id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18373	Crash on Mac waking from sleep	nnmanh542@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x00000001f62b0c80 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)


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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/04-08-25-ctSec63.cxs""

Opened cryosparc_P12_J364_007_volume_map.mrc as #1, grid size 224,224,224,
pixel 1.15, shown at level 0.144, step 1, values float32  
Opened cryosparc_P12_J364_007_volume_map.mrc z flip as #3, grid size
224,224,224, pixel 1.15, shown at level 0.118, step 1, values float32  
Log from Mon Aug 4 13:46:07 2025UCSF 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/tzujingyang/Downloads/cryosparc_P12_J364_007_volume_map.mrc

Opened cryosparc_P12_J364_007_volume_map.mrc as #1, grid size 224,224,224,
pixel 1.15, shown at level 0.0935, step 1, values float32  

> open
> /Users/tzujingyang/Downloads/fold_2025_02_17_ct_post_translocon/fold_2025_02_17_ct_post_translocon_model_0.cif

Chain information for fold_2025_02_17_ct_post_translocon_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
G | .  
  

> set bgColor white

[Repeated 1 time(s)]

> lighting soft

> graphics silhouettes true

> ui mousemode right zoom

> select #1

2 models selected  

> select #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> hide sel atoms

> select #2/A-C

5104 atoms, 5209 bonds, 670 residues, 1 model selected  

> show sel cartoons

Computing secondary structure  

> ui mousemode right ""translate selected models""

> view matrix models #2,1,0,0,22.963,0,1,0,70.289,0,0,1,189.66

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.95513,-0.27821,0.10163,18.017,-0.17707,-0.26127,0.94889,44.495,-0.23743,-0.9243,-0.29881,184.53

> volume #1 level 0.1576

> view matrix models
> #2,-0.97717,0.020318,0.21151,-0.1161,-0.11033,-0.89924,-0.42332,47.062,0.18159,-0.43699,0.88094,186.75

> select #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> show sel cartoons

> select clear

> select #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> view matrix models
> #2,0.34453,0.26283,0.90123,11.89,-0.79557,-0.4279,0.42893,44.798,0.49837,-0.86477,0.061673,186.41

> view matrix models
> #2,0.89857,-0.30549,-0.31503,11.52,0.27215,-0.17521,0.94617,53.87,-0.34424,-0.93594,-0.074298,180.18

> view matrix models
> #2,0.9085,-0.28276,-0.30768,11.488,0.30843,-0.043022,0.95027,53.288,-0.28194,-0.95822,0.048128,181.55

> view matrix models
> #2,0.58344,-0.55494,-0.59299,9.1667,0.67324,-0.077903,0.73531,54.636,-0.45425,-0.82823,0.32816,181.33

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.58344,-0.55494,-0.59299,24.64,0.67324,-0.077903,0.73531,157.92,-0.45425,-0.82823,0.32816,121.65

> view matrix models
> #2,0.58344,-0.55494,-0.59299,99.716,0.67324,-0.077903,0.73531,102.26,-0.45425,-0.82823,0.32816,143.11

> view matrix models
> #2,0.58344,-0.55494,-0.59299,102.63,0.67324,-0.077903,0.73531,125.17,-0.45425,-0.82823,0.32816,125.95

> fitmap #2/A inMap #1

Fit molecule fold_2025_02_17_ct_post_translocon_model_0.cif (#2) to map
cryosparc_P12_J364_007_volume_map.mrc (#1) using 3672 atoms  
average map value = 0.07813, steps = 92  
shifted from previous position = 6.97  
rotated from previous position = 7.15 degrees  
atoms outside contour = 3102, contour level = 0.15761  
  
Position of fold_2025_02_17_ct_post_translocon_model_0.cif (#2) relative to
cryosparc_P12_J364_007_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.66553909 -0.55392862 -0.50022076 106.96152025  
0.60250097 0.00316975 0.79811186 125.68094581  
-0.44051143 -0.83255813 0.33585212 121.20324876  
Axis -0.81533711 -0.02985475 0.57821630  
Axis point 0.00000000 142.79971764 21.66300902  
Rotation angle (degrees) 89.86933805  
Shift along axis -20.88017626  
  

> select clear

> hide #!1 models

> show #!1 models

> hide #2 models

> volume #1 level 0.1443

> show #2 models

> select add #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> ui mousemode right zoom

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.66554,-0.55393,-0.50022,109.51,0.6025,0.0031698,0.79811,70.32,-0.44051,-0.83256,0.33585,155.11

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.18254,0.65455,0.73365,106.32,-0.74328,-0.39658,0.53876,61.958,0.64359,-0.64365,0.41412,161.87

> view matrix models
> #2,-0.9799,-0.087222,0.17942,99.534,0.053281,-0.98111,-0.18596,66.551,0.19225,-0.17266,0.96604,159.27

> view matrix models
> #2,-0.97948,-0.10009,0.1749,99.592,0.035274,-0.93968,-0.34022,65.158,0.19841,-0.32707,0.92394,160.05

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.97948,-0.10009,0.1749,97.345,0.035274,-0.93968,-0.34022,113.48,0.19841,-0.32707,0.92394,130.14

> volume flip #1

Opened cryosparc_P12_J364_007_volume_map.mrc z flip as #3, grid size
224,224,224, pixel 1.15, shown at step 1, values float32  

> view matrix models
> #2,-0.97948,-0.10009,0.1749,72.066,0.035274,-0.93968,-0.34022,57.313,0.19841,-0.32707,0.92394,84.265

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.78926,-0.0074478,-0.61401,78.545,-0.38389,-0.78642,-0.48392,52.497,-0.47927,0.61765,-0.62355,63.428

> view matrix models
> #2,0.5254,-0.0024531,0.85085,86.187,0.67432,-0.60864,-0.41814,59.063,0.51889,0.79344,-0.31812,71.146

> view matrix models
> #2,0.78166,0.071995,0.61953,85.971,0.50316,-0.65976,-0.55817,57.308,0.36856,0.74802,-0.55193,68.89

> view matrix models
> #2,0.75758,0.002533,0.65274,86.471,0.3886,-0.80522,-0.44789,58.178,0.52446,0.59297,-0.611,70.589

> ui mousemode right ""translate selected models""

> view matrix models
> #2,0.75758,0.002533,0.65274,120.55,0.3886,-0.80522,-0.44789,128.77,0.52446,0.59297,-0.611,149.22

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,-0.0024637,0.50637,0.86231,113.4,0.95074,-0.26613,0.15899,133.08,0.30999,0.82022,-0.48077,147.11

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.0024637,0.50637,0.86231,110.46,0.95074,-0.26613,0.15899,126.68,0.30999,0.82022,-0.48077,141.34

> select clear

> fitmap #2/A inMap #3

Fit molecule fold_2025_02_17_ct_post_translocon_model_0.cif (#2) to map
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) using 3672 atoms  
average map value = 0.07028, steps = 88  
shifted from previous position = 2.47  
rotated from previous position = 7.65 degrees  
atoms outside contour = 3288, contour level = 0.14426  
  
Position of fold_2025_02_17_ct_post_translocon_model_0.cif (#2) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.02183192 0.61273735 0.78998501 114.22628435  
0.95843884 -0.23765489 0.15784536 125.93472557  
0.28446154 0.75370625 -0.59245973 141.89463691  
Axis 0.69734812 0.59162440 0.40458149  
Axis point 0.00000000 5.45622083 37.93498054  
Rotation angle (degrees) 154.70788409  
Shift along axis 211.56948323  
  

> select clear

> hide #2 models

> volume #3 level 0.1176

> show #2 models

> ui mousemode right ""rotate selected models""

> select add #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> hide #!3 models

> view matrix models
> #2,-0.69413,0.10211,0.71257,112.11,0.68394,-0.21521,0.69707,127.39,0.22453,0.97122,0.079547,144.42

> show #!3 models

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.69413,0.10211,0.71257,126.88,0.68394,-0.21521,0.69707,114.98,0.22453,0.97122,0.079547,142.76

> fitmap #2/A inMap #3

Fit molecule fold_2025_02_17_ct_post_translocon_model_0.cif (#2) to map
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) using 3672 atoms  
average map value = 0.1228, steps = 84  
shifted from previous position = 7.37  
rotated from previous position = 11.7 degrees  
atoms outside contour = 1867, contour level = 0.11756  
  
Position of fold_2025_02_17_ct_post_translocon_model_0.cif (#2) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
-0.79653569 0.19621692 0.57186522 126.63877416  
0.55507621 -0.13755236 0.82034734 120.62018290  
0.23962744 0.97086471 0.00065002 138.14374615  
Axis 0.29416253 0.64930650 0.70133406  
Axis point 35.95552099 2.31081827 0.00000000  
Rotation angle (degrees) 165.17660668  
Shift along axis 212.45676623  
  

> select clear

> transparency #3 50

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #!3 models

> select ~sel & ##selected

Nothing selected  

> select #2/B:1-95

655 atoms, 667 bonds, 95 residues, 1 model selected  

> hide sel cartoons

> show #!3 models

> view matrix models
> #2,-0.79654,0.19622,0.57187,127.06,0.55508,-0.13755,0.82035,121.54,0.23963,0.97086,0.00065002,136.68

> undo

> select clear

> volume #3 level 0.0962

> volume #3 level 0.1122

> volume #3 level 0.1336

> volume #3 level 0.1296

> volume zone #3 nearAtoms #2/A-C range 5

> hide #2 models

> select #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> show #2 models

> hide sel cartoons

> select #2/A-C

5104 atoms, 5209 bonds, 670 residues, 1 model selected  

> show sel cartoons

> view matrix models
> #2,-0.79654,0.19622,0.57187,126.12,0.55508,-0.13755,0.82035,120.37,0.23963,0.97086,0.00065002,138.33

> undo

> select clear

> volume #3 level 0.09887

> open ""/Users/tzujingyang/Library/Mobile
> Documents/com~apple~CloudDocs/Melanie_Lab/SND/Manuscripts/The SND3
> translocon/PDB deposition/CtSND3-translocon_20250130_rotamer_geo_clash-
> refinement-refined_043.deposit_000.cif""

Summary of feedback from opening /Users/tzujingyang/Library/Mobile
Documents/com~apple~CloudDocs/Melanie_Lab/SND/Manuscripts/The SND3
translocon/PDB deposition/CtSND3-translocon_20250130_rotamer_geo_clash-
refinement-refined_043.deposit_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 617  
Skipping entity category: Missing column 'type' on line 134512  
Missing entity information. Treating each chain as a separate entity.  
Invalid residue range for struct_conf ""1"": invalid chain ""1"", on line 503  
Invalid residue range for struct_conf ""2"": invalid chain ""1"", on line 504  
Invalid residue range for struct_conf ""3"": invalid chain ""1"", on line 505  
Invalid residue range for struct_conf ""4"": invalid chain ""1"", on line 506  
Invalid residue range for struct_conf ""5"": invalid chain ""1"", on line 507  
51 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range ""1 1"": invalid chain ""1"", on line
596  
Invalid sheet range for struct_sheet_range ""2 1"": invalid chain ""1"", on line
597  
Invalid sheet range for struct_sheet_range ""3 1"": invalid chain ""1"", on line
598  
Invalid sheet range for struct_sheet_range ""4 1"": invalid chain ""1"", on line
599  
Invalid sheet range for struct_sheet_range ""5 1"": invalid chain ""1"", on line
600  
14 messages similar to the above omitted  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 147388  
Skipping chem_comp category: Missing column 'type' on line 147673  
Skipping chem_comp category: Missing column 'type' on line 147925  
Skipping chem_comp category: Missing column 'type' on line 148204  
Skipping chem_comp category: Missing column 'type' on line 148465  
2 messages similar to the above omitted  
  
Chain information for CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif #4  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
6 | No description available  
7 | No description available  
L1 | No description available  
L2 | No description available  
L3 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lq | No description available  
  

> mmaker #4/1 to #2/A

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2025_02_17_ct_post_translocon_model_0.cif, chain A (#2) with
CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif, chain 1 (#4), sequence alignment score = 2261.8  
RMSD between 199 pruned atom pairs is 0.912 angstroms; (across all 462 pairs:
4.370)  
  

> select #4

133843 atoms, 143270 bonds, 915 pseudobonds, 11376 residues, 3 models selected  

> hide sel atoms

> select #4/1-3

4821 atoms, 4923 bonds, 625 residues, 1 model selected  

> show sel cartoons

> hide #2 models

> select clear

> fitmap #4/1 inMap #3

Fit molecule CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) to map cryosparc_P12_J364_007_volume_map.mrc
z flip (#3) using 3579 atoms  
average map value = 0.1166, steps = 72  
shifted from previous position = 0.986  
rotated from previous position = 4.53 degrees  
atoms outside contour = 1655, contour level = 0.09887  
  
Position of CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.92522432 -0.20409499 -0.31985183 -27.77065956  
-0.37089772 -0.30883687 -0.87581657 456.34574614  
0.07996774 0.92895910 -0.36144176 16.46517303  
Axis 0.97237838 -0.21541508 -0.08987010  
Axis point 0.00000000 223.33381190 156.11302032  
Rotation angle (degrees) 111.87155816  
Shift along axis -126.78707277  
  

> select #3

2 models selected  

> fitmap #4/1 inMap #3

Fit molecule CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) to map cryosparc_P12_J364_007_volume_map.mrc
z flip (#3) using 3579 atoms  
average map value = 0.1166, steps = 44  
shifted from previous position = 0.00239  
rotated from previous position = 0.0101 degrees  
atoms outside contour = 1654, contour level = 0.09887  
  
Position of CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.92519291 -0.20417123 -0.31989403 -27.74137314  
-0.37097647 -0.30896130 -0.87573933 456.37187789  
0.07996590 0.92890098 -0.36159152 16.50339602  
Axis 0.97236973 -0.21545108 -0.08987739  
Axis point 0.00000000 223.33681553 156.11596185  
Rotation angle (degrees) 111.88099235  
Shift along axis -126.78396642  
  

> select clear

> volume unzone #3

> transparency #3 0

> volume #3 level 0.1162

> show #2 models

> volume #3 level 0.1069

> select #4

133843 atoms, 143270 bonds, 915 pseudobonds, 11376 residues, 3 models selected  

> select #4/6

1444 atoms, 1471 bonds, 188 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> volume #3 level 0.1202

> select #2

17672 atoms, 18080 bonds, 2263 residues, 1 model selected  

> show sel cartoons

> view matrix models
> #2,-0.79654,0.19622,0.57187,124.14,0.55508,-0.13755,0.82035,118.91,0.23963,0.97086,0.00065002,136.7

> undo

> select clear

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #2 models

> hide #!4 models

> hide #2 models

> show #!3 models

> volume #3 level 0.1202

> show #!4 models

> volume #3 level 0.1456

> volume #3 level 0.1403

> show #2 models

> volume #3 color #b2b2b280

> transparency #3 0

> volume #3 level 0.1136

> hide #2 models

> hide #!4 models

> show #!3 models

> volume #3 level 0.1242

> volume #3 level 0.1576

> volume #3 level 0.1536

> volume #3 level 0.1122

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!4 models

> hide #!3 models

> show #!3 models

> volume #3 level 0.1376

> volume #3 level 0.1883

> volume #3 level 0.1389

> open 7AFT

Summary of feedback from opening 7AFT fetched from pdb  
---  
note | Fetching compressed mmCIF 7aft from http://files.rcsb.org/download/7aft.cif  
  
7aft title:  
Cryo-EM structure of the signal sequence-engaged post-translational Sec
translocon [more info...]  
  
Chain information for 7aft #5  
---  
Chain | Description | UniProt  
A | Protein transport protein SEC61 | SC61A_YEAST 1-480  
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82  
C | Protein transport protein SSS1 | SC61G_YEAST 1-80  
D | Protein translocation protein SEC63 | SEC63_YEAST 1-663  
E | Translocation protein SEC66 | SEC66_YEAST 1-206  
F | Translocation protein SEC72 | SEC72_YEAST 1-193  
G | Translocation protein SEC62,Translocation protein SEC62 | SEC62_YEAST -124-149  
H | Mating factor alpha-1,Mating factor alpha-1 | MFAL1_YEAST -164-0  
  

> select #5

6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select #5/A to #4/1

Expected a keyword  

> mmaker #5/A to #4/1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif, chain 1 (#4) with 7aft, chain A (#5), sequence
alignment score = 1590.6  
RMSD between 118 pruned atom pairs is 0.994 angstroms; (across all 388 pairs:
5.498)  
  

> select clear

> select #5

6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 2 models selected  

> select #5/H

65 atoms, 64 bonds, 13 residues, 1 model selected  

> fitmap #5/1 inMap #3

No atoms or maps for #5/1  

> fitmap #5/A inMap #3

Fit molecule 7aft (#5) to map cryosparc_P12_J364_007_volume_map.mrc z flip
(#3) using 1922 atoms  
average map value = 0.149, steps = 84  
shifted from previous position = 2.12  
rotated from previous position = 8.11 degrees  
atoms outside contour = 869, contour level = 0.13892  
  
Position of 7aft (#5) relative to cryosparc_P12_J364_007_volume_map.mrc z flip
(#3) coordinates:  
Matrix rotation and translation  
-0.72201031 -0.56105533 0.40486791 222.89438450  
-0.30547912 0.78354717 0.54105115 18.48906784  
-0.62079273 0.26696582 -0.73711982 237.51717785  
Axis -0.25099834 0.93926632 0.23404830  
Axis point 150.85135772 0.00000000 80.52896731  
Rotation angle (degrees) 146.90763543  
Shift along axis 17.01053023  
  

> select clear

> hide #!5 models

> volume #3 level 0.1456

> volume #3 level 0.1443

> show #!4 models

> show #2 models

> hide #!3 models

> hide #2 models

> show #!5 models

> hide #!4 models

> show #!4 models

> show #!3 models

> hide #!5 models

> hide #!4 models

> volume #3 level 0.1309

> volume #3 level 0.1176

> volume #3 level 0.1136

> volume #3 level 0.1403

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> volume #3 level 0.1296

> volume #3 level 0.1176

> save /Users/tzujingyang/Downloads/ctSec63.cxs includeMaps true

——— End of log from Mon Aug 4 13:46:07 2025 ———

> view name session-start

opened ChimeraX session  

Cell requested for row 4 is out of bounds for table with 6 rows! Resizing
table model.  

> show #!5 models

> rename #5 ""7aft Tsai""

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #2 models

> show #!5 models

> color #3 #b2b2b2d2 models

> color #3 #b2b2b2de models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #2 models

> select #2/A

3672 atoms, 3752 bonds, 476 residues, 1 model selected  

> volume #3 level 0.1416

> show #!5 models

> hide #!5 models

> select #5/B

158 atoms, 157 bonds, 32 residues, 1 model selected  

> hide #!3 models

> hide #2 models

> show #!5 models

> select #5/B

158 atoms, 157 bonds, 32 residues, 1 model selected  

> show #!4 models

> hide #!5 models

> hide #!4 models

> show #!3 models

> show #2 models

> show #!5 models

> hide #2 models

> show #2 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> show #!5 models

> hide #!5 models

> ui tool show ""Side View""

> open /Users/annguyen/Downloads/cryosparc_P12_J369_005_volume_map.mrc

Opened cryosparc_P12_J369_005_volume_map.mrc as #6, grid size 224,224,224,
pixel 1.15, shown at level 0.0937, step 1, values float32  

> hide #!3 models

> hide #2 models

> volume #6 level 0.1367

> volume #6 level 0.1238

> show #!5 models

> hide #!5 models

> volume #6 level 0.08371

> volume #6 level 0.1324

> show #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #!6 models

> show #2 models

> hide #2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> show #2 models

> show #!6 models

> select add #6

158 atoms, 157 bonds, 32 residues, 3 models selected  

> select add #5

6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 4 models selected  

> show #!5 models

> select subtract #5

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,0.91504,-0.34874,0.20269,32.05,-0.39981,-0.71766,0.57019,206.86,-0.053387,-0.60278,-0.79612,301.07

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.91504,-0.34874,0.20269,32.446,-0.39981,-0.71766,0.57019,202.96,-0.053387,-0.60278,-0.79612,314.95

> view matrix models
> #6,0.91504,-0.34874,0.20269,34.814,-0.39981,-0.71766,0.57019,202.52,-0.053387,-0.60278,-0.79612,313.3

> ui tool show ""Fit in Map""

> fitmap #6 inMap #1

Fit map cryosparc_P12_J369_005_volume_map.mrc in map
cryosparc_P12_J364_007_volume_map.mrc using 46864 points  
correlation = 0.7436, correlation about mean = 0.07993, overlap = 603.8  
steps = 60, shift = 3.81, angle = 2.63 degrees  
  
Position of cryosparc_P12_J369_005_volume_map.mrc (#6) relative to
cryosparc_P12_J364_007_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.91602817 -0.32807524 0.23077913 29.45651043  
-0.40100174 -0.73541368 0.54622733 204.65652088  
-0.00948553 -0.59290246 -0.80521839 305.26117423  
Axis -0.97655807 0.20597512 -0.06251874  
Axis point 0.00000000 155.67490962 117.77245564  
Rotation angle (degrees) 144.32145282  
Shift along axis -5.69638643  
  

> color #6 #6a6a6aff models

> undo

> color #6 #6a6a6abf models

> color #6 #6a6a6ad2 models

> color #6 #6a6a6ad1 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #!3 models

> hide #!5 models

> color #6 #a5a5a5d1 models

> hide #2 models

> show #!3 models

> fitmap #6 inMap #3

Fit map cryosparc_P12_J369_005_volume_map.mrc in map
cryosparc_P12_J364_007_volume_map.mrc z flip using 46864 points  
correlation = 0.6934, correlation about mean = 0.08096, overlap = 653.8  
steps = 140, shift = 5.84, angle = 10.2 degrees  
  
Position of cryosparc_P12_J369_005_volume_map.mrc (#6) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.89059252 -0.41985823 0.17482562 45.87397832  
-0.42552460 -0.63354903 0.64617676 184.26921694  
-0.16054203 -0.64987281 -0.74289404 327.71666014  
Axis -0.96810520 0.25050830 -0.00423259  
Axis point 0.00000000 163.07355093 127.22582210  
Rotation angle (degrees) 137.98120473  
Shift along axis 0.36304043  
  

> volume flip #6

Opened cryosparc_P12_J369_005_volume_map.mrc z flip as #7, grid size
224,224,224, pixel 1.15, shown at step 1, values float32  

> fitmap #7 inMap #3

Fit map cryosparc_P12_J369_005_volume_map.mrc z flip in map
cryosparc_P12_J364_007_volume_map.mrc z flip using 46864 points  
correlation = 0.6754, correlation about mean = 0.05638, overlap = 543.7  
steps = 156, shift = 14.5, angle = 7.31 degrees  
  
Position of cryosparc_P12_J369_005_volume_map.mrc z flip (#7) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.91091097 -0.40937649 0.05149827 54.18018317  
-0.33423477 -0.65894287 0.67385560 167.24216477  
-0.24192623 -0.63103498 -0.73706616 347.07625424  
Axis -0.97410180 0.21904161 0.05609335  
Axis point 0.00000000 158.15300023 142.24540846  
Rotation angle (degrees) 137.94900990  
Shift along axis 3.32464895  
  

> close #6

> close #1

> color #7 #a5a5a5ff models

> ui mousemode right ""rotate selected models""

> select add #7

2 models selected  

> view matrix models
> #7,0.98734,0.026146,0.15644,-26.648,-0.025494,0.99966,-0.0061751,3.4773,-0.15655,0.0021087,0.98767,19.815

> fitmap #7 inMap #3

Fit map cryosparc_P12_J369_005_volume_map.mrc z flip in map
cryosparc_P12_J364_007_volume_map.mrc z flip using 46864 points  
correlation = 0.9946, correlation about mean = 0.9205, overlap = 1712  
steps = 92, shift = 2.57, angle = 9.28 degrees  
  
Position of cryosparc_P12_J369_005_volume_map.mrc z flip (#7) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.99976784 0.02110035 -0.00435981 -2.35330290  
-0.02107072 0.99975529 0.00673369 1.86561627  
0.00450082 -0.00664025 0.99996780 0.31585649  
Axis -0.29641125 -0.19638121 -0.93465223  
Axis point 87.57532457 111.98744505 0.00000000  
Rotation angle (degrees) 1.29268927  
Shift along axis 0.03595749  
  

> show #2 models

> hide #!3 models

> color #7 #a5a5a5de models

> show #!5 models

> hide #!5 models

> color #7 #a5a5a5bb models

> color #7 #a5a5a5ba models

> lighting soft

> lighting flat

> color #7 #a5a5a5c4 models

> lighting soft

> volume #7 level 0.1117

> volume #7 level 0.03172

> volume #7 level 0.1304

> volume #7 level 0.1146

> show #!3 models

> hide #!7 models

> volume #3 level 0.1113

> volume #3 level 0.1463

> hide #2 models

> show #!5 models

> select #5/B

158 atoms, 157 bonds, 32 residues, 1 model selected  

> hide #!5 models

> show #2 models

> open 7kal

Summary of feedback from opening 7kal fetched from pdb  
---  
note | Fetching compressed mmCIF 7kal from http://files.rcsb.org/download/7kal.cif  
  
7kal title:  
Cryo-EM structure of the Sec complex from T. lanuginosus, wild-type, class
with Sec62, plug-open conformation [more info...]  
  
Chain information for 7kal #1  
---  
Chain | Description  
A | Protein transport channel Sec61 complex, alpha subunit (Sec61)  
B | Protein transport channel Sec61 complex, beta subunit (Sbh1)  
C | Protein transport channel Sec61 complex, gamma subunit (Sss1)  
D | Protein transport protein Sec63  
E | Protein transport protein Sec66/Sec71  
F | Protein transport protein Sec72  
G | Protein transport protein Sec62  
  

> show #2#!1 cartoons

> hide #2#!1 atoms

> select add #5

6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 2 models selected  

> show #!5 models

> select subtract #5

Nothing selected  

> select add #1

10789 atoms, 11024 bonds, 11 pseudobonds, 1429 residues, 2 models selected  

> hide #2 models

> view matrix models
> #1,0.88239,0.40211,-0.24431,-11.455,0.35912,-0.91107,-0.20246,265.91,-0.30399,0.090914,-0.94833,290.99

> view matrix models
> #1,0.9093,0.33777,-0.24308,-5.751,0.28851,-0.93264,-0.21668,281.45,-0.29989,0.1269,-0.9455,284.53

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.9093,0.33777,-0.24308,-23.762,0.28851,-0.93264,-0.21668,264.93,-0.29989,0.1269,-0.9455,291.41

> view matrix models
> #1,0.9093,0.33777,-0.24308,-17.687,0.28851,-0.93264,-0.21668,263.06,-0.29989,0.1269,-0.9455,291.76

> mmaker 1/A to #5/A

> matchmaker 1/A to #5/A

Missing or invalid ""matchAtoms"" argument: invalid atoms specifier  

> mmaker #1/A to #5/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7aft Tsai, chain A (#5) with 7kal, chain A (#1), sequence alignment
score = 1682.4  
RMSD between 287 pruned atom pairs is 1.164 angstroms; (across all 387 pairs:
2.284)  
  

> hide #!5 models

> volume #3 level 0.1009

> volume #3 level 0.1208

> volume #7 level 0.1117

> volume #7 level 0.1709

> hide #!7 models

> show #2 models

> hide #!1 models

> select subtract #1

Nothing selected  

> rename #1 ""7kal Cryo-EM structure of the Sec complex from T. lanuginosus,
> wild-type, class with Sec62, plug-open conformation""

> rename #1 ""7kal T. lanuginosus WT with Sec62, plug-open conformation""

> rename #1 ""7kal T. lanuginosus WT with Sec62 plug-open conformation""

> open 7kam

Summary of feedback from opening 7kam fetched from pdb  
---  
note | Fetching compressed mmCIF 7kam from http://files.rcsb.org/download/7kam.cif  
  
7kam title:  
Cryo-EM structure of the Sec complex from T. lanuginosus, wild-type, class
with Sec62, plug-closed conformation [more info...]  
  
Chain information for 7kam #6  
---  
Chain | Description  
A | Protein transport channel Sec61 complex, alpha subunit (Sec61)  
B | Protein transport channel Sec61 complex, beta subunit (Sbh1)  
C | Protein transport channel Sec61 complex, gamma subunit (Sss1)  
D | Protein transport protein Sec63  
E | Protein transport protein Sec66/Sec71  
F | Protein transport protein Sec72  
G | Protein transport protein Sec62  
  

> rename #6 ""7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation""

> mmaker #1/A to #6/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347  
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)  
  

> show #2#!6 cartoons

> hide #2#!6 atoms

> select add #6

10916 atoms, 11157 bonds, 9 pseudobonds, 1445 residues, 2 models selected  

> view matrix models #6,1,0,0,36.367,0,1,0,-148.94,0,0,1,-51.128

> view matrix models #6,1,0,0,33.364,0,1,0,-145.72,0,0,1,-55.655

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,-0.56918,0.65785,0.49322,96.147,0.68596,0.71066,-0.15626,-180.81,-0.45331,0.24939,-0.85575,219.94

> view matrix models
> #6,-0.51104,0.85707,-0.065353,131.76,-0.30202,-0.10786,0.94718,-58.919,0.80475,0.50379,0.31397,-158.45

> view matrix models
> #6,0.71818,0.13655,-0.68233,144.65,0.34299,-0.92264,0.17637,74.113,-0.60546,-0.36069,-0.70945,315.72

> view matrix models
> #6,0.70134,0.36268,-0.61366,103.44,0.52853,-0.84223,0.10629,44.117,-0.4783,-0.39889,-0.78238,312.72

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.70134,0.36268,-0.61366,125.48,0.52853,-0.84223,0.10629,132.15,-0.4783,-0.39889,-0.78238,308.63

> view matrix models
> #6,0.70134,0.36268,-0.61366,100.94,0.52853,-0.84223,0.10629,125.12,-0.4783,-0.39889,-0.78238,303.35

> view matrix models
> #6,0.70134,0.36268,-0.61366,59.233,0.52853,-0.84223,0.10629,127.48,-0.4783,-0.39889,-0.78238,309.7

> view matrix models
> #6,0.70134,0.36268,-0.61366,83.991,0.52853,-0.84223,0.10629,165.86,-0.4783,-0.39889,-0.78238,356.63

> mmaker #1/A to #6/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347  
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)  
  

> view matrix models
> #6,0.70134,0.36268,-0.61366,84.018,0.52853,-0.84223,0.10629,149.4,-0.4783,-0.39889,-0.78238,367.32

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,0.36878,0.9289,-0.033825,-31.2,0.91986,-0.36994,-0.1304,51.795,-0.13364,0.016975,-0.99088,281.38

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.36878,0.9289,-0.033825,-67.306,0.91986,-0.36994,-0.1304,60.252,-0.13364,0.016975,-0.99088,284.19

> mmaker #1/A to #6/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347  
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)  
  

> view matrix models
> #6,0.36878,0.9289,-0.033825,-70.459,0.91986,-0.36994,-0.1304,57.715,-0.13364,0.016975,-0.99088,279.62

> view matrix models
> #6,0.36878,0.9289,-0.033825,-66.6,0.91986,-0.36994,-0.1304,59.871,-0.13364,0.016975,-0.99088,287.05

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,0.75101,0.65467,0.085978,-96.5,0.65998,-0.74023,-0.12843,154.03,-0.020434,0.15319,-0.98799,249.36

> mmaker #1/A to #6/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347  
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)  
  

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.75101,0.65467,0.085978,-95.623,0.65998,-0.74023,-0.12843,159.12,-0.020434,0.15319,-0.98799,246.71

> mmaker #1/A to #6/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347  
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)  
  

> mmaker #1 to #6

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain D (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain D (#1), sequence alignment score = 3216.3  
RMSD between 470 pruned atom pairs is 0.543 angstroms; (across all 475 pairs:
0.654)  
  

> hide #2 models

> show #!1 models

> hide #!1 models

> fitmap #6/A inMap #3

Fit molecule 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation
(#6) to map cryosparc_P12_J364_007_volume_map.mrc z flip (#3) using 3386 atoms  
average map value = 0.1176, steps = 84  
shifted from previous position = 4.61  
rotated from previous position = 11.5 degrees  
atoms outside contour = 1840, contour level = 0.12075  
  
Position of 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation
(#6) relative to cryosparc_P12_J364_007_volume_map.mrc z flip (#3)
coordinates:  
Matrix rotation and translation  
0.82602362 0.56150897 -0.04891494 -67.86582856  
0.53971147 -0.81299405 -0.21852274 202.24385256  
-0.16247004 0.15410500 -0.97460512 266.94351827  
Axis 0.95507491 0.29105086 -0.05586872  
Axis point 0.00000000 97.75952528 142.22737827  
Rotation angle (degrees) 168.75073396  
Shift along axis -20.86749542  
  

> select #6/G

354 atoms, 360 bonds, 62 residues, 1 model selected  

> show #2 models

> open 7kai

7kai title:  
Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with
Sec62, conformation 1 (C1) [more info...]  
  
Chain information for 7kai #8  
---  
Chain | Description | UniProt  
A | Protein transport protein SEC61 | SC61A_YEAST 1-480  
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82  
C | Protein transport protein SSS1 | SC61G_YEAST 1-80  
D | Protein translocation protein SEC63 | SEC63_YEAST 2-663  
E | Translocation protein SEC66 | SEC66_YEAST 1-206  
F | Translocation protein SEC72 | SEC72_YEAST 1-193  
G | Protein transport protein Sec62 |   
  

> rename #8 ""7kai Sc, WT, wtSec62, (C1)""

> open 7kaj

7kaj title:  
Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with
Sec62, conformation 2 (C2) [more info...]  
  
Chain information for 7kaj #9  
---  
Chain | Description | UniProt  
A | Protein transport protein SEC61 | SC61A_YEAST 1-480  
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82  
C | Protein transport protein SSS1 | SC61G_YEAST 1-80  
D | Protein translocation protein SEC63 | SEC63_YEAST 2-663  
E | Translocation protein SEC66 | SEC66_YEAST 1-206  
F | Translocation protein SEC72 | SEC72_YEAST 1-193  
G | Protein transport protein Sec62 |   
  

> rename #9 ""7kaj Sc, WT, wtSec62, (C2)""

> show sel cartoons

> hide sel atoms

> select add #6

10916 atoms, 11157 bonds, 9 pseudobonds, 1445 residues, 2 models selected  

> select subtract #6

Nothing selected  

> hide #2#!6,8-9 atoms

> show #2#!6,8-9 cartoons

> select add #8

10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected  

> select add #9

21430 atoms, 21842 bonds, 12 pseudobonds, 2798 residues, 4 models selected  

> view matrix models
> #8,1,0,0,86.197,0,1,0,19.771,0,0,1,25.38,#9,1,0,0,86.197,0,1,0,19.771,0,0,1,25.38

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,0.84265,0.50523,-0.18624,55.887,0.4946,-0.86297,-0.10324,257.07,-0.21288,-0.0051208,-0.97707,341.88,#9,0.84265,0.50523,-0.18624,55.887,0.4946,-0.86297,-0.10324,257.07,-0.21288,-0.0051208,-0.97707,341.88

> view matrix models
> #8,0.82869,0.55371,-0.081747,35.268,0.50771,-0.80512,-0.30661,275.05,-0.23559,0.21258,-0.94832,306.48,#9,0.82869,0.55371,-0.081747,35.268,0.50771,-0.80512,-0.30661,275.05,-0.23559,0.21258,-0.94832,306.48

> ui mousemode right ""translate selected models""

> view matrix models
> #8,0.82869,0.55371,-0.081747,-84.359,0.50771,-0.80512,-0.30661,236.11,-0.23559,0.21258,-0.94832,274.38,#9,0.82869,0.55371,-0.081747,-84.359,0.50771,-0.80512,-0.30661,236.11,-0.23559,0.21258,-0.94832,274.38

> view matrix models
> #8,0.82869,0.55371,-0.081747,-67.287,0.50771,-0.80512,-0.30661,223.18,-0.23559,0.21258,-0.94832,272.07,#9,0.82869,0.55371,-0.081747,-67.287,0.50771,-0.80512,-0.30661,223.18,-0.23559,0.21258,-0.94832,272.07

> mmaker #8 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7aft Tsai, chain D (#5) with 7kai Sc, WT, wtSec62, (C1), chain D
(#8), sequence alignment score = 3040.5  
RMSD between 431 pruned atom pairs is 1.014 angstroms; (across all 486 pairs:
1.292)  
  

> mmaker #9 to #5

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7aft Tsai, chain D (#5) with 7kaj Sc, WT, wtSec62, (C2), chain D
(#9), sequence alignment score = 3037.5  
RMSD between 451 pruned atom pairs is 0.985 angstroms; (across all 486 pairs:
1.187)  
  

> select subtract #8

10712 atoms, 10918 bonds, 6 pseudobonds, 1399 residues, 2 models selected  

> select subtract #9

Nothing selected  

> hide #!8 models

> show #!8 models

> hide #2 models

> hide #!6 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> mmaker #8/A to #9/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7kaj Sc, WT, wtSec62, (C2), chain A (#9) with 7kai Sc, WT, wtSec62,
(C1), chain A (#8), sequence alignment score = 2348.5  
RMSD between 386 pruned atom pairs is 0.512 angstroms; (across all 436 pairs:
1.651)  
  

> show #2 models

> hide #2 models

> select #9/B

229 atoms, 233 bonds, 32 residues, 1 model selected  

> show #2 models

> hide #2 models

> clip off


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
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: Mac14,7
      Model Number: Z16U000NJD/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 50 days, 20 hours, 32 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P3223QE:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    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: 14.1.19
    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: 1.10.1
    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: 1.1.3
    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: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    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: 4.3.2
    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
    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: 4.14.1
    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