![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Last modified 21 months ago
#14604 feedback defect
Crash processing window geometry change event
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard, Tristan Croll | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000203202240 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, 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._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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.linalg._flinalg, 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.__nnls, 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, lxml._elementpath, lxml.etree (total: 131)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
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"captureTime" : "2024-02-16 18:03:30.1752 -0800",
"codeSigningMonitor" : 1,
"incident" : "0C76CC5B-0B69-42AA-9185-D951C42A5D97",
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"procLaunch" : "2024-02-14 12:49:33.5789 -0800",
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"procExitAbsTime" : 51019259683061,
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"crashReporterKey" : "D7658540-E066-2866-40CA-0AAADB07EF70",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 6876,
"sleepWakeUUID" : "238C2671-7AFB-46EE-9270-AA78729639A3",
"sip" : "enabled",
"vmRegionInfo" : "0x77fc148dadc0 is not in any region. Bytes after previous region: 26368759672257 Bytes before following region: 8688431682112\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600080000000-6000a0000000 [512.0M] rw-\/rwx SM=PRV \n---> GAP OF 0x1fe263700000 BYTES\n MALLOC_TINY 7fe303700000-7fe303800000 [ 1024K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x000077fc148dadc0","rawCodes":[1,131924560293312],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000077fc148dadc0"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":72649},
"vmregioninfo" : "0x77fc148dadc0 is not in any region. Bytes after previous region: 26368759672257 Bytes before following region: 8688431682112\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600080000000-6000a0000000 [512.0M] rw-\/rwx SM=PRV \n---> GAP OF 0x1fe263700000 BYTES\n MALLOC_TINY 7fe303700000-7fe303800000 [ 1024K] rw-\/rwx SM=PRV ",
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"uuid" : "6e04c71f-0478-3031-990d-f7a6c732ba2d",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_distance_wrap.cpython-311-darwin.so",
"name" : "_distance_wrap.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6499549184,
"size" : 114688,
"uuid" : "0094c7e3-6996-3477-adf7-3b9117ffaf5c",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_voronoi.cpython-311-darwin.so",
"name" : "_voronoi.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 7521394688,
"size" : 868352,
"uuid" : "7424432a-f8fd-365c-a1e3-87f0a4691a2a",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_qhull.cpython-311-darwin.so",
"name" : "_qhull.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 7124746240,
"size" : 557056,
"uuid" : "edcd63b3-6d86-3462-8685-9e02f1a776e0",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/spatial\/_ckdtree.cpython-311-darwin.so",
"name" : "_ckdtree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6002475008,
"size" : 32768,
"uuid" : "a039992d-891a-3f7b-8250-439a2b70c99c",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_lsap.cpython-311-darwin.so",
"name" : "_lsap.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 7123312640,
"size" : 196608,
"uuid" : "ac477fbb-de0b-389b-a7f8-30698fcc8a55",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_bglu_dense.cpython-311-darwin.so",
"name" : "_bglu_dense.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 7075373056,
"size" : 327680,
"uuid" : "c406e367-c837-3c5f-81e2-1deac9d48e20",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/linalg\/_interpolative.cpython-311-darwin.so",
"name" : "_interpolative.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 5986254848,
"size" : 16384,
"uuid" : "c35f9d95-dbc4-3050-9236-249d498333ec",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_highs\/_highs_constants.cpython-311-darwin.so",
"name" : "_highs_constants.cpython-311-darwin.so"
},
{
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"arch" : "x86_64",
"base" : 7126986752,
"size" : 3047424,
"uuid" : "4e71ccde-f0c3-351a-bd11-22dcd3e3bc9b",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/_highs\/_highs_wrapper.cpython-311-darwin.so",
"name" : "_highs_wrapper.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6040633344,
"size" : 32768,
"uuid" : "4eebcd15-dad1-352a-8fe2-a0c07f554698",
"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/optimize\/__nnls.cpython-311-darwin.so",
"name" : "__nnls.cpython-311-darwin.so"
},
[deleted to fit within ticket limits]
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to SPTBN2 working 7g.pdb #1/J LYS 382 CB
because it is missing heavy-atom bond partners
Not adding hydrogens to SPTBN2 working 7g.pdb #1/J ARG 432 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to SPTBN2 working 7g.pdb #1/K GLU 2268 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to SPTBN2 working 7g.pdb #1/K GLU 2269 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to SPTBN2 working 7g.pdb #1/K THR 2270 CB because it is
missing heavy-atom bond partners
93 messages similar to the above omitted
Skipped 18 atom(s) with bad connectivities; see log for details
Not adding hydrogens to combo #4/J LYS 382 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to combo #4/J ARG 432 CB because it is missing heavy-atom
bond partners
Not adding hydrogens to combo #4/K GLU 2268 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to combo #4/K GLU 2269 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to combo #4/K THR 2270 CB because it is missing heavy-
atom bond partners
93 messages similar to the above omitted
Skipped 18 atom(s) with bad connectivities; see log for details
notes | Termini for SPTBN2 working 7g.pdb (#1) chain B determined from SEQRES
records
Termini for SPTBN2 working 7g.pdb (#1) chain C determined from SEQRES records
Termini for SPTBN2 working 7g.pdb (#1) chain D determined from SEQRES records
Termini for SPTBN2 working 7g.pdb (#1) chain E determined from SEQRES records
Termini for SPTBN2 working 7g.pdb (#1) chain F determined from SEQRES records
4 messages similar to the above omitted
Chain-initial residues that are actual N termini: SPTBN2 working 7g.pdb #1/B
ACE 0, SPTBN2 working 7g.pdb #1/C ACE 0, SPTBN2 working 7g.pdb #1/D ACE 0,
SPTBN2 working 7g.pdb #1/E ACE 0, SPTBN2 working 7g.pdb #1/F ACE 0, SPTBN2
working 7g.pdb #1/J MET 1, SPTBN2 working 7g.pdb #1/K LYS 2038, SPTBN2 working
7g.pdb #1/Q MET 1, SPTBN2 working 7g.pdb #1/S GLU 565
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: SPTBN2 working 7g.pdb #1/B PHE
374, SPTBN2 working 7g.pdb #1/C PHE 374, SPTBN2 working 7g.pdb #1/D PHE 374,
SPTBN2 working 7g.pdb #1/E PHE 374, SPTBN2 working 7g.pdb #1/F PHE 374, SPTBN2
working 7g.pdb #1/K GLY 2416, SPTBN2 working 7g.pdb #1/Q HIS 166, SPTBN2
working 7g.pdb #1/S PRO 1047
Chain-final residues that are not actual C termini: SPTBN2 working 7g.pdb #1/J
GLN 534
3613 hydrogen bonds
No usable SEQRES records for VAVtoSOS 2e.pdb (#2) chain A; guessing termini
instead
Termini for VAVtoSOS 2e.pdb (#2) chain C determined from SEQRES records
Chain-initial residues that are actual N termini: VAVtoSOS 2e.pdb #2/A GLN
189, VAVtoSOS 2e.pdb #2/C MET 1, VAVtoSOS 2e.pdb #2/A GLN 189
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #2/C LEU 177,
VAVtoSOS 2e.pdb #2/A GLU 563
Chain-final residues that are not actual C termini: VAVtoSOS 2e.pdb #2/A GLU
563
Missing OXT added to C-terminal residue VAVtoSOS 2e.pdb #2/A GLU 563
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN
223 OXT
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN
223 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A GLY
279 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN
223 OXT
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #2/A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #2/A ASN
223 O
13 messages similar to the above omitted
539 hydrogen bonds
Termini for 8DNH.pdb (#3) chain B determined from SEQRES records
Termini for 8DNH.pdb (#3) chain C determined from SEQRES records
Termini for 8DNH.pdb (#3) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: 8DNH.pdb #3/B ACE 0,
8DNH.pdb #3/C ACE 0, 8DNH.pdb #3/D ACE 0
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: 8DNH.pdb #3/B PHE 374,
8DNH.pdb #3/C PHE 374, 8DNH.pdb #3/D PHE 374
Chain-final residues that are not actual C termini:
718 hydrogen bonds
Termini for combo (#4) chain B determined from SEQRES records
Termini for combo (#4) chain C determined from SEQRES records
Termini for combo (#4) chain D determined from SEQRES records
Termini for combo (#4) chain E determined from SEQRES records
Termini for combo (#4) chain F determined from SEQRES records
4 messages similar to the above omitted
No usable SEQRES records for combo (#4) chain A; guessing termini instead
Termini for combo (#4) chain G determined from SEQRES records
Termini for combo (#4) chain H determined from SEQRES records
Termini for combo (#4) chain I determined from SEQRES records
Termini for combo (#4) chain L determined from SEQRES records
Chain-initial residues that are actual N termini: combo #4/B ACE 0, combo #4/C
ACE 0, combo #4/D ACE 0, combo #4/E ACE 0, combo #4/F ACE 0, combo #4/J MET 1,
combo #4/K LYS 2038, combo #4/Q MET 1, combo #4/S GLU 565, combo #4/A GLN 189,
combo #4/G MET 1, combo #4/H ACE 0, combo #4/I ACE 0, combo #4/L ACE 0, combo
#4/A GLN 189
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: combo #4/B PHE 374, combo #4/C
PHE 374, combo #4/D PHE 374, combo #4/E PHE 374, combo #4/F PHE 374, combo
#4/K GLY 2416, combo #4/Q HIS 166, combo #4/S PRO 1047, combo #4/G LEU 177,
combo #4/H PHE 374, combo #4/I PHE 374, combo #4/L PHE 374, combo #4/A GLU 563
Chain-final residues that are not actual C termini: combo #4/J GLN 534, combo
#4/A GLU 563
Missing OXT added to C-terminal residue combo #4/A GLU 563
Skipping possible acceptor with bad geometry: combo #4/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 OXT
Skipping possible acceptor with bad geometry: combo #4/A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 O
Skipping possible acceptor with bad geometry: combo #4/A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor combo #4/A GLY 279 O
Skipping possible acceptor with bad geometry: combo #4/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 OXT
Skipping possible acceptor with bad geometry: combo #4/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor combo #4/A ASN 223 OXT
13 messages similar to the above omitted
4874 hydrogen bonds
17383 hydrogens added
> hide #2 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> isolde sim start #4/G
> set selectionWidth 4
Done loading forcefield
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 75 residues in model #4 to IUPAC-IUB
standards.
> 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: started sim
> isolde sim pause
> show sel cartoons
> hide sel atoms
> 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 sim start #4/G,A
ISOLDE: started sim
> show sel cartoons
> hide sel atoms
> show sel atoms
> ui tool show "Ramachandran Plot"
> 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 sim start #4
Loading residue template for ADP from internal database
ISOLDE: started sim
> isolde sim start #4
Simulation already running!
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 329 residues in model #4.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> interfaces #4
26 buried areas: J K 3655, J S 2384, J F 1932, S A 1560, F D 1380, C E 1335, C
H 1304, H L 1239, F B 1228, S Q 1202, A G 1159, C D 976, I L 930, S D 730, J D
725, H I 701, F C 674, S F 649, A D 600, D H 599, F E 559, B E 537, A H 526, J
B 490, J C 329, C K 303
> ui tool show "Show Sequence Viewer"
> sequence chain #4.2/G
Alignment identifier is 4.2/G
> show sel atoms
> ui tool show "Selection Inspector"
> delete atoms (#!4.2 & sel)
/Users/tmckeithan/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py:367: RuntimeWarning:
invalid value encountered in log
logscores = numpy.log(scores)
> delete bonds (#!4.2 & sel)
> delete atoms (#!4.2 & sel)
> delete bonds (#!4.2 & sel)
> delete atoms (#!4.2 & sel)
> delete bonds (#!4.2 & sel)
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8.cxs" format session
opened ChimeraX session
> select
74563 atoms, 75470 bonds, 13 pseudobonds, 5520 residues, 5 models selected
> show sel cartoons
> hide sel atoms
> select #3/A
2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #2/A:583
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:564-583
312 atoms, 315 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/S:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/S:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> select clear
> select #1/S:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/S:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A
5940 atoms, 5995 bonds, 366 residues, 1 model selected
> select sel : combine #1-3 close true name combo
Remapping chain ID 'C' in VAVtoSOS 2e.pdb #2 to 'G'
Remapping chain ID 'B' in 8DNH.pdb #3 to 'H'
Remapping chain ID 'C' in 8DNH.pdb #3 to 'I'
Remapping chain ID 'D' in 8DNH.pdb #3 to 'L'
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain /J
Alignment identifier is 1/J
> sequence chain /K
Alignment identifier is 1/K
> sequence chain /Q
Alignment identifier is 1/Q
> sequence chain /S
Alignment identifier is 1/S
> select /S:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /S:565
17 atoms, 16 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:562
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:562-563
30 atoms, 29 bonds, 2 residues, 1 model selected
> select /S:567
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /S:566-567
34 atoms, 33 bonds, 2 residues, 1 model selected
> name frozen temp sel
> select /A:562
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:562-563
30 atoms, 29 bonds, 2 residues, 1 model selected
> select add temp
64 atoms, 62 bonds, 4 residues, 1 model selected
> select ~sel
71221 atoms, 72060 bonds, 12 pseudobonds, 5118 residues, 2 models selected
> cartoon hide (#!1 & sel)
> show sel atoms
> hide sel cartoons
> color sel byelement
> cofr sel
> interfaces #1
23 buried areas: J K 3441, J S 2289, J F 1813, A G 1482, E C 1287, F D 1245, S
A 1245, F B 1179, C H 1143, H L 1124, S Q 1014, D I 860, C D 614, F C 578, F E
505, B E 493, J B 448, S F 405, S D 398, H I 393, J D 370, I L 319, D H 304
> addh
Summary of feedback from adding hydrogens to combo #1
---
warnings | Not adding hydrogens to /J LYS 382 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /J ARG 432 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /K GLU 2268 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /K GLU 2269 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /K THR 2270 CB because it is missing heavy-atom bond
partners
93 messages similar to the above omitted
Skipped 18 atom(s) with bad connectivities; see log for details
notes | Termini for combo (#1) chain B determined from SEQRES records
Termini for combo (#1) chain C determined from SEQRES records
Termini for combo (#1) chain D determined from SEQRES records
Termini for combo (#1) chain E determined from SEQRES records
Termini for combo (#1) chain F determined from SEQRES records
4 messages similar to the above omitted
No usable SEQRES records for combo (#1) chain A; guessing termini instead
Termini for combo (#1) chain G determined from SEQRES records
Termini for combo (#1) chain H determined from SEQRES records
Termini for combo (#1) chain I determined from SEQRES records
Termini for combo (#1) chain L determined from SEQRES records
Chain-initial residues that are actual N termini: /B ACE 0, /C ACE 0, /D ACE
0, /E ACE 0, /F ACE 0, /J MET 1, /K LYS 2038, /Q MET 1, /A GLN 189, /G MET 1,
/H ACE 0, /I ACE 0, /L ACE 0, /A GLN 189
Chain-initial residues that are not actual N termini: /S GLN 566
Chain-final residues that are actual C termini: /B PHE 374, /C PHE 374, /D PHE
374, /E PHE 374, /F PHE 374, /K GLY 2416, /Q HIS 166, /S PRO 1047, /G LEU 177,
/H PHE 374, /I PHE 374, /L PHE 374, /A GLU 563
Chain-final residues that are not actual C termini: /J GLN 534, /A GLU 563
Missing OXT added to C-terminal residue /A GLU 563
Skipping possible acceptor with bad geometry: /A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O
Skipping possible acceptor with bad geometry: /A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT
Skipping possible acceptor with bad geometry: /A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O
Skipping possible acceptor with bad geometry: /A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT
Skipping possible acceptor with bad geometry: /A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O
13 messages similar to the above omitted
4873 hydrogen bonds
8692 hydrogens added
> isolde sim start /A,S,Q,G
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 75 residues in model #1 to IUPAC-IUB
standards.
ISOLDE: started sim
> show sel cartoons
> hide sel atoms
> ui tool show "Ramachandran Plot"
> show sel cartoons
> show sel atoms
> ui tool show "Ramachandran Plot"
> select clear
> show sel atoms
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 69 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> interfaces #1 areaCutoff 50
26 buried areas: J K 3624, J S 2327, J F 1914, A G 1376, C E 1327, F D 1299, F
B 1228, C H 1191, H L 1190, S A 1123, S Q 1075, D I 922, C D 665, F C 645, F E
551, B E 525, S F 508, J B 479, S D 452, H I 450, J D 374, I L 364, D H 348, C
K 280, J C 248, J Q 63
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8a.pdb"
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8a.pdb" format pdb
SPTBN2 working 8a.pdb title:
Cryo-em structure of nonmuscle β-actin [more info...]
Chain information for SPTBN2 working 8a.pdb #1
---
Chain | Description | UniProt
A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
E F H I L | No description available |
G | No description available |
J | No description available |
K | No description available |
Q | No description available |
S | No description available |
Non-standard residues in SPTBN2 working 8a.pdb #1
---
ACE — acetyl group
ADP — adenosine-5'-diphosphate
GTP — (GTP)
MG — magnesium ion
> isolde sim start /A,S,Q,G,J,K,D,F
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
SPTBN2 working 8a.pdb title:
Cryo-em structure of nonmuscle β-actin [more info...]
Chain information for SPTBN2 working 8a.pdb
---
Chain | Description | UniProt
1.2/A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
1.2/B 1.2/C 1.2/D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN
1-374
1.2/E 1.2/F 1.2/H 1.2/I 1.2/L | No description available |
1.2/G | No description available |
1.2/J | No description available |
1.2/K | No description available |
1.2/Q | No description available |
1.2/S | No description available |
Non-standard residues in SPTBN2 working 8a.pdb #1.2
---
ACE — acetyl group
ADP — adenosine-5'-diphosphate
GTP — (GTP)
MG — magnesium ion
ISOLDE: started sim
> isolde sim pause
> hide sel atoms
> show sel cartoons
> isolde sim resume
> select clear
> select add /A
5941 atoms, 5996 bonds, 366 residues, 1 model selected
> select add /G
8524 atoms, 8609 bonds, 543 residues, 1 model selected
> ui mousemode right "isolde tug selection"
> isolde sim pause
> ui mousemode right "translate selected atoms"
> isolde sim resume
> ui mousemode right "isolde tug selection"
> show sel atoms
> ui mousemode right "isolde tug atom"
> select
79978 atoms, 80817 bonds, 12 pseudobonds, 5122 residues, 18 models selected
> show sel atoms
> hide sel cartoons
> isolde sim pause
> 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 206 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8b.pdb"
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8b.pdb" format pdb
SPTBN2 working 8b.pdb title:
Cryo-em structure of nonmuscle β-actin [more info...]
Chain information for SPTBN2 working 8b.pdb #1
---
Chain | Description | UniProt
A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
E F H I L | No description available |
G | No description available |
J | No description available |
K | No description available |
Q | No description available |
S | No description available |
Non-standard residues in SPTBN2 working 8b.pdb #1
---
ACE — acetyl group
ADP — adenosine-5'-diphosphate
GTP — (GTP)
MG — magnesium ion
> hide atoms
> show cartoons
> interfaces #1 areaCutoff 50
29 buried areas: J K 3357, J S 2483, J F 1682, A G 1361, C E 1274, F D 1261, S
A 1209, C H 1184, F B 1150, H L 1147, D I 1053, S Q 1028, A D 705, F C 683, S
F 583, F E 546, C D 542, B E 493, S D 458, J B 451, D H 439, H I 405, I L 331,
J C 237, C K 195, J Q 183, A H 146, J D 142, J A 52
> select /J
8715 atoms, 8791 bonds, 534 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain /S
Alignment identifier is 1/S
> sequence chain /J
Alignment identifier is 1/J
> sequence chain /K
Alignment identifier is 1/K
> sequence chain /Q
Alignment identifier is 1/Q
> ui tool show "Show Sequence Viewer"
> show sel atoms
> color N cornflowerblue atoms
> color O hotpink atoms
> color :arg,hic,his,lys & sidechain & N blue atoms
> color :asp,glu & sidechain & O red atoms
> ui tool show "Side View"
> interfaces #1 areaCutoff 50
29 buried areas: J K 3357, J S 2483, J F 1682, A G 1361, C E 1274, F D 1261, S
A 1209, C H 1184, F B 1150, H L 1147, D I 1053, S Q 1028, A D 705, F C 683, S
F 583, F E 546, C D 542, B E 493, S D 458, J B 451, D H 439, H I 405, I L 331,
J C 237, C K 195, J Q 183, A H 146, J D 142, J A 52
> dssp
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"
Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for VAVtoSOS 2e.pdb #2
---
Chain | Description
A | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #2/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 SPTBN2 working 8b.pdb, chain A (#1) with VAVtoSOS 2e.pdb, chain A
(#2), sequence alignment score = 1799.5
RMSD between 111 pruned atom pairs is 1.010 angstroms; (across all 366 pairs:
4.868)
> select #1/A
5941 atoms, 5996 bonds, 366 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/G
2583 atoms, 2613 bonds, 177 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:564-565
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:564-583
312 atoms, 315 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIC"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
79564 atoms, 80394 bonds, 5096 residues, 2 models selected
> hide sel target a
> select clear
> select add #2
8523 atoms, 8608 bonds, 543 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.066053,0.85096,-0.52106,95.403,-0.97509,0.055775,0.2147,-59.842,0.21176,0.52226,0.82608,-314.22
> view matrix models
> #2,-0.10676,0.82746,-0.55128,99.813,-0.97792,0.012787,0.20858,-57.088,0.17964,0.56138,0.80783,-314.15
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.10676,0.82746,-0.55128,97.279,-0.97792,0.012787,0.20858,-56.302,0.17964,0.56138,0.80783,-314.65
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.14656,0.80003,-0.58178,101.93,-0.97794,-0.028708,0.20688,-54.17,0.14881,0.59927,0.7866,-314.09
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.14656,0.80003,-0.58178,101.93,-0.97794,-0.028708,0.20688,-53.507,0.14881,0.59927,0.7866,-315.03
> ui mousemode right "rotate selected models"
> select clear
> select add #2
8523 atoms, 8608 bonds, 543 residues, 1 model selected
> view matrix models
> #2,-0.21765,0.81132,-0.54258,94.489,-0.96702,-0.1039,0.23256,-53.398,0.1323,0.5753,0.80717,-317.14
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.21765,0.81132,-0.54258,91.305,-0.96702,-0.1039,0.23256,-50.922,0.1323,0.5753,0.80717,-317.16
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.29199,0.75038,-0.59302,99.523,-0.95413,-0.18566,0.23487,-47.234,0.066143,0.6344,0.77017,-316.12
> view matrix models
> #2,-0.40874,0.63199,-0.65842,111.55,-0.91041,-0.33287,0.24567,-41.084,-0.063904,0.69985,0.71143,-313.7
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8b.pdb" format pdb
SPTBN2 working 8b.pdb title:
Cryo-em structure of nonmuscle β-actin [more info...]
Chain information for SPTBN2 working 8b.pdb #1
---
Chain | Description | UniProt
A | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
E F H I L | No description available |
G | No description available |
J | No description available |
K | No description available |
Q | No description available |
S | No description available |
Non-standard residues in SPTBN2 working 8b.pdb #1
---
ACE — acetyl group
ADP — adenosine-5'-diphosphate
GTP — (GTP)
MG — magnesium ion
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"
Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for VAVtoSOS 2e.pdb #2
---
Chain | Description
A | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #2/C to #1/E pairing ss
Parameters
---
Chain pairing | ss
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 SPTBN2 working 8b.pdb, chain E (#1) with VAVtoSOS 2e.pdb, chain C
(#2), sequence alignment score = 59.9
RMSD between 5 pruned atom pairs is 1.378 angstroms; (across all 131 pairs:
20.379)
> ui tool show Matchmaker
> matchmaker #2/C to #1/G pairing ss
Parameters
---
Chain pairing | ss
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 SPTBN2 working 8b.pdb, chain G (#1) with VAVtoSOS 2e.pdb, chain C
(#2), sequence alignment score = 912.2
RMSD between 121 pruned atom pairs is 1.061 angstroms; (across all 177 pairs:
2.356)
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIC"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
88400 atoms, 89319 bonds, 5659 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #1/G
2583 atoms, 2613 bonds, 177 residues, 1 model selected
> hide sel cartoons
> select #1/A
5941 atoms, 5996 bonds, 366 residues, 1 model selected
> hide sel cartoons
> view matrix models
> #1,0.99677,-0.01188,-0.079408,-9.0815,0.020269,0.99419,0.10568,9.696,0.077691,-0.10695,0.99122,-14.274
> select #2/A:480
7 atoms, 6 bonds, 1 residue, 1 model selected
> cofr sel
> select add #2
8835 atoms, 8924 bonds, 563 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.24209,0.76925,-0.59131,104.63,-0.92355,0.0041076,0.38347,-81.117,0.29741,0.63893,0.70945,-305.94
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select clear
> select #2/A:582-583
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #2/A:564-583
312 atoms, 315 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #2
8523 atoms, 8608 bonds, 543 residues, 1 model selected
> show sel surfaces
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
VAVtoSOS 2e.pdb #2/A LYS 214
VAVtoSOS 2e.pdb #2/C MET 1
VAVtoSOS 2e.pdb #2/C GLN 2
VAVtoSOS 2e.pdb #2/C GLU 31
VAVtoSOS 2e.pdb #2/C ILE 33
VAVtoSOS 2e.pdb #2/C LYS 49
VAVtoSOS 2e.pdb #2/C LYS 123
VAVtoSOS 2e.pdb #2/C ASP 124
VAVtoSOS 2e.pdb #2/C GLU 127
VAVtoSOS 2e.pdb #2/C LYS 128
VAVtoSOS 2e.pdb #2/C GLU 131
VAVtoSOS 2e.pdb #2/C LYS 132
VAVtoSOS 2e.pdb #2/C LYS 133
VAVtoSOS 2e.pdb #2/C LYS 153
VAVtoSOS 2e.pdb #2/C LEU 160
VAVtoSOS 2e.pdb #2/C THR 161
VAVtoSOS 2e.pdb #2/C LYS 166
VAVtoSOS 2e.pdb #2/C ASP 170
VAVtoSOS 2e.pdb #2/C ARG 174
VAVtoSOS 2e.pdb #2/C LEU 177
Using Amber 20 recommended default charges and atom types for standard
residues
copy of VAVtoSOS 2e.pdb #/A LYS 214 CLYS
Nonstandard name for heavy atom copy of VAVtoSOS 2e.pdb #/A LYS 214 OH
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"
Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/VAVtoSOS 2e.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for VAVtoSOS 2e.pdb #1
---
Chain | Description
A | No description available
C | No description available
> show surfaces
> rainbow
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A LYS 214
/C MET 1
/C GLN 2
/C GLU 31
/C ILE 33
/C LYS 49
/C LYS 123
/C ASP 124
/C GLU 127
/C LYS 128
/C GLU 131
/C LYS 132
/C LYS 133
/C LYS 153
/C LEU 160
/C THR 161
/C LYS 166
/C ASP 170
/C ARG 174
/C LEU 177
Using Amber 20 recommended default charges and atom types for standard
residues
/A LYS 214 CLYS
Nonstandard name for heavy atom /A LYS 214 OH
> swapaa /A:214 lys
Using Dunbrack library
/A LYS 214: phi -51.4, psi -27.4 trans
Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 214
> swapaa /C:1 met
Using Dunbrack library
/C MET 1: phi none, psi -163.4 trans
Applying MET rotamer (chi angles: 72.6 -72.0 -71.4) to /C MET 1
> swapaa /C:2 gln
Using Dunbrack library
/C GLN 2: phi 54.0, psi 43.2 trans
Applying GLN rotamer (chi angles: -63.1 -69.2 -63.4) to /C GLN 2
> swapaa /C:31 glu
Using Dunbrack library
/C GLU 31: phi -67.8, psi -17.2 trans
Applying GLU rotamer (chi angles: 66.6 -85.0 17.8) to /C GLU 31
> swapaa /C:33 ile
Using Dunbrack library
/C ILE 33: phi -128.5, psi 129.8 trans
Applying ILE rotamer (chi angles: 66.2 -71.1) to /C ILE 33
> swapaa /C:49 lys
Using Dunbrack library
/C LYS 49: phi -105.8, psi 132.8 trans
Applying LYS rotamer (chi angles: -177.7 178.5 -176.1 -64.2) to /C LYS 49
> swapaa /C:123 lys
Using Dunbrack library
/C LYS 123: phi -59.5, psi -24.4 trans
Applying LYS rotamer (chi angles: -66.0 -66.1 -174.7 -67.0) to /C LYS 123
> swapaa /C:124 asp
Using Dunbrack library
/C ASP 124: phi -65.8, psi -32.0 trans
Applying ASP rotamer (chi angles: -71.2 -15.9) to /C ASP 124
> swapaa /C:127 glu
Using Dunbrack library
/C GLU 127: phi -60.7, psi -29.0 trans
Applying GLU rotamer (chi angles: -69.3 177.9 -8.3) to /C GLU 127
> swapaa /C:128 lys
Using Dunbrack library
/C LYS 128: phi -79.9, psi -47.4 trans
Applying LYS rotamer (chi angles: -66.0 -173.5 -71.5 -66.9) to /C LYS 128
> swapaa /C:131 glu
Using Dunbrack library
/C GLU 131: phi -67.4, psi -28.1 trans
Applying GLU rotamer (chi angles: -68.4 178.8 -8.3) to /C GLU 131
> swapaa /C:132 lys
Using Dunbrack library
/C LYS 132: phi -92.6, psi 6.9 trans
Applying LYS rotamer (chi angles: -64.3 -174.6 -70.2 -66.8) to /C LYS 132
> swapaa /C:133 lys
Using Dunbrack library
/C LYS 133: phi 60.7, psi 17.9 trans
Applying LYS rotamer (chi angles: -83.6 68.4 178.6 177.6) to /C LYS 133
> swapaa /C:153 lys
Using Dunbrack library
/C LYS 153: phi -147.1, psi 155.7 trans
Applying LYS rotamer (chi angles: -61.9 -73.1 -174.8 -67.0) to /C LYS 153
> swapaa /C:160 leu
Using Dunbrack library
/C LEU 160: phi -72.4, psi -31.1 trans
Applying LEU rotamer (chi angles: -67.8 174.1) to /C LEU 160
> swapaa /C:161 thr
Using Dunbrack library
/C THR 161: phi -153.7, psi 150.8 trans
Applying THR rotamer (chi angles: -174.5) to /C THR 161
> swapaa /C:166 lys
Using Dunbrack library
/C LYS 166: phi -57.5, psi -38.2 trans
Applying LYS rotamer (chi angles: -171.7 -89.7 -173.2 -177.4) to /C LYS 166
> swapaa /C:170 asp
Using Dunbrack library
/C ASP 170: phi -62.4, psi -45.3 trans
Applying ASP rotamer (chi angles: -71.6 -15.7) to /C ASP 170
> swapaa /C:174 arg
Using Dunbrack library
/C ARG 174: phi -63.3, psi -17.3 trans
Applying ARG rotamer (chi angles: -172.3 178.2 -63.1 -83.0) to /C ARG 174
> swapaa /C:177 leu
Using Dunbrack library
/C LEU 177: phi -148.8, psi none trans
Applying LEU rotamer (chi angles: -64.7 174.5) to /C LEU 177
> addh
Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1
---
warning | Skipped 18 atom(s) with bad connectivities; see log for details
notes | No usable SEQRES records for VAVtoSOS 2e.pdb (#1) chain A; guessing
termini instead
Termini for VAVtoSOS 2e.pdb (#1) chain C determined from SEQRES records
Chain-initial residues that are actual N termini: /A GLN 189, /C MET 1, /A GLN
189
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASN 583, /C LEU 177, /A ASN
583
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: /A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT
Skipping possible acceptor with bad geometry: /A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O
Skipping possible acceptor with bad geometry: /A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O
Skipping possible acceptor with bad geometry: /A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 OXT
Skipping possible acceptor with bad geometry: /A GLY 279 OXT
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 OXT
13 messages similar to the above omitted
564 hydrogen bonds
161 hydrogens added
> hide surfaces
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAVtoSOS 2e.pdb"
> isolde sim start #1
> set selectionWidth 4
Done loading forcefield
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1 to IUPAC-IUB
standards.
Chain information for VAVtoSOS 2e.pdb
---
Chain | Description
1.2/A | No description available
1.2/C | No description available
> 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: started sim
> isolde sim pause
> isolde sim resume
> ui tool show "Ramachandran Plot"
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 37 days, 2 hours, 52 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (4)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash processing window geometry change event |
comment:2 by , 21 months ago
| Status: | accepted → feedback |
|---|
Hi Tim,
Thanks for reporting this problem. Were you resizing/moving a window when this crash occurred? Was a simulation running?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:3 by , 21 months ago
I'm puzzled why you are running Mac Intel ChimeraX under Rosetta on a Mac M1 machine. You should use the Mac M1 ChimeraX. But this is probably not related to the crash which appears to be from an event on a docked ChimeraX panel.
comment:4 by , 21 months ago
Hi Tim, Thanks for the info. I've seen several cases where the Intel ChimeraX was running on an M1/M2/M3 Mac which puzzles me since the standard Mac ChimeraX download includes both M1/M2/M3 and Intel and it should be running the native version. I will figure out this mystery some day. Thanks for the info. Tom
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Reported by Tim McKeithan