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Opened 16 months ago
Closed 16 months ago
#15558 closed defect (can't reproduce)
Crash in check_for_changes during running simulation
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tristan Croll, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-553.6.1.el8.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007ff168134740 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2232 in changes
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3318 in command_trigger
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/contextlib.py", line 144 in __exit__
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3203 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/home/carsten/.local/share/ChimeraX/1.8/lib/python3.11/site-packages/chimerax/isolde/toolbar.py", line 21 in toolbar_command
File "/home/carsten/.local/share/ChimeraX/1.8/lib/python3.11/site-packages/chimerax/isolde/__init__.py", line 184 in run_provider
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1306 in run_provider
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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, chimerax.mmcif.mmcif_write, PIL._imagingmath, psutil._psutil_linux, psutil._psutil_posix, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, 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._minpack2, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 131)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/W74fitting.cxs
> format session
Opened cryosparc_P30_J109_009_volume_map_sharp.mrc z flip as #4, grid size
416,416,416, pixel 0.65, shown at level 0.0678, step 1, values float32
Opened cryosparc_P30_J106_009_volume_map_sharp.mrc z flip as #5, grid size
416,416,416, pixel 0.65, shown at level 0.0918, step 1, values float32
opened ChimeraX session
> save
> /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitted_J109.cif
Not saving entity_poly_seq for non-authoritative sequences
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ106.pdb
> relModel #5
> ui tool show "Volume Viewer"
> select subtract #3
Nothing selected
> select add #5
3 models selected
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/J106_zflip.mrc
> models #5
> close session
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ106.pdb
Chain information for Y308E_fitJ106.pdb #1
---
Chain | Description
A B C D E F G | No description available
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J106_zflip.mrc
Opened J106_zflip.mrc as #2, grid size 416,416,416, pixel 0.65, shown at level
0.0294, step 2, values float32
> style stick
Changed 17927 atom styles
> volume #2 step 1
> volume #2 level 0.06634
> select add #1
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-17.788,0,1,0,6.5989,0,0,1,-3.3147
> view matrix models #1,1,0,0,-14.856,0,1,0,5.72,0,0,1,-5.906
> view matrix models #1,1,0,0,-13.54,0,1,0,5.4367,0,0,1,-7.398
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98565,-0.16785,0.017995,6.8627,0.1659,0.98286,0.080344,-29.062,-0.031172,-0.076205,0.9966,7.2542
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98565,-0.16785,0.017995,3.2773,0.1659,0.98286,0.080344,-30.682,-0.031172,-0.076205,0.9966,7.0092
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule Y308E_fitJ106.pdb (#1) to map J106_zflip.mrc (#2) using 17927
atoms
average map value = 0.108, steps = 184
shifted from previous position = 7.84
rotated from previous position = 13.4 degrees
atoms outside contour = 5941, contour level = 0.066342
Position of Y308E_fitJ106.pdb (#1) relative to J106_zflip.mrc (#2)
coordinates:
Matrix rotation and translation
0.99652672 -0.03493508 -0.07559124 3.02734528
0.02862809 0.99614098 -0.08296741 18.61911654
0.07819801 0.08051520 0.99368122 -25.93403336
Axis 0.70081014 -0.65925708 0.27247982
Axis point 0.00000000 269.71541336 75.04241941
Rotation angle (degrees) 6.69812883
Shift along axis -17.21969097
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ106.pdb
> relModel #2
> volume #2 color #807777
> volume #2 color #80777785
> volume #2 color #8077779c
> select subtract #1
Nothing selected
> close session
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J106_zflip.mrc
Opened J106_zflip.mrc as #1, grid size 416,416,416, pixel 0.65, shown at level
0.0294, step 2, values float32
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ106.pdb
Chain information for Y308E_fitJ106.pdb #2
---
Chain | Description
A B C D E F G | No description available
> volume #1 step 1
> style stick
Changed 17927 atom styles
> show atoms
> volume #1 level 0.0914
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 56 residues in model #2 to IUPAC-IUB
standards.
Chain information for Y308E_fitJ106.pdb
---
Chain | Description
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E 2.2/F 2.2/G | No description available
> clipper associate #1 toModel #2
Opened J106_zflip.mrc as #2.1.1.1, grid size 416,416,416, pixel 0.65, shown at
step 1, values float32
> volume #2.1.1.1 level 0.008011
> volume #2.1.1.1 level 0.03585
> volume #2.1.1.1 level 0.05207
> select :74
98 atoms, 105 bonds, 7 residues, 1 model selected
> select add #2.2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 10 models selected
> select add #2.2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 10 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select add #2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 17 models selected
> select subtract #2.1
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 12 models selected
> select subtract #2.3
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 11 models selected
> select add #2.2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 11 models selected
> select add #2.2
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 11 models selected
> select :74
98 atoms, 105 bonds, 7 residues, 1 model selected
> clipper spotlight
> isolde sim start /A-G:74
Sim termination reason: None
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to Y308E_fitJ106.pdb #2.2
---
notes | No usable SEQRES records for Y308E_fitJ106.pdb (#2.2) chain A; guessing termini instead
No usable SEQRES records for Y308E_fitJ106.pdb (#2.2) chain B; guessing
termini instead
No usable SEQRES records for Y308E_fitJ106.pdb (#2.2) chain C; guessing
termini instead
No usable SEQRES records for Y308E_fitJ106.pdb (#2.2) chain D; guessing
termini instead
No usable SEQRES records for Y308E_fitJ106.pdb (#2.2) chain E; guessing
termini instead
2 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A ALA 2, /B ALA 2, /C ALA
2, /D ALA 2, /E ALA 2, /F ALA 2, /G ALA 2
Chain-initial residues that are not actual N termini: /A GLY 27, /A PRO 193,
/A THR 313, /B GLY 27, /B PRO 193, /B THR 313, /C GLY 27, /C PRO 193, /C THR
313, /D GLY 27, /D PRO 193, /D THR 313, /E GLY 27, /E PRO 193, /E THR 313, /F
GLY 27, /F PRO 193, /F THR 313, /G GLY 27, /G PRO 193, /G THR 313
Chain-final residues that are actual C termini: /A PRO 362, /B PRO 362, /C PRO
362, /D PRO 362, /E PRO 362, /F PRO 362, /G PRO 362
Chain-final residues that are not actual C termini: /A LEU 17, /A ASP 162, /A
LYS 302, /B LEU 17, /B ASP 162, /B LYS 302, /C LEU 17, /C ASP 162, /C LYS 302,
/D LEU 17, /D ASP 162, /D LYS 302, /E LEU 17, /E ASP 162, /E LYS 302, /F LEU
17, /F ASP 162, /F LYS 302, /G LEU 17, /G ASP 162, /G LYS 302
2373 hydrogen bonds
Adding 'H' to /A GLY 27
Adding 'H' to /A THR 313
Adding 'H' to /B GLY 27
Adding 'H' to /B THR 313
Adding 'H' to /C GLY 27
9 messages similar to the above omitted
18627 hydrogens added
Loading residue template for Y01 from internal database
> cview /A:74
> cview /B:74
> cview /C:74
> isolde sim start /A-G:71-77
ISOLDE: started sim
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A-G:68-80
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> ui mousemode right "isolde tug residue"
> ui mousemode right "isolde tug atom"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A-G:65-83,264
ISOLDE: started sim
> cview /D:74
> isolde sim pause
> isolde tutorial
> select /D:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /E:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> cview /E:74
> cview /F:74
> select /F:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> isolde sim start /F:74
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> cview /G:74
> save
> /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_modelW74AJ106.pdb
> close session
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ106.pdb
Chain information for Y308E_fitJ106.pdb #1
---
Chain | Description
A B C D E F G | No description available
> style stick
Changed 17927 atom styles
> open
> /home/carsten/Desktop/depositions_Panx1/cryosparc_P30_J109_009_volume_map_sharp.mrc
Opened cryosparc_P30_J109_009_volume_map_sharp.mrc as #2, grid size
416,416,416, pixel 0.65, shown at level 0.029, step 2, values float32
> volume #2 step 1
> volume #2 level 0.07067
> volume flip axis z #2
Missing or invalid "volumes" argument: invalid density maps specifier
> flip axis z #2
Unknown command: flip axis z #2
> vop flip axis z #2
> volume flip axis z #2
Missing or invalid "volumes" argument: invalid density maps specifier
> volume #2 flipNormals axis z
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume #2 flipNormals z
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume flip z
Missing or invalid "volumes" argument: invalid density maps specifier
> volume #2 flipNormals z
Invalid "flipNormals" argument: Expected true or false (or 1 or 0)
> volume #2 flipz
Expected a keyword
> volume flip #2 axis z
Opened cryosparc_P30_J109_009_volume_map_sharp.mrc z flip as #3, grid size
416,416,416, pixel 0.65, shown at step 1, values float32
> close #2
> select add #3
4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.73749,0.62799,0.24847,-80.497,0.58491,-0.77784,0.22988,134.92,0.33764,-0.024198,-0.94097,195.49
> view matrix models
> #3,0.77373,0.63337,0.01384,-57.377,0.61736,-0.75871,0.2079,130.61,0.14218,-0.15231,-0.97805,244
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.77373,0.63337,0.01384,-56.037,0.61736,-0.75871,0.2079,127.17,0.14218,-0.15231,-0.97805,268.91
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.66191,0.74942,0.015681,-56.928,0.74218,-0.65815,0.12652,106.51,0.10513,-0.072103,-0.99184,264.68
> view matrix models
> #3,0.68336,0.72992,0.015248,-57.124,0.72293,-0.67944,0.12539,112.16,0.10188,-0.074663,-0.99199,265.49
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit molecule Y308E_fitJ106.pdb (#1) to map
cryosparc_P30_J109_009_volume_map_sharp.mrc z flip (#3) using 17927 atoms
average map value = 0.1062, steps = 132
shifted from previous position = 1.94
rotated from previous position = 7.3 degrees
atoms outside contour = 6443, contour level = 0.070672
Position of Y308E_fitJ106.pdb (#1) relative to
cryosparc_P30_J109_009_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.69906037 0.71505340 0.00363332 -56.37470766
0.71504630 -0.69906973 0.00320673 132.69753142
0.00483292 0.00035629 -0.99998825 268.45910085
Axis -0.92169959 -0.38789765 -0.00229616
Axis point 0.00000000 78.32402036 134.24413736
Rotation angle (degrees) 179.91140398
Shift along axis -0.12894149
> volume #3 color #292828
> volume #3 color #29282867
> volume #3 color #6b686867
> volume #3 color #6b68684e
> ui tool show "Side View"
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ109.pdb
> relModel #3
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/J109_zflip.mrc
> models #3
> close session
> open
> /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitted_J109.cif
Summary of feedback from opening
/home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitted_J109.cif
---
warnings | Unknown polymer entity '1' on line 135
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for Y308E_fitted_J109.cif #1
---
Chain | Description
A B C D E F G | No description available
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J109_zflip.mrc
Opened J109_zflip.mrc as #2, grid size 416,416,416, pixel 0.65, shown at level
0.0291, step 2, values float32
> volume #2 step 1
> style stick
Changed 17927 atom styles
> volume #2 level 0.09072
> select add #1
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-7.5229,0,1,0,11.492,0,0,1,0.39003
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99427,0.0030302,0.10684,-20.851,0.010517,0.99197,-0.126,27.264,-0.10637,0.1264,0.98626,0.56321
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule Y308E_fitted_J109.cif (#1) to map J109_zflip.mrc (#2) using 17927
atoms
average map value = 0.1062, steps = 104
shifted from previous position = 4.2
rotated from previous position = 3.93 degrees
atoms outside contour = 8398, contour level = 0.090716
Position of Y308E_fitted_J109.cif (#1) relative to J109_zflip.mrc (#2)
coordinates:
Matrix rotation and translation
0.99174270 0.01058962 0.12780561 -22.39035465
0.01401152 0.98167154 -0.19006488 33.65586848
-0.12747585 0.19028621 0.97341721 -5.64871133
Axis 0.83029608 0.55727248 0.00746991
Axis point 0.00000000 53.65439667 171.54197477
Rotation angle (degrees) 13.24088049
Shift along axis 0.12267019
> volume #2 color #7a7676
> volume #2 color #7a767678
> volume #2 color #7a76768c
> select subtract #1
Nothing selected
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ109.pdb
> relModel #2
> close session
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J109_zflip.mrc
Opened J109_zflip.mrc as #1, grid size 416,416,416, pixel 0.65, shown at level
0.0291, step 2, values float32
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/Y308E_fitJ109.pdb
Chain information for Y308E_fitJ109.pdb #2
---
Chain | Description
A B C D E F G | No description available
> volume #1 step 1
> volume #1 level 0.02905
> volume #1 level 0.04475
> style stick
Changed 17927 atom styles
> volume #1 color #7a7878
> volume #1 color #7a787886
> volume #1 color #7a787860
> volume #1 level 0.07726
> close session
> open
> /home/carsten/Downloads/cryosparc_P30_J201_component_000/J201_component_000_frame_000.mrc
Opened J201_component_000_frame_000.mrc as #1, grid size 208,208,208, pixel
1.3, shown at level 0.0955, step 1, values float32
> volume #1 level 0.1449
> open
> /home/carsten/Downloads/cryosparc_P30_J201_component_000/J201_component_000_frame_009.mrc
Opened J201_component_000_frame_009.mrc as #2, grid size 208,208,208, pixel
1.3, shown at level 0.0949, step 1, values float32
> volume #2 level 0.1409
> volume #1 color #918e8e
> volume #1 color #918e8e88
> volume #1 color #918e8e65
> volume #2 level 0.1573
> volume #2 level 0.145
> open
> /home/carsten/Desktop/depositions_Panx1/4_Venom_P30_J113_Y308E_2.45Å/4_Venom_P30_J113_Y308E_2.45Å/4_model_Y308E_C7_ChainA_without_K26.cif
Summary of feedback from opening
/home/carsten/Desktop/depositions_Panx1/4_Venom_P30_J113_Y308E_2.45Å/4_Venom_P30_J113_Y308E_2.45Å/4_model_Y308E_C7_ChainA_without_K26.cif
---
warnings | Unknown polymer entity '1' on line 134
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 4_model_Y308E_C7_ChainA_without_K26.cif #3
---
Chain | Description
A B C D E F G | No description available
> style stick
Changed 17927 atom styles
> show cartoons
> hide atoms
> select add #3
17927 atoms, 18368 bonds, 21 pseudobonds, 2205 residues, 2 models selected
> view matrix models
> #3,0.5127,0.85851,-0.0093626,-49.232,0.8562,-0.51046,0.079705,78.865,0.063649,-0.048881,-0.99677,247.71
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.5127,0.85851,-0.0093626,-49.966,0.8562,-0.51046,0.079705,79.576,0.063649,-0.048881,-0.99677,266.05
> view matrix models
> #3,0.5127,0.85851,-0.0093626,-51.199,0.8562,-0.51046,0.079705,80.774,0.063649,-0.048881,-0.99677,270.1
> volume flip #2 axis z
Opened J201_component_000_frame_009.mrc z flip as #4, grid size 208,208,208,
pixel 1.3, shown at step 1, values float32
> volume flip #1 axis z
Opened J201_component_000_frame_000.mrc z flip as #5, grid size 208,208,208,
pixel 1.3, shown at step 1, values float32
> close #1
> close #2
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.72642,-0.68124,-0.090727,336.53,0.66889,-0.73114,0.13425,129.38,-0.15779,0.036833,0.98679,40.479
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.72642,-0.68124,-0.090727,336.61,0.66889,-0.73114,0.13425,129.17,-0.15779,0.036833,0.98679,17.279
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.15442,-0.98414,0.087321,277.76,0.96775,-0.13286,0.21403,-2.6947,-0.19903,0.11755,0.97292,13.653
> ui tool show "Fit in Map"
> fitmap #3 inMap #4
Fit molecule 4_model_Y308E_C7_ChainA_without_K26.cif (#3) to map
J201_component_000_frame_009.mrc z flip (#4) using 17927 atoms
average map value = 0.1802, steps = 112
shifted from previous position = 1.86
rotated from previous position = 14.1 degrees
atoms outside contour = 6972, contour level = 0.145
Position of 4_model_Y308E_C7_ChainA_without_K26.cif (#3) relative to
J201_component_000_frame_009.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.22270278 -0.97488640 0.00008504 297.10625608
0.97488636 -0.22270279 -0.00029953 33.53031205
0.00031094 0.00001620 0.99999997 -0.69388621
Axis 0.00016193 -0.00011586 0.99999998
Axis point 135.18600620 135.20966035 0.00000000
Rotation angle (degrees) 102.86783115
Shift along axis -0.64966141
> volume #4 color #bfbc40
> volume #4 color #bfaf40
> volume #4 color #bfb140
> volume #4 color #bfb340b1
> volume #4 color #bfb340c3
> volume #4 color #bfb34096
> style sel stick
Changed 17927 atom styles
> hide sel cartoons
> show sel atoms
> select subtract #3
Nothing selected
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/3DVA_ECD_Y308E.cxs
> includeMaps true
> volume #5 level 0.1486
> volume #5 level 0.1542
> volume #5 level 0.1764
> volume #5 level 0.145
> volume #5 level 0.1875
> volume #4 level 188
> save
> /home/carsten/Desktop/depositions_Panx1/W74fitting/3DVAFitting_y308E_J201_comp0frame0.pdb
> relModel #5
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/J201comp0_frame0.mrc
> models #5
> volume #4 level 0.1946
> save /home/carsten/Desktop/depositions_Panx1/W74fitting/J201comp0_frame9.mrc
> models #4
> close session
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J201comp0_frame9.mrc
Opened J201comp0_frame9.mrc as #1, grid size 208,208,208, pixel 1.3, shown at
level 0.0949, step 1, values float32
> close #1
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J201comp0_frame0.mrc
Opened J201comp0_frame0.mrc as #1, grid size 208,208,208, pixel 1.3, shown at
level 0.0955, step 1, values float32
> open
> /home/carsten/Desktop/depositions_Panx1/W74fitting/3DVAFitting_y308E_J201_comp0frame0.pdb
Chain information for 3DVAFitting_y308E_J201_comp0frame0.pdb #2
---
Chain | Description
A B C D E F G | No description available
> volume #1 level 0.1372
> style stick
Changed 17927 atom styles
> volume #1 level 0.168
> open /home/carsten/Desktop/depositions_Panx1/W74fitting/J201comp0_frame9.mrc
Opened J201comp0_frame9.mrc as #3, grid size 208,208,208, pixel 1.3, shown at
level 0.0949, step 1, values float32
> volume #3 level 0.1246
> ui mousemode right rotate
> volume #3 level 0.1871
> volume #3 level 0.26
> volume #3 level 0.1826
> volume #1 color #817e7e
> volume #1 color #817e7e83
> volume #3 color #bfbc40
> volume #3 color #bfbe40
> volume #3 color #d2d296
> volume #3 color #d2d296b9
> volume #3 level 0.1692
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> close #2
> open
> /home/carsten/Desktop/depositions_Panx1/W74fitting/3DVAFitting_y308E_J201_comp0frame0.pdb
Chain information for 3DVAFitting_y308E_J201_comp0frame0.pdb #2
---
Chain | Description
A B C D E F G | No description available
> style stick
Changed 17927 atom styles
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 56 residues in model #2 to IUPAC-IUB
standards.
Chain information for 3DVAFitting_y308E_J201_comp0frame0.pdb
---
Chain | Description
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E 2.2/F 2.2/G | No description available
> clipper associate #3 toModel #2
Opened J201comp0_frame9.mrc as #2.1.1.1, grid size 208,208,208, pixel 1.3,
shown at step 1, values float32
> volume #2.1.1.1 style surface
> volume #2.1.1.1 color #40b7bf
> volume #2.1.1.1 color #40b7bfb7
> cview /F:74
> select /F:74
14 atoms, 15 bonds, 1 residue, 1 model selected
> isolde sim start /F:74
Sim termination reason: None
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to
3DVAFitting_y308E_J201_comp0frame0.pdb #2.2
---
notes | No usable SEQRES records for 3DVAFitting_y308E_J201_comp0frame0.pdb (#2.2) chain A; guessing termini instead
No usable SEQRES records for 3DVAFitting_y308E_J201_comp0frame0.pdb (#2.2)
chain B; guessing termini instead
No usable SEQRES records for 3DVAFitting_y308E_J201_comp0frame0.pdb (#2.2)
chain C; guessing termini instead
No usable SEQRES records for 3DVAFitting_y308E_J201_comp0frame0.pdb (#2.2)
chain D; guessing termini instead
No usable SEQRES records for 3DVAFitting_y308E_J201_comp0frame0.pdb (#2.2)
chain E; guessing termini instead
2 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A ALA 2, /B ALA 2, /C ALA
2, /D ALA 2, /E ALA 2, /F ALA 2, /G ALA 2
Chain-initial residues that are not actual N termini: /A GLY 27, /A PRO 193,
/A THR 313, /B GLY 27, /B PRO 193, /B THR 313, /C GLY 27, /C PRO 193, /C THR
313, /D GLY 27, /D PRO 193, /D THR 313, /E GLY 27, /E PRO 193, /E THR 313, /F
GLY 27, /F PRO 193, /F THR 313, /G GLY 27, /G PRO 193, /G THR 313
Chain-final residues that are actual C termini: /A PRO 362, /B PRO 362, /C PRO
362, /D PRO 362, /E PRO 362, /F PRO 362, /G PRO 362
Chain-final residues that are not actual C termini: /A LEU 17, /A ASP 162, /A
LYS 302, /B LEU 17, /B ASP 162, /B LYS 302, /C LEU 17, /C ASP 162, /C LYS 302,
/D LEU 17, /D ASP 162, /D LYS 302, /E LEU 17, /E ASP 162, /E LYS 302, /F LEU
17, /F ASP 162, /F LYS 302, /G LEU 17, /G ASP 162, /G LYS 302
2373 hydrogen bonds
Adding 'H' to /A GLY 27
Adding 'H' to /A THR 313
Adding 'H' to /B GLY 27
Adding 'H' to /B THR 313
Adding 'H' to /C GLY 27
9 messages similar to the above omitted
18627 hydrogens added
Loading residue template for Y01 from internal database
> isolde sim start /F:71-77
ISOLDE: started sim
> select /F:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /F:75
24 atoms, 23 bonds, 1 residue, 1 model selected
> cview /A:75
> select /A:75
24 atoms, 23 bonds, 1 residue, 1 model selected
> volume #2.1.1.1 level 0.1781
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:75
ISOLDE: started sim
> select /A:75
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> cview /B:74
> select /B:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /C:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> cview /C:74
> volume #2.1.1.1 level 0.1738
> cview /D:74
> select /D:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /E:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> cview /E:74
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:74
ISOLDE: started sim
> cview /E:74
> select /E:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /E:75
24 atoms, 23 bonds, 1 residue, 1 model selected
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select /F75
Nothing selected
> select /F:75
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /F:74
24 atoms, 25 bonds, 1 residue, 1 model selected
> isolde sim start /F:74
ISOLDE: started sim
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Stream 8
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 5.8Gi 30Gi 275Mi 25Gi 55Gi
Swap: 31Gi 0B 31Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)
Subsystem: ASUSTeK Computer Inc. Device [1043:8597]
Kernel driver in use: nvidia
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appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
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ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
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ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
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ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
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ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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ChimeraX-Dssp: 2.0
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ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
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ChimeraX-ImageFormats: 1.2
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ChimeraX-IO: 1.0.1
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ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
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ChimeraX-MatchMaker: 2.1.3
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comm: 0.2.2
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MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in check_for_changes during running simulation |
comment:2 by , 16 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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