models
> hide #!23 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4N.png
> width 9439 height 6847 supersample 4 transparentBackground true
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #!23 models
> hide #!24 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4.cxs
> includeMaps true
> hide #!18 models
> hide #!25 models
> hide #!23 models
> show #!20 models
> show #!21 models
> show #!5 models
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> cartoon style (#!5 & sel) modeHelix tube sides 20
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> select subtract #5
32 models selected
> select add #20
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> select add #21
44659 atoms, 45765 bonds, 64 pseudobonds, 5415 residues, 16 models selected
> cartoon style (#!20-21 & sel) modeHelix tube sides 20
> select clear
> turn y 180
> turn x 180
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4.cxs
> includeMaps true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4O.png
> width 9439 height 6847 supersample 4 transparentBackground true
> select add #20
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> cartoon style (#!20 & sel) xsection oval modeHelix default
> undo
> select subtract #20
12 models selected
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> cartoon style (#!5 & sel) xsection oval modeHelix default
> select clear
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4O.png
> width 9439 height 6847 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4.cxs
> includeMaps true
> select add #5
48795 atoms, 49993 bonds, 71 pseudobonds, 5917 residues, 2 models selected
> cartoon style (#!5 & sel) modeHelix tube sides 20
> select subtract #5
32 models selected
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> select add #20
15020 atoms, 15420 bonds, 28 pseudobonds, 1823 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> select clear
> show #!21 models
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4O.png
> width 9439 height 6847 supersample 4 transparentBackground true
> save
> /Users/ivercellino/Desktop/Manuscripts/2026_CIII_RIP1_KO/Figures/Fig4.cxs
> includeMaps true
> close #1-4
> close #6-19
> close #20-25
> hide #!5 models
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J307_006_volume_map.mrc
Opened cryosparc_P436_J307_006_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.82, shown at level 0.0224, step 2, values float32
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J309_004_volume_map.mrc
Opened cryosparc_P436_J309_004_volume_map.mrc as #2, grid size 512,512,512,
pixel 0.82, shown at level 0.0225, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.04301
> volume #2 level 0.06292
> volume #1 level 0.07119
> open
> /Users/ivercellino/Desktop/Group/CIII_project/20251125_VI5_CIII_krios_data_collection/NU_refine/cryosparc_P436_J302_006_volume_map.mrc
Opened cryosparc_P436_J302_006_volume_map.mrc as #3, grid size 512,512,512,
pixel 0.82, shown at level 0.0229, step 2, values float32
> volume #3 level 0.06468
> volume #3 step 1
> volume #1 level 0.07454
> volume #2 level 0.08094
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: Z17J000GSD/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 Performance and 4 Efficiency)
Memory: 32 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 13 days, 9 hours, 52 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (1)
comment:1 by , 49 minutes ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
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Reported by Irene