id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14604	Crash processing window geometry change event	tmckeith@…	Eric Pettersen	"{{{
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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[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

}}}
"	defect	feedback	normal		Window Toolkit				Tom Goddard Tristan Croll				all	ChimeraX