id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20850	Crash on Mac waking from sleep	i.vercellino@…	Tom Goddard	"{{{
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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===== 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

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> hide #!10 models

> show #!11 models

> hide #!11 models

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> 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

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> 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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX