![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 months ago
Last modified 22 months ago
#14604 feedback defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard, Tristan Croll | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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"modelCode" : "MacBookPro18,3",
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"captureTime" : "2024-02-16 18:03:30.1752 -0800",
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"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",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 6876,
"sleepWakeUUID" : "238C2671-7AFB-46EE-9270-AA78729639A3",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x000077fc148dadc0","rawCodes":[1,131924560293312],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000077fc148dadc0"},
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"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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},
"logWritingSignature" : "abc78da7148ba39a8af47839dd2684076451d939",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000361
},
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
},
"deploymentId" : 240000014
}
],
"experiments" : [
{
"treatmentId" : "5d51a80d-93ec-47e1-9027-675002e78e4a",
"experimentId" : "6384d56b96e8d228551ec182",
"deploymentId" : 400000027
}
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8A5D9EA78)"
]
}
===== Log before crash start =====
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
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Alphafold models/SOS1-AF-Q07889.pdb"
SOS1-AF-Q07889.pdb title:
Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
[more info...]
Chain information for SOS1-AF-Q07889.pdb #1
---
Chain | Description | UniProt
A | son of sevenless homolog 1 | SOS1_HUMAN 1-1333
> set bgColor white
> graphics silhouettes true
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> 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
> open /Users/tmckeithan/Downloads/Chimera/PDB/3BJI.pdb
3BJI.pdb title:
Structural basis of promiscuous guanine nucleotide exchange by the T- cell
essential VAV1 [more info...]
Chain information for 3BJI.pdb #2
---
Chain | Description | UniProt
A B | proto-oncogene vav | VAV_HUMAN 189-565
C D | ras-related C3 botulinum toxin substrate 1 precursor | RAC1_HUMAN 1-177
Non-standard residues in 3BJI.pdb #2
---
ZN — zinc ion
> select #2/A
2974 atoms, 2991 bonds, 8 pseudobonds, 409 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/D
1211 atoms, 1229 bonds, 172 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> matchmaker #2/B 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 VAVtoSOS 2e.pdb, chain A (#1) with 3BJI.pdb, chain B (#2), sequence
alignment score = 396.2
RMSD between 134 pruned atom pairs is 1.045 angstroms; (across all 314 pairs:
25.295)
> ui tool show Matchmaker
> matchmaker #2/C to #1/C 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 VAVtoSOS 2e.pdb, chain C (#1) with 3BJI.pdb, chain C (#2), sequence
alignment score = 898.4
RMSD between 158 pruned atom pairs is 0.850 angstroms; (across all 177 pairs:
1.547)
> select #1/C
2583 atoms, 2613 bonds, 177 residues, 1 model selected
> select add #2/C
3902 atoms, 3947 bonds, 368 residues, 2 models selected
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to VAVtoSOS 2e.pdb #1/C MET 1 CA because it is
missing heavy-atom bond partners
Not adding hydrogens to VAVtoSOS 2e.pdb #1/C GLN 2 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to VAVtoSOS 2e.pdb #1/C GLU 31 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to VAVtoSOS 2e.pdb #1/C ILE 33 CB because it is missing
heavy-atom bond partners
Not adding hydrogens to VAVtoSOS 2e.pdb #1/C LYS 49 CB because it is missing
heavy-atom bond partners
14 messages similar to the above omitted
Skipped 18 atom(s) with bad connectivities; see log for details
Not adding hydrogens to 3BJI.pdb #2/B LYS 208 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to 3BJI.pdb #2/B LYS 222 CG because it is missing heavy-
atom bond partners
Not adding hydrogens to 3BJI.pdb #2/B ARG 226 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 3BJI.pdb #2/B ARG 245 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to 3BJI.pdb #2/B LYS 252 CG because it is missing heavy-
atom bond partners
54 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3BJI.pdb #2/B GLU 415 OE2; 3BJI.pdb #2/B ARG 489 NE
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: VAVtoSOS 2e.pdb #1/A GLN
189, VAVtoSOS 2e.pdb #1/C MET 1, VAVtoSOS 2e.pdb #1/A GLN 189
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #1/A ASN 583,
VAVtoSOS 2e.pdb #1/C LEU 177, VAVtoSOS 2e.pdb #1/A ASN 583
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 OXT
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY
279 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 OXT
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY
279 OXT
13 messages similar to the above omitted
550 hydrogen bonds
Termini for 3BJI.pdb (#2) chain B determined from SEQRES records
Termini for 3BJI.pdb (#2) chain C determined from SEQRES records
Chain-initial residues that are actual N termini: 3BJI.pdb #2/B MET 189,
3BJI.pdb #2/C MET 1
Chain-initial residues that are not actual N termini: 3BJI.pdb #2/B ASN 464,
3BJI.pdb #2/B GLN 480
Chain-final residues that are actual C termini: 3BJI.pdb #2/B GLY 566,
3BJI.pdb #2/C LEU 177
Chain-final residues that are not actual C termini: 3BJI.pdb #2/B ASP 457,
3BJI.pdb #2/B GLU 475
Missing OXT added to C-terminal residue 3BJI.pdb #2/B GLY 566
Missing OXT added to C-terminal residue 3BJI.pdb #2/C LEU 177
513 hydrogen bonds
Adding 'H' to 3BJI.pdb #2/B ASN 464
Adding 'H' to 3BJI.pdb #2/B GLN 480
3BJI.pdb #2/B ASP 457 is not terminus, removing H atom from 'C'
3BJI.pdb #2/B GLU 475 is not terminus, removing H atom from 'C'
4072 hydrogens added
> ui tool show Matchmaker
> select add sel : ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #2/B
Alignment identifier is 2/B
> interfaces #1
1 buried areas: A C 1482
> interfaces #2
1 buried areas: B C 1354
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/VAVtoSOS 2e.pdb" format 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
> 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
> hide surfaces
> addh
Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1
---
warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy-
atom bond partners
Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond
partners
14 messages similar to the above omitted
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 ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor /A ASN 223 O
13 messages similar to the above omitted
550 hydrogen bonds
0 hydrogens added
> swapaa /A:223 asn
Using Dunbrack library
/A ASN 223: phi -140.8, psi 26.7 trans
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
Skipped 70 atom(s) with bad connectivities; see log for details
Applying ASN rotamer (chi angles: -163.3 -54.4) to /A ASN 223
> addh
Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1
---
warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy-
atom bond partners
Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond
partners
14 messages similar to the above omitted
Skipped 17 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 GLY 279 OXT
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 OXT
Skipping possible acceptor with bad geometry: /A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor /A GLY 279 O
12 messages similar to the above omitted
551 hydrogen bonds
4 hydrogens added
> swapaa /A:279 gly
Using Dunbrack library
Swapping /A GLY 279 to GLY
> addh
Summary of feedback from adding hydrogens to VAVtoSOS 2e.pdb #1
---
warnings | Not adding hydrogens to /C MET 1 CA because it is missing heavy-
atom bond partners
Not adding hydrogens to /C GLN 2 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C GLU 31 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ILE 33 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C LYS 49 CB because it is missing heavy-atom bond
partners
14 messages similar to the above omitted
Skipped 17 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 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
12 messages similar to the above omitted
551 hydrogen bonds
3 hydrogens added
> show surfaces
> 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
> hide surfaces
> show surfaces
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
/A LYS 214 O
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for VAVtoSOS 2e.pdb_A SES surface #1.1: minimum, -22.41, mean
-1.75, maximum 15.42
Coulombic values for VAVtoSOS 2e.pdb_C SES surface #1.2: minimum, -14.81, mean
-0.22, maximum 9.43
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> select /C
2639 atoms, 2669 bonds, 177 residues, 1 model selected
> select /A
6240 atoms, 6299 bonds, 386 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Alphafold models/SOS1-AF-Q07889.pdb"
SOS1-AF-Q07889.pdb title:
Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
[more info...]
Chain information for SOS1-AF-Q07889.pdb #2
---
Chain | Description | UniProt
A | son of sevenless homolog 1 | SOS1_HUMAN 1-1333
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/C
Alignment identifier is 1/C
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:1040-1041
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:1040-1333
2241 atoms, 2331 bonds, 294 residues, 1 model selected
> cartoon hide sel
> select clear
> select #2/A:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:554-565
100 atoms, 99 bonds, 12 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2/A & sel 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 VAVtoSOS 2e.pdb, chain A (#1) with SOS1-AF-Q07889.pdb, chain A
(#2), sequence alignment score = 61.6
RMSD between 12 pruned atom pairs is 0.349 angstroms; (across all 12 pairs:
0.349)
> select #2/A:565
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:271-565
2380 atoms, 2424 bonds, 295 residues, 1 model selected
> cartoon hide sel
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-315
2556 atoms, 2610 bonds, 315 residues, 1 model selected
> cartoon hide sel
> select #2/A:563@CA
1 atom, 1 residue, 1 model selected
> cofr sel
No displayed objects specified.
> select #1/A:563@CA
1 atom, 1 residue, 1 model selected
> cofr sel
> ui mousemode right zoom
> select add #1
8879 atoms, 8968 bonds, 563 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.70271,-0.27973,0.65418,-92.749,0.51877,0.8307,-0.20204,54.743,-0.48691,0.48134,0.72886,1.1474
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.70271,-0.27973,0.65418,-120.91,0.51877,0.8307,-0.20204,77.907,-0.48691,0.48134,0.72886,-7.8518
> roll x 2 180
> cofr sel
> roll x 1 60
> roll x 1 300
> roll x 1 90
> show sel surfaces
> hide #!1 models
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warning | Skipped 17 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: VAVtoSOS 2e.pdb #1/A GLN
189, VAVtoSOS 2e.pdb #1/C MET 1, VAVtoSOS 2e.pdb #1/A GLN 189
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: VAVtoSOS 2e.pdb #1/A ASN 583,
VAVtoSOS 2e.pdb #1/C LEU 177, VAVtoSOS 2e.pdb #1/A ASN 583
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 OXT
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A GLY 279 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A GLY
279 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 O
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 O
Skipping possible acceptor with bad geometry: VAVtoSOS 2e.pdb #1/A ASN 223 OXT
Wrong number of grandchild atoms for phi/psi acceptor VAVtoSOS 2e.pdb #1/A ASN
223 OXT
12 messages similar to the above omitted
565 hydrogen bonds
Termini for SOS1-AF-Q07889.pdb (#2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini: SOS1-AF-Q07889.pdb #2/A MET
1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: SOS1-AF-Q07889.pdb #2/A SER
1333
Chain-final residues that are not actual C termini:
1018 hydrogen bonds
10869 hydrogens added
Drag select of 474 residues
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for SOS1-AF-Q07889.pdb_A SES surface #2.1: minimum, -18.25,
mean -0.78, maximum 27.88
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> select add #1
16908 atoms, 9129 bonds, 1037 residues, 3 models selected
> select subtract #1
7868 atoms, 474 residues, 4 models selected
> show #!1 models
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 4n.pdb"
Chain information for SPTBN2 working 4n.pdb #3
---
Chain | Description
A B C D F G | No description available
H | No description available
J | No description available
K | No description available
Q | No description available
b | No description available
> select #2/A:1085
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:1085
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:819
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:819-864
786 atoms, 791 bonds, 46 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3/H to #2/A & sel 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 SOS1-AF-Q07889.pdb, chain A (#2) with SPTBN2 working 4n.pdb, chain
H (#3), sequence alignment score = 242.8
RMSD between 46 pruned atom pairs is 0.746 angstroms; (across all 46 pairs:
0.746)
> hide sel atoms
> select
98252 atoms, 99312 bonds, 10 pseudobonds, 6212 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select #2/A:1289-1333
705 atoms, 720 bonds, 45 residues, 1 model selected
> select #2/A:1040-1333
4434 atoms, 4524 bonds, 294 residues, 1 model selected
> cartoon hide (#!2 & sel)
> select #2/A:564-565
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #2/A:271-565
4737 atoms, 4781 bonds, 295 residues, 1 model selected
> cartoon hide (#!2 & sel)
> select #2/A:313-314
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #2/A:138-314
2837 atoms, 2865 bonds, 177 residues, 1 model selected
> select #2/A:93
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:1-93
1476 atoms, 1493 bonds, 93 residues, 1 model selected
> select #2/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:1-246
4024 atoms, 4064 bonds, 246 residues, 1 model selected
> cartoon hide (#!2 & sel)
> select #2/A:566
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:271-566
4754 atoms, 4798 bonds, 296 residues, 1 model selected
> select clear
> select #2/A:566
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:271-566
4754 atoms, 4798 bonds, 296 residues, 1 model selected
> cartoon hide (#!2 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #3/H
Alignment identifier is 3/H
> select #3/H:520-565
738 atoms, 741 bonds, 46 residues, 1 model selected
> select #3/H:201-565
5911 atoms, 5966 bonds, 365 residues, 1 model selected
> cartoon hide sel
> select clear
> select #2/A
21448 atoms, 21723 bonds, 1333 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> view matrix models
> #2,-0.16721,0.025947,0.98558,-73.706,0.98583,0.018113,0.16677,74.81,-0.013525,0.9995,-0.028608,160.35
> select #1/A
6251 atoms, 6310 bonds, 386 residues, 1 model selected
> hide sel surfaces
> select #3/Q
2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> close #2
> select #3/H:519-565
760 atoms, 763 bonds, 47 residues, 1 model selected
> select #3/H:201-565
5911 atoms, 5966 bonds, 365 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> combine #1,3 name SOS-RacGEF
Remapping chain ID 'A' in SPTBN2 working 4n.pdb #3 to 'E'
Remapping chain ID 'C' in SPTBN2 working 4n.pdb #3 to 'I'
> close #1-2
> close session
> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 7g.pdb"
Chain information for SPTBN2 working 7g.pdb #1
---
Chain | Description
B C D E F | No description available
J | No description available
K | No description available
Q | No description available
S | No description available
> select ::name="ADP"
195 atoms, 205 bonds, 5 residues, 1 model selected
> color sel byelement
> select clear
> select ::name="ADP"
195 atoms, 205 bonds, 5 residues, 1 model selected
> show sel atoms
> select clear
> 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 "Show Sequence Viewer"
> sequence chain #1/S
Alignment identifier is 1/S
> select #1/S:570
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/S:565-570
108 atoms, 108 bonds, 6 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2/A to #1/S 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 7g.pdb, chain S (#1) with VAVtoSOS 2e.pdb, chain A
(#2), sequence alignment score = 117
RMSD between 8 pruned atom pairs is 1.292 angstroms; (across all 276 pairs:
36.428)
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:563
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:563-569
117 atoms, 117 bonds, 7 residues, 1 model selected
> select #1/S:570
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/S:565-570
108 atoms, 108 bonds, 6 residues, 1 model selected
> name frozen temp sel
> select #2/A:569
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:564-569
102 atoms, 102 bonds, 6 residues, 1 model selected
> select add temp
210 atoms, 210 bonds, 12 residues, 2 models selected
> matchmaker #2/A & sel to #1/S & sel 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 7g.pdb, chain S (#1) with VAVtoSOS 2e.pdb, chain A
(#2), sequence alignment score = 24.2
RMSD between 5 pruned atom pairs is 0.794 angstroms; (across all 5 pairs:
0.794)
> select #1/S
8017 atoms, 8116 bonds, 483 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select add #2
8835 atoms, 8924 bonds, 563 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.81869,0.30503,0.48652,-105.62,-0.32525,-0.94456,0.044877,60.514,0.47324,-0.1215,0.87251,-275.68
> undo
> view matrix models
> #2,-0.33213,0.84204,-0.42503,19.323,-0.92921,-0.21469,0.30078,-30.599,0.16202,0.49484,0.85374,-311.62
> view matrix models
> #2,-0.17531,0.79237,-0.58431,50.14,-0.96584,-0.023367,0.2581,-34.351,0.19086,0.60959,0.7694,-303.58
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.17531,0.79237,-0.58431,95.476,-0.96584,-0.023367,0.2581,-65.593,0.19086,0.60959,0.7694,-309.48
> open /Users/tmckeithan/Downloads/Chimera/PDB/6ZNL.pdb
6ZNL.pdb title:
Cryo-em structure of the dynactin complex [more info...]
Chain information for 6ZNL.pdb #3
---
Chain | Description | UniProt
A B C D E F G I | ARP1 actin related protein 1 homolog A | F2Z5G5_PIG 1-376
H | β-actin | ACTB_PIG 1-375
J | ARP11 | I3LHK5_PIG 1-417
K | capping protein (actin filament) muscle Z-line, α 1 | A0PFK5_PIG 1-286
L | F-actin capping protein β subunit | A9XFX6_PIG 1-272
M N m n | dynactin subunit 2 |
O o | dynactin subunit 3 isoform 1 | F1SEC0_PIG 1-186
U | dynactin 6 | D0G6S1_PIG 1-190
V | dynactin subunit 5 |
Y | dynactin subunit 4 |
Z z | dynactin subunit 1 |
Non-standard residues in 6ZNL.pdb #3
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
ZN — zinc ion
> close #3
> open /Users/tmckeithan/Downloads/Chimera/PDB/8DNH.pdb
8DNH.pdb title:
Cryo-em structure of nonmuscle β-actin [more info...]
Chain information for 8DNH.pdb #3
---
Chain | Description | UniProt
A B C D | actin, cytoplasmic 1, N-terminally processed | ACTB_HUMAN 1-374
Non-standard residues in 8DNH.pdb #3
---
ACE — acetyl group
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> ui tool show Matchmaker
> matchmaker #3/A to #1/B 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 7g.pdb, chain B (#1) with 8DNH.pdb, chain A (#3),
sequence alignment score = 1845.7
RMSD between 263 pruned atom pairs is 1.168 angstroms; (across all 374 pairs:
2.458)
> matchmaker #3/A to #1/D 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 7g.pdb, chain D (#1) with 8DNH.pdb, chain A (#3),
sequence alignment score = 1823.5
RMSD between 224 pruned atom pairs is 1.340 angstroms; (across all 374 pairs:
2.714)
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8.pdb"
> ui mousemode right zoom
> show sel atoms
> style sel sphere
Changed 8835 atom styles
> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SPTBN2 working 8.cxs"
> select
74563 atoms, 75470 bonds, 13 pseudobonds, 5520 residues, 5 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select #1/S:586-588,601-604,947-950,953-956
272 atoms, 269 bonds, 15 residues, 1 model selected
> select add #2
9107 atoms, 9193 bonds, 578 residues, 2 models selected
> select sel : ui tool show "Show Sequence Viewer"
> sequence chain #1/S
Destroying pre-existing alignment with identifier 1/S
Alignment identifier is 1/S
> sequence chain #1/J
Alignment identifier is 1/J
> sequence chain #1/K
Alignment identifier is 1/K
> sequence chain #1/Q
Alignment identifier is 1/Q
> select clear
> select #2/A
6252 atoms, 6311 bonds, 386 residues, 1 model selected
> select sel : select add #1
60614 atoms, 61233 bonds, 9 pseudobonds, 3865 residues, 3 models selected
> select subtract #1
6682 atoms, 6739 bonds, 416 residues, 1 model selected
> select add #2
8835 atoms, 8924 bonds, 563 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> select sel : undo
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99927,0.033374,0.018352,2.1816,-0.033789,0.99917,0.022784,6.2974,-0.017577,-0.023387,0.99957,1.8691,#2,-0.20392,0.8022,-0.56115,89.719,-0.95476,-0.036233,0.29516,-69.519,0.21644,0.59595,0.7733,-307.62
> undo
> select add #1
62767 atoms, 63418 bonds, 9 pseudobonds, 4012 residues, 3 models selected
> select subtract #1
8835 atoms, 8924 bonds, 563 residues, 1 model selected
> view matrix models
> #2,-0.12312,0.77457,-0.62039,102.93,-0.97518,0.021485,0.22035,-62.423,0.18401,0.63212,0.7527,-308.28
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.12312,0.77457,-0.62039,105.45,-0.97518,0.021485,0.22035,-62.22,0.18401,0.63212,0.7527,-308.29
> view matrix models
> #2,-0.12312,0.77457,-0.62039,105.25,-0.97518,0.021485,0.22035,-61.883,0.18401,0.63212,0.7527,-308.73
> select sel : view matrix models
> #1,1,0,0,2.5099,0,1,0,-5.5645,0,0,1,5.9637,#2,-0.12312,0.77457,-0.62039,107.76,-0.97518,0.021485,0.22035,-67.448,0.18401,0.63212,0.7527,-302.77
> undo
> ui mousemode right zoom
> select add #1
62767 atoms, 63418 bonds, 9 pseudobonds, 4012 residues, 3 models selected
> select subtract #1
8835 atoms, 8924 bonds, 563 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.12312,0.77457,-0.62039,104.94,-0.97518,0.021485,0.22035,-59.617,0.18401,0.63212,0.7527,-307.1
> ui mousemode right zoom
> select sel : select #3/A
2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected
> select clear
> select #3/A
2949 atoms, 3013 bonds, 1 pseudobond, 377 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select #2/A:582-583
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #2/A:567-583
254 atoms, 257 bonds, 17 residues, 1 model selected
> select #2/A:564-583
312 atoms, 315 bonds, 20 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 5097 residues
> select add ::name="ACE"::name="ADP"::name="GTP"::name="MG"
71302 atoms, 369 bonds, 10 pseudobonds, 5123 residues, 5 models selected
> cartoon hide (#2#!1,3 & sel)
> select ~sel
Nothing selected
> cartoon
> select ~sel
71302 atoms, 72141 bonds, 12 pseudobonds, 5123 residues, 5 models selected
> select ~sel
Nothing selected
> combine #1,2,3 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'
> 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
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