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Opened 6 hours ago
#19948 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-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fa59b100 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 56 in display
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 144 in show_save_file_dialog
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 133 in
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.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-1.11.1.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, PIL._imaging, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, 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, 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, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath (total: 114)
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x7c6b0603149a1570","rawCodes":[1,8965266093511415152],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x7c6b0603149a1570"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":10473},
"vmregioninfo" : "0x603149a1570 is not in any region.
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
UNUSED SPACE AT END",
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/Fig9_10_new.cxs
Opened cryosparc_P14_J135__localfilter.mrc as #8, grid size 256,256,256, pixel
0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 0 as #2.1, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 1 as #2.2, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 2 as #2.3, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 3 as #2.4, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 4 as #2.5, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 5 as #2.6, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 6 as #2.7, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 7 as #2.8, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 8 as #2.9, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 9 as #2.10, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 10 as #2.11, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 11 as #2.12, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 12 as #2.13, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 13 as #2.14, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
> view name session-start
opened ChimeraX session
> hide #5 models
> select add #2
29 models selected
> close
QAccessibleTree::indexFromLogical: invalid index: 0 0 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 0
QAccessibleTree::indexFromLogical: invalid index: 0 1 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 1
QAccessibleTree::indexFromLogical: invalid index: 0 2 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 2
QAccessibleTree::indexFromLogical: invalid index: 0 3 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 3
QAccessibleTree::indexFromLogical: invalid index: 0 4 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 4
QAccessibleTree::indexFromLogical: invalid index: 0 5 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 5
QAccessibleTree::indexFromLogical: invalid index: 0 0 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 0
QAccessibleTree::indexFromLogical: invalid index: 0 1 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 1
QAccessibleTree::indexFromLogical: invalid index: 0 2 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 2
QAccessibleTree::indexFromLogical: invalid index: 0 3 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 3
QAccessibleTree::indexFromLogical: invalid index: 0 4 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 4
QAccessibleTree::indexFromLogical: invalid index: 0 5 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 5
QAccessibleTree::indexFromLogical: invalid index: 0 0 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 0
QAccessibleTree::indexFromLogical: invalid index: 0 1 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 1
QAccessibleTree::indexFromLogical: invalid index: 0 2 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 2
QAccessibleTree::indexFromLogical: invalid index: 0 3 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 3
QAccessibleTree::indexFromLogical: invalid index: 0 4 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 4
QAccessibleTree::indexFromLogical: invalid index: 0 5 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 5
QAccessibleTree::indexFromLogical: invalid index: 0 0 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 0
QAccessibleTree::indexFromLogical: invalid index: 0 1 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 1
QAccessibleTree::indexFromLogical: invalid index: 0 2 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 2
QAccessibleTree::indexFromLogical: invalid index: 0 3 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 3
QAccessibleTree::indexFromLogical: invalid index: 0 4 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 4
QAccessibleTree::indexFromLogical: invalid index: 0 5 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 5
QAccessibleTree::indexFromLogical: invalid index: 0 0 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 0
QAccessibleTree::indexFromLogical: invalid index: 0 1 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 1
QAccessibleTree::indexFromLogical: invalid index: 0 2 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 2
QAccessibleTree::indexFromLogical: invalid index: 0 3 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 3
QAccessibleTree::indexFromLogical: invalid index: 0 4 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 4
QAccessibleTree::indexFromLogical: invalid index: 0 5 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 5
QAccessibleTree::indexFromLogical: invalid index: 0 0 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 0
QAccessibleTree::indexFromLogical: invalid index: 0 1 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 1
QAccessibleTree::indexFromLogical: invalid index: 0 2 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 2
QAccessibleTree::indexFromLogical: invalid index: 0 3 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 3
QAccessibleTree::indexFromLogical: invalid index: 0 4 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 4
QAccessibleTree::indexFromLogical: invalid index: 0 5 for
SizedTreeWidget(0x7d51afde0)
Requested invalid tree cell: 0 5
> open
> /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/Fig9_10_new.cxs
Opened cryosparc_P14_J135__localfilter.mrc as #8, grid size 256,256,256, pixel
0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 0 as #2.1, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 1 as #2.2, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 2 as #2.3, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 3 as #2.4, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 4 as #2.5, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 5 as #2.6, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 6 as #2.7, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 7 as #2.8, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 8 as #2.9, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 9 as #2.10, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 10 as #2.11, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 11 as #2.12, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 12 as #2.13, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
Opened cryosparc_P14_J135__localfilter.mrc 13 as #2.14, grid size 256,256,256,
pixel 0.84, shown at level 0.0368, step 1, values float32
> view name session-start
opened ChimeraX session
Called attribute on invalid object: 2147511799
> close #2
> select #5/D
785 atoms, 799 bonds, 97 residues, 1 model selected
Called attribute on invalid object: 2147521053
Called attribute on invalid object: 2147524278
> save /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/D.pdb
> selectedOnly true relModel #5
> open /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/D.pdb
> /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/DH.pdb
Summary of feedback from opening
/Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/D.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU B 95 CYS B 105 1 11
Start residue of secondary structure not found: HELIX 2 2 TRP B 112 GLN B 118
1 7
Start residue of secondary structure not found: HELIX 3 3 ASP B 123 ARG B 132
1 10
Start residue of secondary structure not found: HELIX 4 4 LEU B 137 THR B 151
1 15
Start residue of secondary structure not found: HELIX 5 5 VAL B 158 SER B 167
1 10
73 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
3 messages similar to the above omitted
Summary of feedback from opening
/Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/DH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU B 95 CYS B 105 1 11
Start residue of secondary structure not found: HELIX 2 2 TRP B 112 GLN B 118
1 7
Start residue of secondary structure not found: HELIX 3 3 ASP B 123 ARG B 132
1 10
Start residue of secondary structure not found: HELIX 4 4 LEU B 137 THR B 151
1 15
Start residue of secondary structure not found: HELIX 5 5 VAL B 158 SER B 167
1 10
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
Cannot find LINK/SSBOND residue CYS (601 )
2 messages similar to the above omitted
Chain information for D.pdb #2
---
Chain | Description
D | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for DH.pdb #3
---
Chain | Description
D | No description available
H | No description available
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> select add #2
1570 atoms, 1598 bonds, 194 residues, 2 models selected
> select add #3
3131 atoms, 3187 bonds, 387 residues, 3 models selected
> select add #5
12290 atoms, 12479 bonds, 1520 residues, 3 models selected
> select subtract #5
2346 atoms, 2388 bonds, 290 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> cartoon style sel modeHelix tube sides 20
> select #3/D
785 atoms, 799 bonds, 97 residues, 1 model selected
> cartoon hide sel
> select #3/H
776 atoms, 790 bonds, 96 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pink
> color sel light pink
> select #2/D
785 atoms, 799 bonds, 97 residues, 1 model selected
> color sel yellow
Called attribute on invalid object: 2147588560
> save
> /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/Fig9_10_new.cxs
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #3 models
> hide #2 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #2 models
> hide #2 models
> show #5 models
> open
> /Users/TLA1/Documents/Man_RIPK1/38_data_2025/38_deposited_9XSH_A667_roted.pdb
Chain information for 38_deposited_9XSH_A667_roted.pdb #7
---
Chain | Description
A B C G H I J | No description available
D | No description available
E | No description available
F | No description available
K | No description available
L | No description available
M | No description available
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Called attribute on invalid object: 2147680120
> select subtract #2
Nothing selected
> select add #7
9944 atoms, 10091 bonds, 1230 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> cartoon style sel modeHelix tube sides 20
> select #7/D
785 atoms, 799 bonds, 97 residues, 1 model selected
> color sel yellow
> select #7/H
776 atoms, 790 bonds, 96 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light pink
> color sel pink
> select #7
9944 atoms, 10091 bonds, 1230 residues, 1 model selected
> cartoon hide sel
> select #7/D,H
1561 atoms, 1589 bonds, 193 residues, 1 model selected
> cartoon sel
> hide #5 models
Called attribute on invalid object: 2147748719
Called attribute on invalid object: 2147752723
Called attribute on invalid object: 2147756618
> save
> /Users/TLA1/Documents/Man_RIPK1/NC_figures/NewFigureFrom_P14_J135/Fig9_10_new.cxs
Called attribute on invalid object: 2147760520
> select #7/D,H 574
Expected a keyword
> select #7/D 574-583
Expected a keyword
> select #7/D 574,583
Expected a keyword
> select #7/D574,583
Nothing selected
> select #7/D574
Nothing selected
> select #7/D
785 atoms, 799 bonds, 97 residues, 1 model selected
> select #7/D 574
Expected a keyword
> select #7/D:574-583
75 atoms, 75 bonds, 10 residues, 1 model selected
> cartoon hide sel
> select #7/H:574-583
75 atoms, 75 bonds, 10 residues, 1 model selected
> cartoon hide sel
> select #7/H:665-669
41 atoms, 41 bonds, 5 residues, 1 model selected
> cartoon hide sel
> select #7/D:665-669
41 atoms, 41 bonds, 5 residues, 1 model selected
> cartoon hide sel
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,6
Model Number: Z1FF001R3TA/A
Chip: Apple M4 Max
Total Number of Cores: 16 (12 Performance and 4 Efficiency)
Memory: 64 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (25D2128)
Kernel Version: Darwin 25.3.0
Time since boot: 11 hours, 42 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
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: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
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: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
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: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
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: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
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: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
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: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
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: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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