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Opened 96 minutes ago
#20312 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-15.7.5-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.
Opened and moved matchmaker gui window led to crash
Fatal Python error: Segmentation fault
Thread 0x000000039dc53000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x00000001f7e62240 (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/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, chimerax.map._map, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, PIL._imaging, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, 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.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, kiwisolver._cext, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.alignment_algs._sw (total: 124)
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"codeSigningMonitor" : 1,
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"procLaunch" : "2026-05-07 17:28:23.0709 -0400",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102ac8000-102acc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5774},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4339826680
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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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/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/DHX29_43S_2026may7fit2J1716_1.pdb
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/cryosparc_P43_J1717_005_volume_map_sharp_DHX_local.mrc
Chain information for DHX29_43S_2026may7fit2J1716_1.pdb #1
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j | No description available
k | No description available
l | No description available
n | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
x | No description available
y | No description available
z | No description available
Opened cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc as #2, grid size
512,512,512, pixel 0.825, shown at level 0.0792, step 2, values float32
Opened cryosparc_P43_J1717_005_volume_map_sharp_DHX_local.mrc as #3, grid size
512,512,512, pixel 0.825, shown at level 0.081, step 2, values float32
> style stick
Changed 140977 atom styles
> select /G:1-263
2083 atoms, 2125 bonds, 263 residues, 1 model selected
> delete /1:B
> select /B:52-473
3214 atoms, 3267 bonds, 422 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /C:2-226
1774 atoms, 1811 bonds, 225 residues, 1 model selected
> select /C:2-226
1774 atoms, 1811 bonds, 225 residues, 1 model selected
> select /C:2-226
1774 atoms, 1811 bonds, 225 residues, 1 model selected
> select /A:6-271
2147 atoms, 2178 bonds, 266 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /C:2-226
1774 atoms, 1811 bonds, 225 residues, 1 model selected
> select /C:2-226
1774 atoms, 1811 bonds, 225 residues, 1 model selected
> select /A:6-271
Nothing selected
> select /A:6-271
Nothing selected
> select /B:52-473
Nothing selected
> select /C:2-226
1774 atoms, 1811 bonds, 225 residues, 1 model selected
> select /D:11-526
3666 atoms, 3748 bonds, 1 pseudobond, 456 residues, 2 models selected
> select /E:38-263
1743 atoms, 1779 bonds, 226 residues, 1 model selected
> select /E:38-263
1743 atoms, 1779 bonds, 226 residues, 1 model selected
> select /E:38-263
1743 atoms, 1779 bonds, 226 residues, 1 model selected
> select /F:1-227
1765 atoms, 1793 bonds, 227 residues, 1 model selected
> select /G:1-263
2083 atoms, 2125 bonds, 263 residues, 1 model selected
> select /H:14-204
1509 atoms, 1531 bonds, 191 residues, 1 model selected
Drag select of 955 atoms, 1075 bonds
> delete atoms sel
> delete bonds sel
Drag select of 1 atoms
Drag select of 100 atoms, 7 pseudobonds, 92 bonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 168 atoms, 184 bonds
> delete atoms sel
> delete bonds sel
Drag select of 44 atoms, 3 pseudobonds, 38 bonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 13 atoms, 1 pseudobonds, 12 bonds
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /U:6-144
1154 atoms, 1172 bonds, 139 residues, 1 model selected
> select /1:42@N3
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
334 atoms, 366 bonds, 17 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save DHX29_40S_eIF3_U70_2026may7fit2J1716_1.pdb models #1
> volume #2 step 1
> volume #2 level 0.1579
> volume #2 level 0.09947
> volume #2 color #b2b2b2a2
> volume #3 step 1
> volume #3 level 0.1717
> volume #3 level 0.1349
> volume #3 color #b2b2b2b8
> volume #2 level 0.08149
> volume gaussian #2 bfactor 150
Opened cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc gaussian as #4, grid
size 512,512,512, pixel 0.825, shown at step 1, values float32
> volume #4 level 0.09173
> volume #4 level 0.06133
> volume #4 level 0.06459
> volume #2 level 0.07454
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 707 residues in model #1 to IUPAC-IUB
standards.
Chain information for DHX29_43S_2026may7fit2J1716_1.pdb #1.2
---
Chain | Description
0 | No description available
2 | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
n | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
x | No description available
y | No description available
z | No description available
> clipper associate #2 toModel #1
Opened cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc as #1.1.1.1, grid size
512,512,512, pixel 0.825, shown at step 1, values float32
> select clear
> volume #1.1.1.1 level 0.01532
> clipper associate #3 toModel #1
Opened cryosparc_P43_J1717_005_volume_map_sharp_DHX_local.mrc as #1.1.1.2,
grid size 512,512,512, pixel 0.825, shown at step 1, values float32
> volume #1.1.1.2 level 0.08577
> volume #1.1.1.2 level 0.02221
> cofr sel
> volume #1.1.1.2 level 0.1659
> clipper associate #4 toModel #1
Opened cryosparc_P43_J1716_map2.9Afilt_DHXribomask.mrc gaussian as #1.1.1.3,
grid size 512,512,512, pixel 0.825, shown at step 1, values float32
> addh
Summary of feedback from adding hydrogens to DHX29_43S_2026may7fit2J1716_1.pdb
#1.2
---
warnings | Not adding hydrogens to /h HIS 362 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /2 A 2 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /d MET 1 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /d ASP 2 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /d THR 3 CB because it is missing heavy-atom bond
partners
102 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /j PRO 261 N; /b PRO 103 N; /k PRO 288 N; /b PRO 108 N; /b PRO
99 N; /k PRO 294 N
notes | Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain 0 determined from SEQRES records
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain 2 determined from
SEQRES records
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain C determined from
SEQRES records
No usable SEQRES records for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain D;
guessing termini instead
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain E determined from
SEQRES records
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain F determined from
SEQRES records
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain G determined from
SEQRES records
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain H determined from
SEQRES records
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain I determined from
SEQRES records
37 messages similar to the above omitted
No usable SEQRES records for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain y;
guessing termini instead
Termini for DHX29_43S_2026may7fit2J1716_1.pdb (#1.2) chain z determined from
SEQRES records
Chain-initial residues that are actual N termini: /0 SER 16, /C SER 2, /D ALA
11, /E GLY 38, /F MET 1, /G MET 1, /H THR 14, /I MET 1, /J SER 5, /K GLY 2, /L
TRP 7, /M MET 1, /N MET 1, /O GLY 9, /P GLY 2, /Q ASN 16, /R VAL 4, /S PRO 6,
/T MET 1, /U PRO 6, /V VAL 4, /W ALA 16, /X MET 1, /Y VAL 2, /Z MET 1, /a ASP
3, /b MET 1, /c MET 1, /d MET 1, /e GLN 4, /f LYS 82, /g THR 2, /i LEU 80, /j
ASN 238, /k VAL 287, /l MET 1, /n ARG 41, /p GLY 73, /q PHE 86, /r GLY 29, /s
ALA 2, /t GLN 181, /u PHE 6, /x LYS 14, /y ALA 3, /z MET 1, /D ALA 11, /D VAL
162, /y ALA 3, /y GLN 676
Chain-initial residues that are not actual N termini: /D VAL 162, /h LEU 81,
/h PRO 361, /h SER 534, /h PRO 824, /y GLN 676
Chain-final residues that are actual C termini: /0 LEU 151, /C GLU 226, /E THR
263, /F LYS 227, /G GLY 263, /H ARG 204, /I LEU 237, /J LEU 194, /K GLY 207,
/L GLY 181, /M ARG 98, /N PHE 158, /O LYS 132, /P ALA 151, /Q TYR 462, /R GLY
134, /S ARG 146, /T MET 126, /U ARG 144, /V LYS 144, /W ALA 119, /X ASN 82, /Y
PHE 130, /Z ARG 142, /a GLY 128, /b PRO 108, /c HIS 84, /d LEU 68, /e ASP 56,
/f LYS 152, /g ILE 314, /h ASN 1369, /i SER 133, /j TRP 314, /k GLY 870, /l
LYS 25, /n GLY 115, /p VAL 685, /q LEU 357, /r ASN 352, /s SER 216, /t GLU
552, /u SER 370, /x GLY 233, /z HIS 342, /D ALA 101, /D THR 526, /y ARG 605,
/y GLN 728
Chain-final residues that are not actual C termini: /D THR 526, /D ALA 101, /h
GLU 178, /h GLN 505, /h CYS 784, /y GLN 728, /y ARG 605
Missing OXT added to C-terminal residue /C GLU 226
Missing OXT added to C-terminal residue /L GLY 181
Missing OXT added to C-terminal residue /R GLY 134
Missing OXT added to C-terminal residue /T MET 126
Missing OXT added to C-terminal residue /U ARG 144
16 messages similar to the above omitted
11541 hydrogen bonds
Adding 'H' to /D VAL 162
Adding 'H' to /y GLN 676
98947 hydrogens added
> isolde restrain ligands #1
> ui tool show "Ramachandran Plot"
> select #1:h
Nothing selected
> select ~sel & ##selected
Nothing selected
> cofr sel
> volume #1.1.1.3 level 0.08847
> isolde sim start /h:449
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.2 level 0.02175
> volume #1.1.1.3 level 0.08886
> volume #1.1.1.2 level 0.1214
> isolde sim start /h:494
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.09648
> isolde sim start /L:180/h:503
ISOLDE: started sim
> volume #1.1.1.2 level 0.1301
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start /h:505
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto first
> volume #1.1.1.2 level 0.1011
> isolde sim start /h:81
ISOLDE: started sim
> volume #1.1.1.2 level 0.06163
> volume #1.1.1.2 level 0.09295
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde stepto
> isolde sim start /h:82
ISOLDE: started sim
> isolde stepto
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto
> volume #1.1.1.2 level 0.156
> isolde stepto
> isolde sim start /h:92
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.2 level 0.2863
> volume #1.1.1.1 level 0.08576
> volume #1.1.1.1 level 0.106
> volume #1.1.1.1 level 0.1792
> isolde sim start /2:580
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /i:98
ISOLDE: started sim
> volume #1.1.1.1 level 0.2642
> volume #1.1.1.1 level 0.1772
> volume #1.1.1.1 level 0.1377
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip /i:98
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde pepflip /i:99
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.1781
> isolde sim start /2:580
ISOLDE: started sim
> volume #1.1.1.1 level 0.1184
> volume #1.1.1.1 level 0.1936
> volume #1.1.1.1 level 0.1126
> volume #1.1.1.2 level 0.1406
> volume #1.1.1.2 level 0.2339
> volume #1.1.1.2 level 0.4029
> volume #1.1.1.1 level 0.2379
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /2:577-583
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /h:118
ISOLDE: started sim
> volume #1.1.1.2 level 0.2747
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /2:547
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /h:123
ISOLDE: started sim
> volume #1.1.1.2 level 0.1873
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.2 level 0.2137
> volume #1.1.1.2 level 0.1291
> volume #1.1.1.1 level 0.1566
> volume #1.1.1.1 level 0.09639
> isolde sim start /2:547
ISOLDE: started sim
> volume #1.1.1.1 level 0.1242
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /h:123
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/DHX29_40S_eIF3_U70_2026may7fit2J1716_2.pdb
> relModel #1.1.1.1
> save
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/40S-eIF3-DHX29-ATPgammaS/maps_after_polish/islode_session2026May8.cxs
Taking snapshot of stepper: DHX29_43S_2026may7fit2J1716_1.pdb
> select clear
> open
> /Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected_ma-u3zgf.cif
Summary of feedback from opening
/Users/adesgeorges/Documents/Collaborations/Initiation/DHX29_newdata/DEAHelicase_reference_models/RabbitCorrected_ma-u3zgf.cif
---
warnings | Unknown polymer entity '1' on line 299
Unable to fetch template for '.': will connect using distance criteria
Unknown polymer entity '1' on line 299
Unknown polymer entity '2' on line 116841
Unknown polymer entity '3' on line 121877
Unknown polymer entity '4' on line 125711
Unknown polymer entity '5' on line 129672
77 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
notes | PDBx/mmCIF styling lost on line 300. Rereading mmCIF file from the beginning.
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
RabbitCorrected_ma-u3zgf.cif title:
rabbit-80S-corrected [more info...]
Chain information for RabbitCorrected_ma-u3zgf.cif #2
---
Chain | Description
A | 28S ribosomal RNA
A3 | 5.8S ribosomal RNA
A4 | 5S ribosomal RNA
AA | ribosomal protein uL2
AB | ribosomal protein uL3
AC | ribosomal protein uL4
AD | ribosomal protein uL18
AE | ribosomal protein eL6
AF | ribosomal protein uL30
AG | ribosomal protein eL8
AH | ribosomal protein uL6
AI | ribosomal protein uL16
AJ | ribosomal protein uL5
AK | ribosomal protein uL10
AL | ribosomal protein eL13
AM | ribosomal protein eL14
AN | ribosomal protein eL15
AO | ribosomal protein uL13
AP | ribosomal protein uL22
AQ | ribosomal protein eL18
AR | ribosomal protein eL19
AS | ribosomal protein eL20
AT | ribosomal protein eL21
AU | ribosomal protein eL22
AV | ribosomal protein uL14
AW | ribosomal protein eL24
AX | ribosomal protein uL23
AY | ribosomal protein uL24
AZ | ribosomal protein eL27
Aa | ribosomal protein uL15
Ab | ribosomal protein eL29
Ac | ribosomal protein eL30
Ad | ribosomal protein eL31
Ae | ribosomal protein eL32
Af | ribosomal protein eL33
Ag | ribosomal protein eL34
Ah | ribosomal protein uL29
Ai | ribosomal protein eL36
Aj | ribosomal protein eL37
Ak | ribosomal protein eL38
Al | ribosomal protein eL39
Am | ribosomal protein eL40
An | ribosomal protein eL41
Ao | ribosomal protein eL42
Ap | ribosomal protein eL43
Aq | ribosomal protein uL11
At | ribosomal protein eL28
Au | ribosomal protein uL1
B | 18S ribosomal RNA
BA | ribosomal protein uS2
BB | ribosomal protein eS1
BC | ribosomal protein uS5
BD | ribosomal protein uS3
BE | ribosomal protein eS4
BF | ribosomal protein uS7
BG | ribosomal protein eS6
BH | ribosomal protein eS7
BI | ribosomal protein eS8
BJ | ribosomal protein uS4
BK | ribosomal protein eS10
BL | ribosomal protein uS17
BM | ribosomal protein eS12
BN | ribosomal protein uS15
BO | ribosomal protein uS11
BP | ribosomal protein uS19
BQ | ribosomal protein uS9
BR | ribosomal protein eS17
BS | ribosomal protein uS13
BT | ribosomal protein eS19
BU | ribosomal protein uS10
BV | ribosomal protein eS21
BW | ribosomal protein uS8
BX | ribosomal protein uS12
BY | ribosomal protein eS24
BZ | ribosomal protein eS25
Ba | ribosomal protein eS26
Bb | ribosomal protein eS27
Bc | ribosomal protein eS28
Bd | ribosomal protein uS14
Be | ribosomal protein eS30
Bf | ribosomal protein eS31
Bg | ribosomal protein RACK 1
Non-standard residues in RabbitCorrected_ma-u3zgf.cif #2
---
MG — (MG)
ZN — (ZN)
> style stick
Changed 609438 atom styles
> show cartoons
> hide atoms
> ui tool show Matchmaker
> select #2/B
54866 atoms, 59177 bonds, 6 pseudobonds, 1708 residues, 2 models selected
> select #1.2/2
59813 atoms, 64497 bonds, 1863 residues, 1 model selected
> matchmaker #!2 & sel to #1.2 & sel
No molecules/chains to match specified
> ui tool show Matchmaker
===== 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 - 89.4
OpenGL renderer: Apple M2 Pro
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: Mac mini
Model Identifier: Mac14,12
Model Number: Z170000G0LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: mBoot-18000.101.7
OS Loader Version: 11881.140.96.701.1
Software:
System Software Overview:
System Version: macOS 15.7.5 (24G624)
Kernel Version: Darwin 24.6.0
Time since boot: 12 days, 19 hours, 2 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: H70HGX7Y9X
Display Firmware Version: Version 17.0 (Build 21A329)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
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-Clipper: 0.26.1
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-ISOLDE: 1.11.1
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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