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Opened 3 hours ago
#19379 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-13.6.5-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x00000001f173e100 (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, chimerax.surface._surface, chimerax.map._map, 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, 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, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, kiwisolver._cext, 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, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.special.cython_special, scipy.stats._stats, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._ansari_swilk_statistics, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.stats._unuran.unuran_wrapper, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 189)
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"procRole" : "Foreground",
"version" : 2,
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"captureTime" : "2025-11-17 11:00:24.2178 +0100",
"incident" : "1C61A837-DEB2-4DD6-A687-5A40A5FFD319",
"pid" : 681,
"translated" : false,
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"procLaunch" : "2025-11-14 10:47:26.4937 +0100",
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"procExitAbsTime" : 955408848009,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
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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.
How to cite UCSF ChimeraX
> open "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251110_Analysis_XL-
> MS_SMG5-SMG6-RNA_high-BS3-conc.cxs"
> set bgColor #ffffff00
> view name session-start
opened ChimeraX session
> close #9-27
> close #2
> close #32
> close #31
> hide #3 models
> show #6 models
> show #7 models
> show #8 models
> mmaker #6-8 to #1.8/B
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 Session_Export.cif, chain B (#1.8) with ranked_0.pdb, chain B (#6),
sequence alignment score = 1090.5
RMSD between 197 pruned atom pairs is 0.813 angstroms; (across all 217 pairs:
1.696)
Matchmaker Session_Export.cif, chain B (#1.8) with ranked_1.pdb, chain B (#7),
sequence alignment score = 1098.3
RMSD between 181 pruned atom pairs is 0.745 angstroms; (across all 217 pairs:
2.210)
Matchmaker Session_Export.cif, chain B (#1.8) with ranked_2.pdb, chain B (#8),
sequence alignment score = 1091.1
RMSD between 200 pruned atom pairs is 0.694 angstroms; (across all 217 pairs:
1.628)
> mmaker #6-8 to #1.8/A:700-900
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 Session_Export.cif, chain A (#1.8) with ranked_0.pdb, chain A (#6),
sequence alignment score = 994.1
RMSD between 185 pruned atom pairs is 0.722 angstroms; (across all 201 pairs:
1.196)
Matchmaker Session_Export.cif, chain A (#1.8) with ranked_1.pdb, chain A (#7),
sequence alignment score = 1026.5
RMSD between 190 pruned atom pairs is 0.648 angstroms; (across all 201 pairs:
0.973)
Matchmaker Session_Export.cif, chain A (#1.8) with ranked_2.pdb, chain A (#8),
sequence alignment score = 1003.1
RMSD between 190 pruned atom pairs is 0.658 angstroms; (across all 201 pairs:
0.993)
> mmaker #28-30 to #1.8/A:700-900
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 Session_Export.cif, chain A (#1.8) with ranked_22.pdb, chain A
(#28), sequence alignment score = 997.7
RMSD between 185 pruned atom pairs is 0.803 angstroms; (across all 201 pairs:
1.176)
Matchmaker Session_Export.cif, chain A (#1.8) with ranked_23.pdb, chain A
(#29), sequence alignment score = 997.7
RMSD between 182 pruned atom pairs is 0.765 angstroms; (across all 201 pairs:
1.202)
Matchmaker Session_Export.cif, chain A (#1.8) with ranked_24.pdb, chain A
(#30), sequence alignment score = 1015.7
RMSD between 187 pruned atom pairs is 0.821 angstroms; (across all 201 pairs:
1.132)
> show #28 models
> show #29 models
> show #30 models
> show #4 models
> show #5 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #29 models
> hide #30 models
> hide #7 models
> hide #8 models
> hide #6 models
> hide #28 models
> show #28 models
> hide #28 models
> ui tool show XMAS
> show #4 models
> hide #5 models
> hide #4 models
> show #5 models
> hide #5 models
> select subtract #5
Nothing selected
> show #4 models
> close #7-8
> close #29-30
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL-
> MS_SMG5-SMG6-RNA_high-BS3-conc.cxs"
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Intralinks_cut-
off_AF3-pred_sample-04.pb
> hide #4 models
> select subtract #4
Nothing selected
> select add #2
56 pseudobonds, 1 model selected
> show #5 models
> hide #2 models
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL-
> MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"
> select add #5
12 pseudobonds, 1 model selected
> select add #4
175 pseudobonds, 2 models selected
> close #2-5
> close #1.1-7
> close #1.10-11#1.9
> rename #1.8 id #1
> hide #!1 models
> show #!1 models
> rename #6 id #2
> rename #28 id #3
Peptide pair mapping of XlinkX evidence file:
/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample02_Crosslinks.txt
Unique peptide pairs: 194 out of 194
Unique peptide pairs with pseudobonds: 188
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample02_Crosslinks_1.8.pb
Mapping information is stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample02_Crosslinks_1.8.tsv
Peptide pair mapping of XlinkX evidence file:
/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample04_Crosslinks.txt
Unique peptide pairs: 183 out of 183
Unique peptide pairs with pseudobonds: 177
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample04_Crosslinks_1.8.pb
Mapping information is stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/20251024_ECL1_ENO9_68min_NiKr_SA_F-45-55_Orbi5918_Sample04_Crosslinks_1.8.tsv
> rename #4 20251024_Orbi5918_02_Crosslinks_1.8.pb
> rename #5 20251024_Orbi5918_04_Crosslinks_1.8.pb
> hide #5 models
Please select pseudobonds
Please select pseudobonds
> select add #4
187 pseudobonds, 1 model selected
> show #5 models
> select add #5
362 pseudobonds, 2 models selected
> hide #4 models
> select subtract #4
175 pseudobonds, 1 model selected
> select add #4
362 pseudobonds, 2 models selected
> show #4 models
> hide #5 models
> hide #4 models
> select subtract #5
187 pseudobonds, 1 model selected
> select subtract #4
Nothing selected
> hide #1.8 models
> show #1.8 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #6 models
> show #7 models
> show #6 models
> select add #6
187 pseudobonds, 1 model selected
> select add #7
362 pseudobonds, 2 models selected
> close #6-7
Traceback (most recent call last):
File "/Users/kurscheidt/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py", line
1015, in
self.get_names(names_menu, pbs_dict, f))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kurscheidt/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py", line
1246, in get_names
function(pbs_dict, names)
File "/Users/kurscheidt/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py", line
1115, in create_distance_plot
plt.yticks(plt.yticks()[0], names)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/pyplot.py", line 2324, in yticks
labels_out = ax.set_yticklabels(labels, minor=minor, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/axes/_base.py", line 74, in wrapper
return get_method(self)(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/axis.py", line 2106, in set_ticklabels
raise ValueError(
ValueError: The number of FixedLocator locations (6), usually from a call to
set_ticks, does not match the number of labels (2).
ValueError: The number of FixedLocator locations (6), usually from a call to
set_ticks, does not match the number of labels (2).
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/axis.py", line 2106, in set_ticklabels
raise ValueError(
See log for complete Python traceback.
> select add #4
187 pseudobonds, 1 model selected
> select add #5
362 pseudobonds, 2 models selected
Traceback (most recent call last):
File "/Users/kurscheidt/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py", line
1015, in
self.get_names(names_menu, pbs_dict, f))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kurscheidt/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py", line
1246, in get_names
function(pbs_dict, names)
File "/Users/kurscheidt/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/XMAS/tool.py", line
1115, in create_distance_plot
plt.yticks(plt.yticks()[0], names)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/pyplot.py", line 2324, in yticks
labels_out = ax.set_yticklabels(labels, minor=minor, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/axes/_base.py", line 74, in wrapper
return get_method(self)(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/axis.py", line 2106, in set_ticklabels
raise ValueError(
ValueError: The number of FixedLocator locations (6), usually from a call to
set_ticks, does not match the number of labels (2).
ValueError: The number of FixedLocator locations (6), usually from a call to
set_ticks, does not match the number of labels (2).
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/matplotlib/axis.py", line 2106, in set_ticklabels
raise ValueError(
See log for complete Python traceback.
> show #4 models
> show #5 models
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb"
> #4,5
Saved 362 pseudobonds to file /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb"
> #4,5
Saved 362 pseudobonds to file /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb
> open "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Visualization_02-vs-04_CO-31A.pb"
Opened Pseudobonds 20251117_Visualization_02-vs-04_CO-31A.pb, 362 bonds
> hide #5 models
> hide #4 models
> select subtract #5
187 pseudobonds, 1 model selected
> select subtract #4
Nothing selected
> select add #5
175 pseudobonds, 1 model selected
> select add #4
362 pseudobonds, 2 models selected
> select subtract #4
175 pseudobonds, 1 model selected
> select subtract #5
Nothing selected
> close #6
> show #4 models
> show #5 models
> select add #5
175 pseudobonds, 1 model selected
> select add #4
362 pseudobonds, 2 models selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02-vs-04_AF3-model_CO-31A.pb
> hide #5 models
> hide #4 models
> select add #6
433 pseudobonds, 3 models selected
> select subtract #5
258 pseudobonds, 2 models selected
> select subtract #4
71 pseudobonds, 1 model selected
Venn diagrams can only be plotted for two or three groups
> select add #5
246 pseudobonds, 2 models selected
> select add #4
433 pseudobonds, 3 models selected
> select subtract #6
362 pseudobonds, 2 models selected
> hide #6 models
> show #5 models
> show #4 models
> hide #5 models
> select subtract #5
187 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_AF3-model_CO-31A.pb
> select add #5
362 pseudobonds, 2 models selected
> show #5 models
> hide #4 models
> select subtract #4
175 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_04_AF3-model_CO-31A.pb
> hide #5 models
> select subtract #5
Nothing selected
> select add #7
66 pseudobonds, 1 model selected
> select add #8
124 pseudobonds, 2 models selected
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL-
> MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"
> show #6 models
> hide #7 models
> hide #8 models
> select subtract #8
66 pseudobonds, 1 model selected
> select subtract #7
Nothing selected
> hide #6 models
> show #6 models
> select subtract #6
66 pseudobonds, 1 model selected
> select subtract #7
Nothing selected
> hide #6 models
> show #7 models
> select add #7
66 pseudobonds, 1 model selected
> show #8 models
> select add #8
124 pseudobonds, 2 models selected
> select intersect #7 & #8
Nothing selected
> show #6 models
> hide #8 models
> hide #7 models
> hide #6 models
> show #8 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #8 models
> hide #6 models
> show #6 models
> select add #6
71 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02-vs-04_Intralinks_AF3-model_CO-31A.pb
> hide #6 models
> select subtract #6
Nothing selected
> select add #6
71 pseudobonds, 1 model selected
> show #6 models
> hide #9 models
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02-vs-04_Interlinks_AF3-model_CO-31A.pb
> color #10 #ffd479ff models
> hide #6 models
> show #9 models
> hide #10 models
> show #10 models
> select add #10
73 pseudobonds, 2 models selected
> select add #9
142 pseudobonds, 3 models selected
> select subtract #6
71 pseudobonds, 2 models selected
> hide #10 models
> select subtract #10
69 pseudobonds, 1 model selected
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL-
> MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"
> show #10 models
> hide #9 models
> select #1.8/B
1716 atoms, 1744 bonds, 44 pseudobonds, 217 residues, 7 models selected
> ui tool show "Renumber Residues"
> renumber #1.8/B start 800
217 residues renumbered
> select #1.8/A
6859 atoms, 6981 bonds, 556 pseudobonds, 855 residues, 7 models selected
> ui tool show "Renumber Residues"
> renumber #1.8/A start 565
855 residues renumbered
> select clear
> select add #7
66 pseudobonds, 1 model selected
> hide #10 models
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_Interlinks_AF3-model_CO-31A.pb
> select add #8
124 pseudobonds, 2 models selected
> select subtract #7
58 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_04_Interlinks_AF3-model_CO-31A.pb
> select subtract #8
Nothing selected
> hide #12 models
> show #12 models
> hide #11 models
> show #11 models
> hide #12 models
> show #12 models
> select add #11
1 pseudobond, 1 model selected
> select add #12
3 pseudobonds, 2 models selected
> hide #12 models
> hide #11 models
> show #9 models
> select subtract #11
2 pseudobonds, 1 model selected
> select subtract #12
Nothing selected
> select add #7
66 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_Intralinks_AF3-model_CO-31A.pb
> select add #8
124 pseudobonds, 2 models selected
> select subtract #7
58 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_04_Intralinks_AF3-model_CO-31A.pb
> hide #9 models
> select add #13
123 pseudobonds, 2 models selected
> select add #14
179 pseudobonds, 3 models selected
> ui mousemode right select
> select clear
> select add #13
65 pseudobonds, 1 model selected
> select subtract #13
Nothing selected
> hide #14 models
> show #14 models
> hide #14 models
> show #14 models
> hide #14 models
> show #14 models
> hide #14 models
> select add #13
65 pseudobonds, 1 model selected
> select add #14
121 pseudobonds, 2 models selected
> show #14 models
> hide #13 models
> select subtract #13
56 pseudobonds, 1 model selected
> select add #13
121 pseudobonds, 2 models selected
> show #13 models
> hide #14 models
> select subtract #14
65 pseudobonds, 1 model selected
> select clear
> select #1.8/B & #13
7 pseudobonds, 1 model selected
> hide #13 models
> select add #13
65 pseudobonds, 1 model selected
> select subtract #13
Nothing selected
> select add #13
65 pseudobonds, 1 model selected
> select add #14
121 pseudobonds, 2 models selected
> show #13 models
> show #14 models
> select add #14
57 pseudobonds, 2 models selected
> select subtract #14
1 pseudobond, 1 model selected
> select add #13
65 pseudobonds, 1 model selected
> select subtract #13
Nothing selected
> select add #14
56 pseudobonds, 1 model selected
> hide #14 models
> hide #13 models
> select subtract #14
Nothing selected
> show #13 models
> select add #13
65 pseudobonds, 1 model selected
Pseudobonds are stored in /Users/kurscheidt/Documents/MassSpec core
facility/Crosslinking-
MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Crosslinks_02_Intralinks_Interdomain-
links_AF3-model_CO-31A.pb
> hide #13 models
> select subtract #13
Nothing selected
> delete sel
> hide sel pseudobonds
> show sel pseudobonds
> delete sel pseudobond
Expected a keyword
> delete sel pseudobonds
Expected a keyword
> hide sel pseudobonds
Venn diagrams can only be plotted for two or three groups
> select pbond delete
Expected an objects specifier or a keyword
> save "/Users/kurscheidt/Documents/MassSpec core facility/Crosslinking-
> MS/20251022_SMG5-SMG6+RNA_BS3/Results/Analysis/20251117_Analysis_XL-
> MS_Comparison_SMG5-SMG6-RNA_high-BS3-conc.cxs"
> pbond delete sel
Must specify exactly 2 atoms to delete pseudobond between; you specified 0
> pbond delete
Missing or invalid "atoms" argument: empty atom specifier
> hide sel pseudobonds
===== 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 - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: MacBookPro17,1
Model Number: MYDA2D/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.101.3
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.5 (22G621)
Kernel Version: Darwin 22.6.0
Time since boot: 3 days, 18 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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
ASUS PA279:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 50.00Hz
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-XMAS: 1.1.3
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
et_xmlfile: 2.0.0
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
openpyxl: 3.1.5
openvr: 1.26.701
packaging: 24.2
pandas: 2.3.3
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
QtRangeSlider: 0.1.5
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
seaborn: 0.13.2
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
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