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Opened 73 minutes ago
#20828 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001f14d1d80 (most recent call first):
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2848 in update_buffer_data
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1923 in update_buffers
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1935 in activate_bindings
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 791 in draw_self
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 784 in draw
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1572 in _draw_multiple
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559 in draw_opaque
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259 in _draw_scene
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 424 in event_loop
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 56)
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"codeSigningMonitor" : 2,
"incident" : "4B895C88-C0A2-4AF1-ADE3-F1AD00A2D628",
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"procLaunch" : "2026-08-05 13:45:52.1562 -0500",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"sleepWakeUUID" : "839165B2-9065-4F67-BDC1-F01101A22A90",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
mapped file 13b720000-13b79c000 [ 496K] r--\/r-x SM=PRV Object_id=54274126
GAP OF 0x40000 BYTES
---> mapped file 13b7dc000-13b840000 [ 400K] r--\/rwx SM=COW Object_id=dc566967
CG image 13b840000-13b850000 [ 64K] rw-\/rwx SM=COW ",
"exception" : {"codes":"0x0000000000000002, 0x000000013b7dc000","rawCodes":[2,5293064192],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x000000013b7dc000"},
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
mapped file 13b720000-13b79c000 [ 496K] r--\/r-x SM=PRV Object_id=54274126
GAP OF 0x40000 BYTES
---> mapped file 13b7dc000-13b840000 [ 400K] r--\/rwx SM=COW Object_id=dc566967
CG image 13b840000-13b850000 [ 64K] rw-\/rwx SM=COW ",
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"name" : "libsystem_c.dylib"
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"arch" : "arm64e",
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"uuid" : "160fd864-8d15-36fc-9e97-9725388cfafe",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
"name" : "GLEngine"
},
{
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"size" : 74280,
"uuid" : "ed35de10-ac5d-3468-9986-10c0c12b0562",
"path" : "\/usr\/lib\/libffi.dylib",
"name" : "libffi.dylib"
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{
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},
"vmSummary" : "ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%)
Writable regions: Total=18.3G written=4.6G(25%) resident=10.3M(0%) swapped_out=4.6G(25%) unallocated=13.7G(75%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 1
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 5440K 16
CG raster data 3296K 7
ColorSync 128K 6
CoreAnimation 2192K 114
CoreGraphics 32K 2
CoreServices 624K 2
CoreUI image data 5120K 39
Foundation 32K 2
Kernel Alloc Once 32K 1
MALLOC 13.2G 365
MALLOC guard page 3824K 4
Mach message 64K 3
Memory Tag 22 64.0M 1
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 592K 37
Stack 192.3M 38
Stack Guard 56.0M 1
VM_ALLOCATE 4.8G 169
VM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)
__AUTH 6172K 649
__AUTH_CONST 91.5M 1044
__CTF 824 1
__DATA 42.7M 1126
__DATA_CONST 62.4M 1181
__DATA_DIRTY 8495K 899
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 605.3M 134
__OBJC_RO 79.1M 1
__OBJC_RW 2598K 1
__TEXT 1.5G 1203
__TPRO_CONST 128K 2
dyld private memory 304K 5
mapped file 661.0M 83
page table in kernel 10.3M 1
shared memory 3248K 30
=========== ======= =======
TOTAL 21.4G 7177
TOTAL, minus reserved VM space 21.3G 7177
",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "b65b1f77c00f53bfa1ca36cf1573345e4a98358c",
"roots_installed" : 0,
"bug_type" : "309",
"trmStatus" : 8192,
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : [
],
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},
{
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class001.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class002.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class003.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class004.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class005.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class006.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class007.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class008.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class009.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class010.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class011.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class012.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class013.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class014.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J274/run_it030_class015.mrc"
Opened run_it030_class001.mrc as #1.1, grid size 132,132,132, pixel 3.8, shown
at level 0.109, step 1, values float32
Opened run_it030_class002.mrc as #1.2, grid size 132,132,132, pixel 3.8, shown
at level 0.0956, step 1, values float32
Opened run_it030_class003.mrc as #1.3, grid size 132,132,132, pixel 3.8, shown
at level 0.112, step 1, values float32
Opened run_it030_class004.mrc as #1.4, grid size 132,132,132, pixel 3.8, shown
at level 0.123, step 1, values float32
Opened run_it030_class005.mrc as #1.5, grid size 132,132,132, pixel 3.8, shown
at level 0.0932, step 1, values float32
Opened run_it030_class006.mrc as #1.6, grid size 132,132,132, pixel 3.8, shown
at level 0.146, step 1, values float32
Opened run_it030_class007.mrc as #1.7, grid size 132,132,132, pixel 3.8, shown
at level 0.122, step 1, values float32
Opened run_it030_class008.mrc as #1.8, grid size 132,132,132, pixel 3.8, shown
at level 0.158, step 1, values float32
Opened run_it030_class009.mrc as #1.9, grid size 132,132,132, pixel 3.8, shown
at level 0.155, step 1, values float32
Opened run_it030_class010.mrc as #1.10, grid size 132,132,132, pixel 3.8,
shown at level 0.109, step 1, values float32
Opened run_it030_class011.mrc as #1.11, grid size 132,132,132, pixel 3.8,
shown at level 0.117, step 1, values float32
Opened run_it030_class012.mrc as #1.12, grid size 132,132,132, pixel 3.8,
shown at level 0.132, step 1, values float32
Opened run_it030_class013.mrc as #1.13, grid size 132,132,132, pixel 3.8,
shown at level 0.114, step 1, values float32
Opened run_it030_class014.mrc as #1.14, grid size 132,132,132, pixel 3.8,
shown at level 0.0897, step 1, values float32
Opened run_it030_class015.mrc as #1.15, grid size 132,132,132, pixel 3.8,
shown at level 0.0946, step 1, values float32
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J147/run_class001.mrc"
Opened run_class001.mrc as #2, grid size 132,132,132, pixel 3.8, shown at
level 0.144, step 1, values float32
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.04639
> close #2
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J72/run_class001.mrc"
Opened run_class001.mrc as #2, grid size 132,132,132, pixel 3.8, shown at
level 0.146, step 1, values float32
> volume #2 level 0.01607
> volume #2 level 0.004311
> hide #!2 models
> show #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!1.6 models
> hide #!1.8 models
> hide #!1.9 models
> hide #!1.11 models
> hide #!1.10 models
> hide #!1.12 models
> hide #!1.13 models
> hide #!1.14 models
> hide #!1.15 models
> hide #!1.7 models
> show #!1.1 models
> volume #1.1 level 0.07023
> hide #!1.1 models
> show #!1.2 models
> volume #1.2 level 0.08899
> volume #1.3 level 0.1092
> volume #1.4 level 0.1144
> volume #1.5 level 0.08286
> volume #1.6 level 0.06483
> volume #1.7 level 0.08601
> volume #1.8 level 0.04623
> volume #1.9 level 0.02378
> volume #1.9 level 0.03209
> volume #1.10 level 0.09574
> volume #1.11 level 0.1087
> volume #1.12 level 0.08388
> volume #1.13 level 0.09786
> volume #1.14 level 0.06696
> volume #1.15 level 0.07941
> volume #1.8 level 0.04832
> volume #1.9 level 0.04766
> volume #1.9 color #99bfe56d
> volume #1.8 level 0.04623
> set bgColor white
> volume #1.8 level 0.07753
> fitmap #1.8 inMap #1.9
Fit map run_it030_class008.mrc in map run_it030_class009.mrc using 60555
points
correlation = 0.9476, correlation about mean = 0.7108, overlap = 1322
steps = 48, shift = 0.0755, angle = 0.173 degrees
Position of run_it030_class008.mrc (#1.8) relative to run_it030_class009.mrc
(#1.9) coordinates:
Matrix rotation and translation
0.99999620 0.00275361 0.00009176 -0.72703580
-0.00275372 0.99999546 0.00122730 0.38991949
-0.00008838 -0.00122755 0.99999924 0.39428729
Axis -0.40694588 0.02986360 -0.91296397
Axis point 141.71728136 271.97823767 0.00000000
Rotation angle (degrees) 0.17281490
Shift along axis -0.05246147
> volume #1.8 level 0.06397
> volume #1.9 level 0.01962
> volume #1.8 level 0.0196
> open 2938 fromDatabase emdb_fits format ccp4
Opened emdb 2938 as #3, grid size 300,300,300, pixel 1.1, shown at level 0.01,
step 2, values float32, fit PDB 4ug0
4ug0 title:
Structure of the human 80S ribosome [more info...]
Chain information for 4ug0 #4
---
Chain | Description | UniProt
L5 | 28S ribosomal RNA |
L7 | 5S ribosomal RNA |
L8 | 5.8S ribosomal RNA |
LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN 1-257
LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN 1-403
LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN 1-427
LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN 1-297
LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN 1-288
LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN 1-248
LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN 1-266
LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN 1-192
LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN 1-214
LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN 1-178
LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN 1-211
LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN 1-215
LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN 1-204
LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN 1-203
LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN 1-184
LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN 1-188
LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN 1-196
LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN 1-176
LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN 1-160
LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN 1-128
LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN 1-140
LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN 1-157
LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN 1-156
LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN 1-145
LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN 1-136
La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN 1-148
Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN 1-159
Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN 1-115
Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN 1-125
Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN 1-135
Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN 1-110
Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN 1-117
Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN 1-123
Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN 1-105
Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN 1-97
Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN 1-70
Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN 1-51
Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN 1-128
Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN 1-25
Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN 1-106
Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN 1-92
Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN 1-137
Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN 1-217
S2 | 18S ribosomal RNA |
S6 | HUMAN INITIATOR MET-TRNA-I |
SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN 1-295
SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN 1-264
SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN 1-293
SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN 1-243
SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN 1-263
SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN 1-204
SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN 1-249
SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN 1-194
SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN 1-208
SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN 1-194
SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN 1-165
SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN 1-158
SM | 40S RIBOSOMAL PROTEIN |
SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN 1-151
SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN 1-151
SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN 1-145
SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN 1-146
SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN 1-135
SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN 1-152
ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN 1-145
SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN 1-119
SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN 1-83
SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN 1-130
SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN 1-143
SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN 1-133
SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN 1-125
Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN 1-115
Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN 1-84
Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN 1-69
Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN 1-56
Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN 1-59
Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN 1-156
Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN 1-317
Non-standard residues in 4ug0 #4
---
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> show #!1 models
> hide #!1.8 models
> hide #!1.9 models
> show #!1.9 models
> ui mousemode right "translate selected models"
> select add #1.9
2 models selected
> select subtract #1.9
Nothing selected
> select add #3
2 models selected
> view matrix models #3,1,0,0,234.5,0,1,0,-108.89,0,0,1,203.59
> hide #!4 models
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.64728,0.7546,0.10771,165.83,-0.6714,0.49751,0.54927,-3.4539,0.36089,-0.42785,0.82867,231.92
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.64728,0.7546,0.10771,-40.953,-0.6714,0.49751,0.54927,131.44,0.36089,-0.42785,0.82867,126.69
> view matrix models
> #3,0.64728,0.7546,0.10771,-35.325,-0.6714,0.49751,0.54927,127.46,0.36089,-0.42785,0.82867,126.7
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.60622,0.79505,-0.01999,-14.397,-0.6655,0.52088,0.53461,125.23,0.43545,-0.31078,0.84487,93.819
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.60622,0.79505,-0.01999,10.062,-0.6655,0.52088,0.53461,130.48,0.43545,-0.31078,0.84487,92.774
> view matrix models
> #3,0.60622,0.79505,-0.01999,0.61422,-0.6655,0.52088,0.53461,191.25,0.43545,-0.31078,0.84487,96.108
> view matrix models
> #3,0.60622,0.79505,-0.01999,11.522,-0.6655,0.52088,0.53461,207.93,0.43545,-0.31078,0.84487,106.28
> view matrix models
> #3,0.60622,0.79505,-0.01999,19.766,-0.6655,0.52088,0.53461,193.39,0.43545,-0.31078,0.84487,96.149
> view matrix models
> #3,0.60622,0.79505,-0.01999,13.291,-0.6655,0.52088,0.53461,197.78,0.43545,-0.31078,0.84487,89.914
> view matrix models
> #3,0.60622,0.79505,-0.01999,14.505,-0.6655,0.52088,0.53461,189.88,0.43545,-0.31078,0.84487,88.285
> volume #1.9 level 0.06635
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.04329,0.89717,0.43955,24.833,-0.90285,-0.15325,0.40171,352.28,0.42776,-0.41424,0.80338,111.53
> fitmap #3 inMap #1.9
Fit map emdb 2938 in map run_it030_class009.mrc using 276391 points
correlation = 0.8096, correlation about mean = 0.4125, overlap = 1486
steps = 72, shift = 7.05, angle = 8.58 degrees
Position of emdb 2938 (#3) relative to run_it030_class009.mrc (#1.9)
coordinates:
Matrix rotation and translation
0.11044066 0.87140076 0.47797864 15.05832056
-0.83965281 -0.17551188 0.51398321 324.09906243
0.53177629 -0.45810075 0.71229045 122.89843290
Axis -0.49378438 -0.02732731 -0.86915488
Axis point 127.00318891 182.13019739 -0.00000000
Rotation angle (degrees) 100.15958016
Shift along axis -123.11009096
> select subtract #3
Nothing selected
> ui tool show "Map Filter"
> volume gaussian #1.9 sDev 5
Opened run_it030_class009.mrc gaussian as #5, grid size 132,132,132, pixel
3.8, shown at step 1, values float32
> volume gaussian #3 sDev 5
Opened emdb 2938 gaussian as #6, grid size 300,300,300, pixel 1.1, shown at
step 1, values float32
> volume #5 color #99bfe56a
> volume #5 level 0.02137
> volume #6 level 0.001368
> volume #5 level 0.00369
> volume #6 level 0.0005542
> hide #!5 models
> volume gaussian #1.8 sDev 5
Opened run_it030_class008.mrc gaussian as #7, grid size 132,132,132, pixel
3.8, shown at step 1, values float32
> volume #7 level 0.03372
> volume #7 color #b2b2b261
> volume #7 level 0.01584
> volume #7 level 0.01548
> volume #7 level 0.007453
> fitmap #6 inMap #7
Fit map emdb 2938 gaussian in map run_it030_class008.mrc gaussian using
4427296 points
correlation = 0.8592, correlation about mean = 0.4955, overlap = 2135
steps = 64, shift = 0.79, angle = 0.851 degrees
Position of emdb 2938 gaussian (#6) relative to run_it030_class008.mrc
gaussian (#7) coordinates:
Matrix rotation and translation
0.11848464 0.87686597 0.46590499 14.67054389
-0.84246768 -0.15957123 0.51457286 321.09892241
0.52555646 -0.45347888 0.71982450 121.78882014
Axis -0.49039387 -0.03021813 -0.87097688
Axis point 127.99389496 180.71524594 0.00000000
Rotation angle (degrees) 99.24352617
Shift along axis -122.97260008
> volume #7 level 0.00344
> select add #6
2 models selected
> view matrix models
> #6,0.18167,0.78043,0.59827,-2.5466,-0.8535,-0.17704,0.4901,329.48,0.4884,-0.59966,0.63393,163.54
> view matrix models
> #6,0.27344,0.81226,0.51523,-10.324,-0.86734,-0.023378,0.49717,307.81,0.41587,-0.58283,0.69811,163.64
> fitmap #6 inMap #7
Fit map emdb 2938 gaussian in map run_it030_class008.mrc gaussian using
4427296 points
correlation = 0.8591, correlation about mean = 0.4954, overlap = 2135
steps = 96, shift = 3.35, angle = 11.6 degrees
Position of emdb 2938 gaussian (#6) relative to run_it030_class008.mrc
gaussian (#7) coordinates:
Matrix rotation and translation
0.11847464 0.87701545 0.46562610 14.73234999
-0.84233180 -0.15953277 0.51480718 321.00785616
0.52577647 -0.45320326 0.71983742 121.76568938
Axis -0.49037127 -0.03047076 -0.87098080
Axis point 127.97469225 180.64253016 0.00000000
Rotation angle (degrees) 99.24232524
Shift along axis -123.06125166
> ui mousemode right select
> select clear
> volume #6 level 0.001205
> volume #7 level 0.00417
> select add #6
2 models selected
Drag select of 6 emdb 2938 gaussian , 7 run_it030_class008.mrc gaussian
> select subtract #7
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.1162,0.87653,0.46711,18.838,-0.84201,-0.1625,0.51441,322.06,0.5268,-0.45308,0.71916,122.79
> view matrix models
> #6,0.1162,0.87653,0.46711,28.152,-0.84201,-0.1625,0.51441,317.18,0.5268,-0.45308,0.71916,109
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.52451,0.48672,0.69857,162.3,-0.5553,-0.81752,0.15266,421.15,0.64539,-0.30785,0.69907,69.715
> view matrix models
> #6,-0.067504,0.83098,0.55219,53.814,-0.62437,-0.46687,0.62626,307.48,0.77821,-0.30249,0.55035,68.774
> volume #7 level 0.05779
> volume #6 level 0.007631
> view matrix models
> #6,0.24152,0.88925,0.38846,17.058,-0.74457,-0.086904,0.66186,265.9,0.62232,-0.44909,0.64112,103.58
> volume #6 level 0.01145
> volume #7 level 0.07676
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.24152,0.88925,0.38846,-8.8046,-0.74457,-0.086904,0.66186,283.47,0.62232,-0.44909,0.64112,119.74
> view matrix models
> #6,0.24152,0.88925,0.38846,5.7392,-0.74457,-0.086904,0.66186,276.82,0.62232,-0.44909,0.64112,119.98
> fitmap #6 inMap #7
Fit map emdb 2938 gaussian in map run_it030_class008.mrc gaussian using 439744
points
correlation = 0.9633, correlation about mean = 0.161, overlap = 645.8
steps = 84, shift = 6.17, angle = 11.2 degrees
Position of emdb 2938 gaussian (#6) relative to run_it030_class008.mrc
gaussian (#7) coordinates:
Matrix rotation and translation
0.11832101 0.87438568 0.47058456 14.46080081
-0.84242884 -0.16248398 0.51372424 321.71114518
0.52565557 -0.45721838 0.71738245 122.55013223
Axis -0.49208418 -0.02791058 -0.87010009
Axis point 127.67813445 181.27221694 0.00000000
Rotation angle (degrees) 99.40373450
Shift along axis -122.72595760
> volume #6 level 0.002018
> volume #7 level 0.0173
> volume #7 level 0.006723
> ui mousemode right select
> select clear
> hide #!7 models
> show #!5 models
> hide #!6 models
> show #!7 models
> fitmap #5 inMap #7
Fit map run_it030_class009.mrc gaussian in map run_it030_class008.mrc gaussian
using 206038 points
correlation = 0.9779, correlation about mean = 0.9311, overlap = 860.7
steps = 44, shift = 0.547, angle = 1.11 degrees
Position of run_it030_class009.mrc gaussian (#5) relative to
run_it030_class008.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.99977338 -0.01998631 -0.00733106 6.70309138
0.01993842 0.99977976 -0.00654918 -3.70691835
0.00746034 0.00640153 0.99995168 -3.65351947
Axis 0.29100959 -0.33237097 0.89713040
Axis point 191.19714002 334.59859595 0.00000000
Rotation angle (degrees) 1.27501380
Shift along axis -0.09494744
> fitmap #5 inMap #7
Fit map run_it030_class009.mrc gaussian in map run_it030_class008.mrc gaussian
using 206038 points
correlation = 0.9779, correlation about mean = 0.9312, overlap = 860.7
steps = 40, shift = 0.0462, angle = 0.011 degrees
Position of run_it030_class009.mrc gaussian (#5) relative to
run_it030_class008.mrc gaussian (#7) coordinates:
Matrix rotation and translation
0.99977335 -0.01996585 -0.00739062 6.69350672
0.01991894 0.99978132 -0.00636747 -3.71201740
0.00751614 0.00621881 0.99995242 -3.64417758
Axis 0.28347039 -0.33573251 0.89829184
Axis point 192.22203916 334.90960501 0.00000000
Rotation angle (degrees) 1.27209110
Shift along axis -0.12987909
> volume #7 level 0.0246
> volume #7 color #b2b2b2
> volume #7 level 0.008547
> volume #7 level 0.04648
> save "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J274/J274.cxs"
> close #5
> close
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J276/J276.cxs"
Opened sphereonire1.mrc as #3, grid size 132,132,132, pixel 3.8, shown at
level 5e-05, step 1, values float32
Opened sec61mask3.mrc as #4, grid size 132,132,132, pixel 3.8, shown at level
5e-05, step 1, values float32
Opened run_class001.mrc as #1, grid size 132,132,132, pixel 3.8, shown at
level 0.0592, step 1, values float32
Opened run_it100_class001.mrc as #2.1, grid size 132,132,132, pixel 3.8, shown
at level 1.27e-06, step 1, values float32
Opened run_it100_class002.mrc as #2.2, grid size 132,132,132, pixel 3.8, shown
at level 1.94e-06, step 1, values float32
Opened run_it100_class003.mrc as #2.3, grid size 132,132,132, pixel 3.8, shown
at level 1.57e-06, step 1, values float32
Opened run_class001.mrc gaussian as #5, grid size 132,132,132, pixel 3.8,
shown at level 0.0344, step 1, values float32
> view name session-start
opened ChimeraX session
> close #2
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J279/run_it100_class001.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J279/run_it100_class002.mrc"
> "/Users/fsf3282/Library/CloudStorage/OneDrive-NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J279/run_it100_class003.mrc"
Opened run_it100_class001.mrc as #2.1, grid size 132,132,132, pixel 3.8, shown
at level 9.52e-07, step 1, values float32
Opened run_it100_class002.mrc as #2.2, grid size 132,132,132, pixel 3.8, shown
at level 2.79e-07, step 1, values float32
Opened run_it100_class003.mrc as #2.3, grid size 132,132,132, pixel 3.8, shown
at level 2.23e-06, step 1, values float32
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> show #!2.2 models
> hide #!2.2 models
> hide #!2.3 models
> show #!2.3 models
> hide #!2.3 models
> show #!2.1 models
> save "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J279/J279.cxs"
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J274/J274.cxs" format
> session
Opened run_it030_class001.mrc as #1.1, grid size 132,132,132, pixel 3.8, shown
at level 0.0702, step 1, values float32
Opened run_it030_class002.mrc as #1.2, grid size 132,132,132, pixel 3.8, shown
at level 0.089, step 1, values float32
Opened run_it030_class003.mrc as #1.3, grid size 132,132,132, pixel 3.8, shown
at level 0.109, step 1, values float32
Opened run_it030_class004.mrc as #1.4, grid size 132,132,132, pixel 3.8, shown
at level 0.114, step 1, values float32
Opened run_it030_class005.mrc as #1.5, grid size 132,132,132, pixel 3.8, shown
at level 0.0829, step 1, values float32
Opened run_it030_class006.mrc as #1.6, grid size 132,132,132, pixel 3.8, shown
at level 0.0648, step 1, values float32
Opened run_it030_class007.mrc as #1.7, grid size 132,132,132, pixel 3.8, shown
at level 0.086, step 1, values float32
Opened run_it030_class008.mrc as #1.8, grid size 132,132,132, pixel 3.8, shown
at level 0.0196, step 1, values float32
Opened run_it030_class009.mrc as #1.9, grid size 132,132,132, pixel 3.8, shown
at level 0.0664, step 1, values float32
Opened run_it030_class010.mrc as #1.10, grid size 132,132,132, pixel 3.8,
shown at level 0.0957, step 1, values float32
Opened run_it030_class011.mrc as #1.11, grid size 132,132,132, pixel 3.8,
shown at level 0.109, step 1, values float32
Opened run_it030_class012.mrc as #1.12, grid size 132,132,132, pixel 3.8,
shown at level 0.0839, step 1, values float32
Opened run_it030_class013.mrc as #1.13, grid size 132,132,132, pixel 3.8,
shown at level 0.0979, step 1, values float32
Opened run_it030_class014.mrc as #1.14, grid size 132,132,132, pixel 3.8,
shown at level 0.067, step 1, values float32
Opened run_it030_class015.mrc as #1.15, grid size 132,132,132, pixel 3.8,
shown at level 0.0794, step 1, values float32
Opened run_class001.mrc as #2, grid size 132,132,132, pixel 3.8, shown at
level 0.00431, step 1, values float32
Opened emdb 2938 as #3, grid size 300,300,300, pixel 1.1, shown at level 0.01,
step 2, values float32
Opened run_it030_class009.mrc gaussian as #5, grid size 132,132,132, pixel
3.8, shown at level 0.00369, step 1, values float32
Opened emdb 2938 gaussian as #6, grid size 300,300,300, pixel 1.1, shown at
level 0.00202, step 1, values float32
Opened run_it030_class008.mrc gaussian as #7, grid size 132,132,132, pixel
3.8, shown at level 0.0465, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!6 models
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J281/run_class001.mrc"
Opened run_class001.mrc as #8, grid size 600,600,600, pixel 0.835, shown at
level 0.00148, step 4, values float32
> hide #!7 models
> hide #!6 models
> close #8
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J281/run_class001.mrc"
Opened run_class001.mrc as #8, grid size 132,132,132, pixel 3.8, shown at
level 0.0537, step 1, values float32
> volume #8 level 0.002968
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J150/J147reconstruct.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened run_class001.mrc gaussian as #5, grid size 132,132,132, pixel 3.8,
shown at level 0.06, step 1, values float32
Opened job150_reconstruct.mrc as #6, grid size 600,600,600, pixel 0.835, shown
at level 0.00921, step 4, values float32
Opened job147test_reconstruct.mrc as #7, grid size 132,132,132, pixel 3.8,
shown at level 0.0513, step 1, values float32
> view name session-start
opened ChimeraX session
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion
> Chimera/immuno2_jobs/J130/job130_reconstruct.mrc"
Opened job130_reconstruct.mrc as #1, grid size 600,600,600, pixel 0.835, shown
at level 0.0151, step 4, values float32
> hide #!7 models
> volume #1 level 0.01509
> close
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J274/J274.cxs" format
> session
Opened run_it030_class001.mrc as #1.1, grid size 132,132,132, pixel 3.8, shown
at level 0.0702, step 1, values float32
Opened run_it030_class002.mrc as #1.2, grid size 132,132,132, pixel 3.8, shown
at level 0.089, step 1, values float32
Opened run_it030_class003.mrc as #1.3, grid size 132,132,132, pixel 3.8, shown
at level 0.109, step 1, values float32
Opened run_it030_class004.mrc as #1.4, grid size 132,132,132, pixel 3.8, shown
at level 0.114, step 1, values float32
Opened run_it030_class005.mrc as #1.5, grid size 132,132,132, pixel 3.8, shown
at level 0.0829, step 1, values float32
Opened run_it030_class006.mrc as #1.6, grid size 132,132,132, pixel 3.8, shown
at level 0.0648, step 1, values float32
Opened run_it030_class007.mrc as #1.7, grid size 132,132,132, pixel 3.8, shown
at level 0.086, step 1, values float32
Opened run_it030_class008.mrc as #1.8, grid size 132,132,132, pixel 3.8, shown
at level 0.0196, step 1, values float32
Opened run_it030_class009.mrc as #1.9, grid size 132,132,132, pixel 3.8, shown
at level 0.0664, step 1, values float32
Opened run_it030_class010.mrc as #1.10, grid size 132,132,132, pixel 3.8,
shown at level 0.0957, step 1, values float32
Opened run_it030_class011.mrc as #1.11, grid size 132,132,132, pixel 3.8,
shown at level 0.109, step 1, values float32
Opened run_it030_class012.mrc as #1.12, grid size 132,132,132, pixel 3.8,
shown at level 0.0839, step 1, values float32
Opened run_it030_class013.mrc as #1.13, grid size 132,132,132, pixel 3.8,
shown at level 0.0979, step 1, values float32
Opened run_it030_class014.mrc as #1.14, grid size 132,132,132, pixel 3.8,
shown at level 0.067, step 1, values float32
Opened run_it030_class015.mrc as #1.15, grid size 132,132,132, pixel 3.8,
shown at level 0.0794, step 1, values float32
Opened run_class001.mrc as #2, grid size 132,132,132, pixel 3.8, shown at
level 0.00431, step 1, values float32
Opened emdb 2938 as #3, grid size 300,300,300, pixel 1.1, shown at level 0.01,
step 2, values float32
Opened run_it030_class009.mrc gaussian as #5, grid size 132,132,132, pixel
3.8, shown at level 0.00369, step 1, values float32
Opened emdb 2938 gaussian as #6, grid size 300,300,300, pixel 1.1, shown at
level 0.00202, step 1, values float32
Opened run_it030_class008.mrc gaussian as #7, grid size 132,132,132, pixel
3.8, shown at level 0.0465, step 1, values float32
> view name session-start
opened ChimeraX session
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J282/run_class001.mrc"
Opened run_class001.mrc as #8, grid size 132,132,132, pixel 3.8, shown at
level 0.157, step 1, values float32
> hide #!1 models
> hide #!7 models
> hide #!5 models
> volume #8 level 0.02648
> color #8 #e5bf9961 models
> show #!6 models
> close #1
> hide #!6 models
> volume #8 color #e5bf99
> volume #8 level 0.02849
> save "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J282/J282.cxs"
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J284/run_class001.mrc"
Opened run_class001.mrc as #1, grid size 132,132,132, pixel 3.8, shown at
level 0.154, step 1, values float32
> hide #!8 models
> close #8
> show #!2 models
> hide #!2 models
> volume #1 level 0.01739
> volume #1 level 0.01642
> save "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J284/J284.cxs"
> close
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/J267/run_class001.mrc"
Opened run_class001.mrc as #1, grid size 600,600,600, pixel 0.835, shown at
level 0.00148, step 4, values float32
> volume #1 step 1
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/j260/postprocess.mrc"
Opened postprocess.mrc as #2, grid size 600,600,600, pixel 0.835, shown at
level 0.014, step 4, values float32
> close #1
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/j265/postprocess.mrc"
Opened postprocess.mrc as #1, grid size 600,600,600, pixel 0.835, shown at
level 0.00447, step 4, values float32
> open "/Users/fsf3282/Library/CloudStorage/OneDrive-
> NorthwesternUniversity/Relion Chimera/immuno2_jobs/j250/postprocess.mrc"
Opened postprocess.mrc as #3, grid size 600,600,600, pixel 0.835, shown at
level 0.0102, step 4, values float32
> volmax #1,2,3
Unknown command: volmax #1,2,3
> volume maximum #1,2,3
Opened volume maximum as #4, grid size 600,600,600, pixel 0.835, shown at step
1, values float32
> hide #!4 models
> show #!4 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: Mac16,2
Model Number: Z1E40008WLL/A
Chip: Apple M4
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 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: 21 days, 4 hours, 49 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
iMac:
Resolution: 4480 x 2520
UI Looks like: 2240 x 1260 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
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: 1.2.2
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
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