ChimeraX bug report submission

[tmckeith@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
I was trying to combine two different versions of the same protein and inadvertently left some duplicate sequences. When I tried to delete one of the duplicate residues, the program crashed. Hope that helped.
Fatal Python error: Segmentation fault

Thread 0x0000000310e4b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000200afb240 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 107 in _make_ribbon_graphics
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 600 in compute_ribbons
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 667 in _create_ribbon_graphics
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 357 in update_graphics_if_needed
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1891 in _update_graphics_if_needed
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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, chimerax.pdb_lib._load_libs, chimerax.map._map, 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.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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, 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, numpy.linalg.lapack_lite, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 132)


{"app_name":"ChimeraX","timestamp":"2024-04-01 00:42:24.00 -0700","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"36A1E742-67AB-4B5C-8850-BFB9C61F4CCD"}
{
  "uptime" : 630000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 1248,
  "osVersion" : {
    "train" : "macOS 14.2.1",
    "build" : "23C71",
    "releaseType" : "User"
  },
  "captureTime" : "2024-04-01 00:42:20.9494 -0700",
  "codeSigningMonitor" : 1,
  "incident" : "36A1E742-67AB-4B5C-8850-BFB9C61F4CCD",
  "pid" : 21873,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-03-29 00:29:11.0360 -0700",
  "procStartAbsTime" : 11613163313908,
  "procExitAbsTime" : 15272794284039,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"A3A24E3E-6232-5DE6-A66A-3508864FEE6F","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D7658540-E066-2866-40CA-0AAADB07EF70",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 6001,
  "sleepWakeUUID" : "41497BE0-CDC8-438E-983F-1BFF3DFD5BFA",
  "sip" : "enabled",
  "vmRegionInfo" : "0x210 is not in any region.  Bytes before following region: 140722925305328\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9bf98000-7ffcc49b0000 [650.1M] r-x\/r-x SM=COW  ...t_id=3baf4017",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000210","rawCodes":[1,528],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000210"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":21873},
  "vmregioninfo" : "0x210 is not in any region.  Bytes before following region: 140722925305328\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9bf98000-7ffcc49b0000 [650.1M] r-x\/r-x SM=COW  ...t_id=3baf4017",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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}
===== 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: 1.7.1 (2024-01-23)  
© 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/Working models/RacGEF working1h.pdb" format pdb

Chain information for RacGEF working1h.pdb #1  
---  
Chain | Description  
C D F H I J L M | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> set bgColor white

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> interfaces #1 areaCutoff 20

30 buried areas: R O 2213, R G 2211, F K 1724, C J 1274, F D 1246, C H 1177, F
M 1174, H L 1166, O Q 1094, R Q 1081, I D 1073, F C 699, O K 675, D K 614, F J
544, C D 522, J M 493, H D 492, O E 480, O D 478, O F 462, H I 452, F E 397, C
K 396, C E 321, D E 320, I L 310, E K 300, R D 298, H E 24  

> select ::name="4IP"

36 atoms, 36 bonds, 1 residue, 1 model selected  

> select ::name="4IP"

36 atoms, 36 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> interfaces #1 areaCutoff 20

30 buried areas: R O 2213, R G 2211, F K 1724, C J 1274, F D 1246, C H 1177, F
M 1174, H L 1166, O Q 1094, R Q 1081, I D 1073, F C 699, O K 675, D K 614, F J
544, C D 522, J M 493, H D 492, O E 480, O D 478, O F 462, H I 452, F E 397, C
K 396, C E 321, D E 320, I L 310, E K 300, R D 298, H E 24  

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> select /E

2637 atoms, 2665 bonds, 166 residues, 1 model selected  

> show sel cartoons

> hide 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

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:160-165

93 atoms, 93 bonds, 6 residues, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:152-165

211 atoms, 211 bonds, 14 residues, 1 model selected  

> select /E:151

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select /E:0-151

2426 atoms, 2453 bonds, 152 residues, 1 model selected  

> show sel atoms

> isolde sim start /E

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for RacGEF working1h.pdb  
---  
Chain | Description  
1.2/C 1.2/D 1.2/F 1.2/H 1.2/I 1.2/J 1.2/L 1.2/M | No description available  
1.2/E | No description available  
1.2/G | No description available  
1.2/K | No description available  
1.2/O | No description available  
1.2/Q | No description available  
1.2/R | 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  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select

74199 atoms, 74989 bonds, 12 pseudobonds, 4715 residues, 18 models selected  

> show sel cartoons

> isolde sim pause

> select clear

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:164-165

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:153-165

197 atoms, 197 bonds, 13 residues, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug selection"

> isolde sim resume

> select

74199 atoms, 74989 bonds, 12 pseudobonds, 4715 residues, 18 models selected  

> hide sel cartoons

> select clear

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:163-165

46 atoms, 45 bonds, 3 residues, 1 model selected  

> ui mousemode right "isolde tug atom"

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select /F

5848 atoms, 5912 bonds, 1 pseudobond, 377 residues, 2 models selected  

> select /E

2637 atoms, 2665 bonds, 166 residues, 1 model selected  

> style sel sphere

Changed 2637 atom styles  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:160

24 atoms, 24 bonds, 1 residue, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:160-165

93 atoms, 93 bonds, 6 residues, 1 model selected  

> 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

> color S yellow atoms

> color P purple atoms

> hide H atoms

> show sel atoms

> show (#!1.2 & sel) target ab

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1i.pdb"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1i.pdb" format pdb

Chain information for RacGEF working1i.pdb #1  
---  
Chain | Description  
C D F H I J L M | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel red target apf

> select clear

> interfaces #1 areaCutoff 20

29 buried areas: R O 2213, R G 2211, F K 1730, C J 1274, F D 1246, C H 1177, F
M 1174, H L 1166, O Q 1094, R Q 1081, I D 1073, F C 699, O K 673, D K 614, F J
544, C D 522, J M 493, H D 492, O E 489, O D 477, O F 459, H I 452, F E 412, C
K 396, E K 327, I L 310, C E 303, R D 298, D E 285  

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /E:165

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select /R

9136 atoms, 9223 bonds, 564 residues, 1 model selected  

> select /R

9136 atoms, 9223 bonds, 564 residues, 1 model selected  

> hide sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /O

Alignment identifier is 1/O  

> select /E

2637 atoms, 2665 bonds, 166 residues, 1 model selected  

> hide sel atoms

> combine /C,K name K2

> ui tool show Matchmaker

> select clear

> select add #2

74199 atoms, 74989 bonds, 12 pseudobonds, 4715 residues, 2 models selected  

> select subtract #2/C

68352 atoms, 69078 bonds, 11 pseudobonds, 4338 residues, 2 models selected  

> select subtract #2/K

66159 atoms, 66870 bonds, 11 pseudobonds, 4197 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> ui tool show Matchmaker

> matchmaker #2/C 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 RacGEF working1i.pdb, chain D (#1) with K2, chain C (#2), sequence
alignment score = 1843.3  
RMSD between 204 pruned atom pairs is 1.175 angstroms; (across all 374 pairs:
3.061)  
  

> select #1/E

2637 atoms, 2665 bonds, 166 residues, 1 model selected  

> show sel cartoons

> matchmaker #2/C to #1/F 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 RacGEF working1i.pdb, chain F (#1) with K2, chain C (#2), sequence
alignment score = 1791.7  
RMSD between 252 pruned atom pairs is 1.233 angstroms; (across all 374 pairs:
2.046)  
  

> show sel atoms

> hide #!2 models

> show #!2 models

> matchmaker #2/C to #1/I 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 RacGEF working1i.pdb, chain I (#1) with K2, chain C (#2), sequence
alignment score = 1809.7  
RMSD between 289 pruned atom pairs is 1.066 angstroms; (across all 374 pairs:
1.772)  
  

> matchmaker #2/C to #1/F 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 RacGEF working1i.pdb, chain F (#1) with K2, chain C (#2), sequence
alignment score = 1791.7  
RMSD between 252 pruned atom pairs is 1.233 angstroms; (across all 374 pairs:
2.046)  
  

> hide sel atoms

> hide sel cartoons

> show sel atoms

> select clear

> matchmaker #2/C 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 RacGEF working1i.pdb, chain D (#1) with K2, chain C (#2), sequence
alignment score = 1843.3  
RMSD between 204 pruned atom pairs is 1.175 angstroms; (across all 374 pairs:
3.061)  
  

> select #1/E

2637 atoms, 2665 bonds, 166 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #2/K

2193 atoms, 2208 bonds, 141 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #1/G:15@CA

1 atom, 1 residue, 1 model selected  

> select #1/E

2637 atoms, 2665 bonds, 166 residues, 1 model selected  

> hide sel cartoons

> select clear

> matchmaker #2/C to #1/F 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 RacGEF working1i.pdb, chain F (#1) with K2, chain C (#2), sequence
alignment score = 1791.7  
RMSD between 252 pruned atom pairs is 1.233 angstroms; (across all 374 pairs:
2.046)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/K

Alignment identifier is 1/K  

> select #1/K:802

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/K:802-822

274 atoms, 275 bonds, 21 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #2/K

Alignment identifier is 2/K  

> select #2/K:803

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2/K:803-822

259 atoms, 260 bonds, 20 residues, 1 model selected  

> show sel atoms

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1i.pdb" format pdb

Chain information for RacGEF working1i.pdb #1  
---  
Chain | Description  
C D F H I J L M | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/SOS-DHa.pdb" format pdb

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Working models/SOS-DHa.pdb  
---  
warnings | Cannot find LINK/SSBOND residue SER (1263 )  
Cannot find LINK/SSBOND residue MSE (1264 )  
Cannot find LINK/SSBOND residue HIS (1333 )  
Cannot find LINK/SSBOND residue MSE (1334 )  
Cannot find LINK/SSBOND residue LEU (1062 )  
35 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 ASP A 1037 GLN A
1071 1 35  
Start residue of secondary structure not found: HELIX 2 2 GLN A 1078 PHE A
1085 1 8  
Start residue of secondary structure not found: HELIX 3 3 LEU A 1088 ARG A
1107 1 20  
Start residue of secondary structure not found: HELIX 4 4 LEU A 1112 LYS A
1114 1 3  
Start residue of secondary structure not found: HELIX 5 5 VAL A 1118 TYR A
1135 1 18  
7 messages similar to the above omitted  
  
SOS-DHa.pdb title:  
Crystal structure of RAC1 In complex with the guanine nucleotide exchange
region of TIAM1 [more info...]  
  
Chain information for SOS-DHa.pdb  
---  
Chain | Description | UniProt  
1.1/A | T-lymphoma invasion and metastasis inducing protein 1 | TIAM1_MOUSE
1030-1406  
1.2/A | T-lymphoma invasion and metastasis inducing protein 1 | TIAM1_MOUSE
1030-1406  
1.2/B | ras-related C3 botulinum toxin substrate | RAC1_HUMAN 1-177  
  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.cxs"

opened ChimeraX session  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.cxs"

opened ChimeraX session  

> select ::name="4IP"

36 atoms, 36 bonds, 1 residue, 1 model selected  

> view sel

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1g.cxs" format session

opened ChimeraX session  

> show #2.3 models

> hide #1.3,5#!1.1,4,6-8,10-11 target m

> hide #!6 models

> hide #1.12 models

> show #2.4 models

> show #1.13#2.1,3-4#!1.14#!8.2 cartoons

> ui tool show Matchmaker

> matchmaker #2.4/D to #1.12/O 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 RacGEF working1b.pdb O, chain O (#1.12) with SOS1-AF-split.pdb D,
chain D (#2.4), sequence alignment score = 2416  
RMSD between 197 pruned atom pairs is 1.301 angstroms; (across all 483 pairs:
4.276)  
  

> show #1.12 models

> hide #1.12-13#2.1,3-4#!1.14#!8.2 atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #2.4/D

Alignment identifier is 2.4/D  

> select #2.4/D:819

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.4/D:819

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.4/D:819-864

385 atoms, 390 bonds, 46 residues, 1 model selected  

> matchmaker #2.4/D & sel to #1.12/O 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 RacGEF working1b.pdb O, chain O (#1.12) with SOS1-AF-split.pdb D,
chain D (#2.4), sequence alignment score = 239.8  
RMSD between 46 pruned atom pairs is 0.632 angstroms; (across all 46 pairs:
0.632)  
  

> select #2.1/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:1-23

196 atoms, 202 bonds, 23 residues, 1 model selected  
Drag select of 143 residues  

> select clear

Drag select of 59 residues  

> show sel atoms

> style sel stick

Changed 644 atom styles  

> select

95223 atoms, 96417 bonds, 13 pseudobonds, 6996 residues, 56 models selected  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="MSE"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

94465 atoms, 95650 bonds, 6929 residues, 22 models selected  

> hide sel & #1.12#2.1,3-4#!1.14#!8.2 atoms

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.pdb"

Chain information for RacGEF working1h.pdb #1  
---  
Chain | Description  
C D F H I J L M | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select /Q

2653 atoms, 2672 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.cxs"

opened ChimeraX session  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.pdb" format pdb

Chain information for RacGEF working1h.pdb #1  
---  
Chain | Description  
C D F H I J L M | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> select ::name="4IP"

36 atoms, 36 bonds, 1 residue, 1 model selected  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.cxs" format session

opened ChimeraX session  

> interfaces #1 areaCutoff 20

30 buried areas: R O 2401, R G 2318, F K 1861, C J 1315, F D 1285, F M 1219, C
H 1216, H L 1210, O Q 1179, R Q 1177, I D 1131, F C 766, O K 748, D K 672, F J
587, C D 585, O D 536, H D 533, J M 525, O E 524, O F 498, H I 491, C K 438, F
E 419, I L 355, C E 350, R D 347, D E 333, E K 320, H E 27  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1g.cxs"

opened ChimeraX session  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1g.pdb"

> close #3

> close #5#4

> close #7

> close #2.2

> close #2.5

> close #8.2

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  

> close #8

Deleting atomic symmetry model...  

> combine 1,2,6 close true name working

Expected a keyword  

> combine #1,2,6 close true name working

Remapping chain ID 'C' in SOS1-AF-split.pdb C #2.3 to 'D'  
Remapping chain ID 'D' in SOS1-AF-split.pdb D #2.4 to 'K'  
Remapping chain ID 'D' in RacGEF working1b.pdb #6 to 'N'  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1g.pdb" relModel #1

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1g.pdb" format pdb

Chain information for RacGEF working1g.pdb #1  
---  
Chain | Description  
A | No description available  
C F H I J L M N | No description available  
D | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> split #1

Split RacGEF working1g.pdb (#1) into 17 models  
Chain information for RacGEF working1g.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for RacGEF working1g.pdb C #1.2  
---  
Chain | Description  
C | No description available  
  
Chain information for RacGEF working1g.pdb D #1.3  
---  
Chain | Description  
D | No description available  
  
Chain information for RacGEF working1g.pdb E #1.4  
---  
Chain | Description  
E | No description available  
  
Chain information for RacGEF working1g.pdb F #1.5  
---  
Chain | Description  
F | No description available  
  
Chain information for RacGEF working1g.pdb G #1.6  
---  
Chain | Description  
G | No description available  
  
Chain information for RacGEF working1g.pdb H #1.7  
---  
Chain | Description  
H | No description available  
  
Chain information for RacGEF working1g.pdb I #1.8  
---  
Chain | Description  
I | No description available  
  
Chain information for RacGEF working1g.pdb J #1.9  
---  
Chain | Description  
J | No description available  
  
Chain information for RacGEF working1g.pdb K #1.10  
---  
Chain | Description  
K | No description available  
  
Chain information for RacGEF working1g.pdb L #1.11  
---  
Chain | Description  
L | No description available  
  
Chain information for RacGEF working1g.pdb M #1.12  
---  
Chain | Description  
M | No description available  
  
Chain information for RacGEF working1g.pdb N #1.13  
---  
Chain | Description  
N | No description available  
  
Chain information for RacGEF working1g.pdb O #1.14  
---  
Chain | Description  
O | No description available  
  
Chain information for RacGEF working1g.pdb Q #1.16  
---  
Chain | Description  
Q | No description available  
  
Chain information for RacGEF working1g.pdb R #1.17  
---  
Chain | Description  
R | No description available  
  

> hide #1.1 models

> select add #1.1

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> show #1.1 models

> select subtract #1.1

Nothing selected  

> hide #!1.2 models

> show #!1.2 models

> close #1.3#1.2

> hide #1.4,6#!1.5,7-9 target m

> close #1.4,6#1.5,7-9

> close #1.11-12

> hide #!1.13 models

> show #!1.13 models

> close #1.13

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Alphafold models/SOS1-AF-split.pdb"

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Alphafold models/SOS1-AF-split.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 176 UNP Q07889 SOS1_HUMAN 1 1333  
  
SOS1-AF-split.pdb title:  
Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
[more info...]  
  
Chain information for SOS1-AF-split.pdb #2  
---  
Chain | Description  
A | son of sevenless homolog 1  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> split #2

Split SOS1-AF-split.pdb (#2) into 5 models  
Chain information for SOS1-AF-split.pdb A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for SOS1-AF-split.pdb B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for SOS1-AF-split.pdb C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for SOS1-AF-split.pdb D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for SOS1-AF-split.pdb E #2.5  
---  
Chain | Description  
E | No description available  
  

> close #2.5

> ui tool show Matchmaker

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A

Alignment identifier is 1.1/A  

> sequence chain #1.10/K

Alignment identifier is 1.10/K  

> sequence chain #1.14/O

Alignment identifier is 1.14/O  

> sequence chain #1.16/Q

Alignment identifier is 1.16/Q  

> sequence chain #1.17/R

Alignment identifier is 1.17/R  

> sequence chain #2.1/A

Alignment identifier is 2.1/A  

> select #1.14/O:819

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.14/O:819-864

786 atoms, 791 bonds, 46 residues, 1 model selected  

> matchmaker #2.4/D & sel to #1.14/O pairing ss

No molecules/chains to match specified  

> matchmaker #2.4/D to #1.14/O & 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 RacGEF working1g.pdb O, chain O (#1.14) with SOS1-AF-split.pdb D,
chain D (#2.4), sequence alignment score = 239.8  
RMSD between 46 pruned atom pairs is 0.632 angstroms; (across all 46 pairs:
0.632)  
  

> matchmaker #1.1/A to #1.17/R 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 RacGEF working1g.pdb R, chain R (#1.17) with RacGEF working1g.pdb
A, chain A (#1.1), sequence alignment score = 822.2  
RMSD between 99 pruned atom pairs is 1.129 angstroms; (across all 176 pairs:
9.119)  
  

> matchmaker #2.2/B to #1.17/R 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 RacGEF working1g.pdb R, chain R (#1.17) with SOS1-AF-split.pdb B,
chain B (#2.2), sequence alignment score = 1025.4  
RMSD between 34 pruned atom pairs is 1.097 angstroms; (across all 231 pairs:
19.032)  
  

> matchmaker #2.3/C to #1.17/R 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 RacGEF working1g.pdb R, chain R (#1.17) with SOS1-AF-split.pdb C,
chain C (#2.3), sequence alignment score = 786.4  
RMSD between 77 pruned atom pairs is 1.241 angstroms; (across all 157 pairs:
5.489)  
  

> hide #1.17 models

> hide #1.1 models

> show #1.1 models

> ui tool show "Side View"

> ui tool show Matchmaker

> matchmaker #2.1/A to #1.17/R 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 RacGEF working1g.pdb R, chain R (#1.17) with SOS1-AF-split.pdb A,
chain A (#2.1), sequence alignment score = 822.2  
RMSD between 99 pruned atom pairs is 1.129 angstroms; (across all 176 pairs:
9.119)  
  

> select clear

> view

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

Drag select of 124 atoms, 28 bonds  

> ui tool show "Show Sequence Viewer"

> sequence chain #2.1/A

Destroying pre-existing alignment with identifier 2.1/A  
Alignment identifier is 2.1/A  

> select up

277 atoms, 265 bonds, 25 residues, 5 models selected  

> select #2.1/A:151

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2.1/A:150-151

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #2.1/A:155

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #2.1/A:155

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide #1.10 models

> show #1.10 models

> hide #!1.16 models

> show #!1.16 models

> hide #2.2 models

> hide #2.4 models

> show #2.4 models

> hide #2.4 models

> show #2.4 models

> hide #1.14 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1.1/A

Destroying pre-existing alignment with identifier 1.1/A  
Alignment identifier is 1.1/A  

> sequence chain #1.10/K

Destroying pre-existing alignment with identifier 1.10/K  
Alignment identifier is 1.10/K  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.14/O

Alignment identifier is 1.14/O  

> hide #1.1 models

> hide #1.15 models

> hide #!1.16 models

> hide #2.1 models

> hide #2.3 models

> show #1.14 models

Drag select of 12007 atoms  

> hide sel atoms

> show sel cartoons

> select clear

> close #1.10

> show #1.1 models

> show #!1.16 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #1.1 models

> hide #2.1 models

> show #1.1 models

> show #2.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> close #1.1

> select add #2.1

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #2.1/A:176

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2.1/A:24-176

1230 atoms, 1252 bonds, 153 residues, 1 model selected  

> show sel atoms

> select clear

> select add #2.1

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2.1,0.17068,0.54934,-0.81798,318.84,-0.9487,0.31585,0.014162,343.48,0.26614,0.77361,0.57507,360.73

> ui mousemode right "rotate selected models"

> view matrix models
> #2.1,0.10598,0.56231,-0.82011,316.47,-0.95727,0.28088,0.06888,342.72,0.26908,0.77776,0.56805,360.89

> select clear

> select add #2.4

4003 atoms, 4102 bonds, 484 residues, 1 model selected  

> ui mousemode right zoom

> show sel atoms

> hide sel cartoons

> select clear

> hide #1.14 models

> select add #2.1

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> combine #2/A name HH2

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:24

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:24-176

1230 atoms, 1252 bonds, 153 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide #2.1 models

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-23

196 atoms, 202 bonds, 23 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 196 atom styles  

> select #3/A:18

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:18-20

34 atoms, 35 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 34 atom styles  

> select #3/A:21

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:21

4 atoms, 3 bonds, 1 residue, 1 model selected  

> cofr sel

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.72646,0.55151,0.41,277.31,-0.41402,-0.82742,0.37942,346.72,0.5485,0.10588,0.82942,360.98

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.72646,0.55151,0.41,297.17,-0.41402,-0.82742,0.37942,343.23,0.5485,0.10588,0.82942,360.05

> view matrix models
> #3,-0.72646,0.55151,0.41,297.09,-0.41402,-0.82742,0.37942,342.59,0.5485,0.10588,0.82942,359.52

> select #3/A:15

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:15

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> setattr sel r psi 100

Assigning psi attribute to 1 item  

> setattr sel r omega 180

Assigning omega attribute to 1 item  

> select clear

> select add #2.1

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> select clear

> select add #3

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> view matrix models
> #3,-0.72646,0.55151,0.41,305.49,-0.41402,-0.82742,0.37942,353.45,0.5485,0.10588,0.82942,368.37

> view matrix models
> #3,-0.72646,0.55151,0.41,306.78,-0.41402,-0.82742,0.37942,355.38,0.5485,0.10588,0.82942,369.95

> view matrix models
> #3,-0.72646,0.55151,0.41,304.37,-0.41402,-0.82742,0.37942,350.22,0.5485,0.10588,0.82942,365.66

> view matrix models
> #3,-0.72646,0.55151,0.41,299.25,-0.41402,-0.82742,0.37942,340.69,0.5485,0.10588,0.82942,357.76

> select #3/A:19

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:19

14 atoms, 15 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TRP rotLib Dunbrack

HH2 #3/A TRP 19: phi -109.3, psi -36.1 trans  
Changed 468 bond radii  

> select clear

> select add #2.1

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> select add #3

3284 atoms, 3378 bonds, 388 residues, 39 models selected  

> select subtract #2.1

1858 atoms, 1923 bonds, 212 residues, 38 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.60169,0.56869,0.56085,307.94,-0.51229,-0.8135,0.27528,334.5,0.6128,-0.12169,0.78081,356.56

> cofr sel

> view matrix models
> #3,-0.0011605,-0.040014,0.9992,334.15,-0.95571,-0.29401,-0.012884,316.81,0.29429,-0.95496,-0.0379,315.28

> view matrix models
> #3,-0.99512,-0.087469,-0.045593,268.42,0.060843,-0.90813,0.41425,364.62,-0.077638,0.40946,0.90902,331.18

> view matrix models
> #3,-0.57009,0.61068,-0.54961,296.79,-0.63597,-0.75153,-0.17537,323.6,-0.52014,0.24956,0.81681,304.04

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.57009,0.61068,-0.54961,294,-0.63597,-0.75153,-0.17537,331.14,-0.52014,0.24956,0.81681,308.23

> view matrix models
> #3,-0.57009,0.61068,-0.54961,297.48,-0.63597,-0.75153,-0.17537,330.31,-0.52014,0.24956,0.81681,316.07

> select #!3/A:19@CZ3

1 atom, 1 residue, 1 model selected  

> cofr sel

> roll z 180 1 models #3

> select add #3

1858 atoms, 1923 bonds, 212 residues, 38 models selected  

> view matrix models
> #3,-0.88787,-0.34582,-0.30346,266.38,-0.23952,0.91057,-0.33689,375.39,0.39282,-0.22643,-0.8913,335.58

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.896,-0.33912,-0.28666,266.28,-0.24114,0.91368,-0.32717,375.48,0.37287,-0.22402,-0.90043,334.47

> undo

> view matrix models
> #3,-0.81524,0.20603,-0.54124,276.95,0.34937,0.92033,-0.1759,408.43,0.46188,-0.33249,-0.82227,338.19

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.81524,0.20603,-0.54124,280.02,0.34937,0.92033,-0.1759,405.45,0.46188,-0.33249,-0.82227,337.18

> clashes #!3 & ~#!3/A:19 & ~solvent radius 0.075 reveal true restrict #3.1 &
> ~@c,ca,n

1042 clashes  

> swapaa #!3/A:19 TRP criteria 3 rotLib Dunbrack retain false

Using Dunbrack library  
HH2 #!3/A TRP 19: phi -109.3, psi -36.1 trans  
Applying TRP rotamer (chi angles: 60.9 -93.0) to HH2 #!3/A TRP 19  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.16/Q

Alignment identifier is 1.16/Q  

> select #1.16/Q:46

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1.16/Q:40-46

135 atoms, 135 bonds, 7 residues, 1 model selected  

> view matrix models #1.16,1,0,0,-0.15577,0,1,0,-0.49524,0,0,1,0.22752

> undo

> ui mousemode right zoom

> interfaces #1 areaCutoff 20

3 buried areas: #1.17/R #1.14/O 2215, #1.14/O #1.16/Q 1094, #1.17/R #1.16/Q
1081  

> show #1.14 models

> hide #2.4 models

> select clear

> select add #1.14

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> show sel atoms

> close #4

> hide #3 models

> show #3 models

> select #1.16/Q:40

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1.16/Q:40-46

135 atoms, 135 bonds, 7 residues, 1 model selected  

> select #3/A:20

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:20

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:18

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:18

9 atoms, 8 bonds, 1 residue, 1 model selected  

> swapaa #1/Q:64 tyr

Using Dunbrack library  
RacGEF working1g.pdb Q #1.16/Q ALA 64: phi -78.6, psi -7.7 trans  
Applying TYR rotamer (chi angles: -68.6 -18.1) to RacGEF working1g.pdb Q
#1.16/Q TYR 64  

> select #1.16/Q:64-65

25 atoms, 25 bonds, 2 residues, 1 model selected  

> select #1.16/Q:64-65

25 atoms, 25 bonds, 2 residues, 1 model selected  

> select #1.16/Q:64

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.16/Q:64

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.16/Q:71

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1.16/Q:71

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1.16/Q:73

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #1.16/Q:73

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #1.14/O:884-885

45 atoms, 45 bonds, 2 residues, 1 model selected  

> select #1.14/O:884-885

45 atoms, 45 bonds, 2 residues, 1 model selected  

> select #1.14/O:884

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #1.14/O:884

21 atoms, 21 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel TYR rotLib Dunbrack

RacGEF working1g.pdb O #1.14/O TYR 884: phi -63.4, psi -29.0 trans  
Changed 180 bond radii  

> swapaa #!1.14/O:884 TYR criteria 2 rotLib Dunbrack retain false

Using Dunbrack library  
RacGEF working1g.pdb O #!1.14/O TYR 884: phi -63.4, psi -29.0 trans  
Applying TYR rotamer (chi angles: 72.9 89.3) to RacGEF working1g.pdb O
#!1.14/O TYR 884  

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-23

196 atoms, 202 bonds, 23 residues, 1 model selected  

> select #3/A:24

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:24-176

1230 atoms, 1252 bonds, 153 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> combine #1/Q,O#3 close true name HH2

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #3/O

Alignment identifier is 3/O  

> sequence chain #3/Q

Alignment identifier is 3/Q  

> isolde sim start #3/A

> 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 #3 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  
Sim termination reason: None  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Skipped 4 atom(s) with bad connectivities; see log for details  
Skipped 6 atom(s) with bad connectivities; see log for details  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
No usable SEQRES records for RacGEF working1g.pdb R (#1.17) chain R; guessing
termini instead  
Chain-initial residues that are actual N termini: RacGEF working1g.pdb R
#1.17/R MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: RacGEF working1g.pdb R
#1.17/R GLU 564  
Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
GLY 280 O  
Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
#1.17/R GLY 280 O  
  
Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
GLY 280 OXT  
Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
#1.17/R GLY 280 OXT  
  
Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
GLY 280 O  
Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
#1.17/R GLY 280 O  
  
Skipping possible acceptor with bad geometry: RacGEF working1g.pdb R #1.17/R
GLY 280 OXT  
Wrong number of grandchild atoms for phi/psi acceptor RacGEF working1g.pdb R
#1.17/R GLY 280 OXT  
  
498 hydrogen bonds  
RacGEF working1g.pdb R #1.17/R GLU 564 is not terminus, removing H atom from
'C'  
No usable SEQRES records for SOS1-AF-split.pdb A (#2.1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: SOS1-AF-split.pdb A #2.1/A
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: SOS1-AF-split.pdb A #2.1/A
PHE 176  
158 hydrogen bonds  
SOS1-AF-split.pdb A #2.1/A PHE 176 is not terminus, removing H atom from 'C'  
No usable SEQRES records for SOS1-AF-split.pdb B (#2.2) chain B; guessing
termini instead  
Chain-initial residues that are actual N termini: SOS1-AF-split.pdb B #2.2/B
HIS 177  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: SOS1-AF-split.pdb B #2.2/B
PHE 407  
209 hydrogen bonds  
SOS1-AF-split.pdb B #2.2/B PHE 407 is not terminus, removing H atom from 'C'  
No usable SEQRES records for SOS1-AF-split.pdb C (#2.3) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: SOS1-AF-split.pdb C #2.3/C
TYR 408  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: SOS1-AF-split.pdb C #2.3/C
GLU 564  
128 hydrogen bonds  
SOS1-AF-split.pdb C #2.3/C GLU 564 is not terminus, removing H atom from 'C'  
No usable SEQRES records for SOS1-AF-split.pdb D (#2.4) chain D; guessing
termini instead  
Chain-initial residues that are actual N termini: SOS1-AF-split.pdb D #2.4/D
GLU 565  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: SOS1-AF-split.pdb D #2.4/D
GLY 1048  
467 hydrogen bonds  
SOS1-AF-split.pdb D #2.4/D GLY 1048 is not terminus, removing H atom from 'C'  
No usable SEQRES records for HH2 (#3.2) chain O; guessing termini instead  
No usable SEQRES records for HH2 (#3.2) chain Q; guessing termini instead  
No usable SEQRES records for HH2 (#3.2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: HH2 #3.2/Q MET 1, HH2 #3.2/A
MET 1  
Chain-initial residues that are not actual N termini: HH2 #3.2/O GLU 565  
Chain-final residues that are actual C termini: HH2 #3.2/O PRO 1047, HH2
#3.2/Q HIS 166  
Chain-final residues that are not actual C termini: HH2 #3.2/A LEU 23  
Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 OXT  
Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 OXT  
  
Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 O  
Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 O  
  
Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 OXT  
Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 OXT  
  
Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 O  
Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 O  
  
Skipping possible acceptor with bad geometry: HH2 #3.2/O GLU 565 OXT  
Wrong number of grandchild atoms for phi/psi acceptor HH2 #3.2/O GLU 565 OXT  
  
1 messages similar to the above omitted  
684 hydrogen bonds  
HH2 #3.2/A LEU 23 is not terminus, removing H atom from 'C'  
8792 hydrogens added  
  

> isolde sim start #3/A

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start #3/A,O,Q

ISOLDE: started sim  

> hide sel atoms

> show sel cartoons

> select #3.2/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> show sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #3.2/A

Alignment identifier is 3.2/A  

> show sel atoms

> select #3.2/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> style sel sphere

Changed 8016 atom styles  

> select #3.2/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> style sel sphere

Changed 2664 atom styles  

> select #3.2/A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3.2/A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3.2/A:14-15

29 atoms, 28 bonds, 2 residues, 1 model selected  

> select #3.2/A:1-15

244 atoms, 247 bonds, 15 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #3.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #3.2/A:8

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/A:8

21 atoms, 21 bonds, 1 residue, 1 model selected  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> select #3.2/O:799

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3.2/O:668-799

2231 atoms, 2260 bonds, 132 residues, 1 model selected  

> select #3.2/A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #3.2/A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #3.2/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #3.2/A:21-23

45 atoms, 44 bonds, 3 residues, 1 model selected  

> select #3.2/A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3.2/A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 24 atom styles  

> ui mousemode right "isolde tug atom"

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:19-20

48 atoms, 49 bonds, 2 residues, 1 model selected  

> select #3.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/Q:40

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3.2/Q:40-46

135 atoms, 135 bonds, 7 residues, 1 model selected  

> style sel stick

Changed 135 atom styles  

> style sel sphere

Changed 135 atom styles  

> select #3.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #3.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 19 atom styles  

> style sel sphere

Changed 19 atom styles  

> style sel sphere

Changed 19 atom styles  

> ui mousemode right "isolde tug selection"

> select #3.2/A:19-20

48 atoms, 49 bonds, 2 residues, 1 model selected  

> select #3.2/A:19-20

48 atoms, 49 bonds, 2 residues, 1 model selected  

> ui mousemode right "isolde tug atom"

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #3.2/A:18-20

70 atoms, 71 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 70 atom styles  

Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.  

> select #3.2/A:22-23

38 atoms, 37 bonds, 2 residues, 1 model selected  

> select #3.2/A:21-23

45 atoms, 44 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 45 atom styles  

> select #3.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #3.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 19 atom styles  

> style sel stick

Changed 17 atom styles  

> style sel stick

Changed 22 atom styles  

> style sel stick

Changed 14 atom styles  

> style sel stick

Changed 15 atom styles  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 21 residues in model #3.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/temp.pdb"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/temp.pdb" format pdb

Chain information for temp.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.7/A | No description available  
1.4/B | No description available  
1.5/C | No description available  
1.6/D | No description available  
1.7/O | No description available  
1.7/Q | No description available  
1.2/R | No description available  
  

> select add #1.1

36 atoms, 36 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #1.2

9136 atoms, 9223 bonds, 564 residues, 1 model selected  

> hide #1.3 models

> show #1.3 models

> ui tool show "Show Sequence Viewer"

> hide #1.2 models

> hide #1.4 models

> hide #1.5 models

> hide #1.3 models

> hide #1.6 models

> select add #1.3

12024 atoms, 12140 bonds, 740 residues, 2 models selected  

> select subtract #1.3

9136 atoms, 9223 bonds, 564 residues, 1 model selected  

> select #1.3/A#1.7/A

3271 atoms, 3306 bonds, 199 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.7/A

Alignment identifier is 1.7/A  

> show sel & #!1.7 atoms

> select #1.7/A:6

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1.7/A:1-6

99 atoms, 98 bonds, 6 residues, 1 model selected  

> select #1.7/A:7

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.7/A:7

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #1.7

11063 atoms, 11188 bonds, 4 pseudobonds, 674 residues, 2 models selected  

> isolde sim start #1.7

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for temp.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/O | No description available  
2.2/Q | No description available  
  
ISOLDE: started sim  

> isolde sim pause

> select #2.2/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> style sel sphere

Changed 8016 atom styles  

> select #2.2/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select #2.2/A:7

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:7

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug selection"

> 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 17 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/temp.pdb" format pdb

Chain information for temp.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.7/A | No description available  
1.4/B | No description available  
1.5/C | No description available  
1.6/D | No description available  
1.7/O | No description available  
1.7/Q | No description available  
1.2/R | No description available  
  

> hide #1.1-6 target m

> select #1.3/A

2888 atoms, 2917 bonds, 176 residues, 1 model selected  

> show #1.3 models

> select subtract #1.3

Nothing selected  

> hide #1.3 models

> select add #1.7

11063 atoms, 11188 bonds, 4 pseudobonds, 674 residues, 2 models selected  

> show sel atoms

> style sel sphere

Changed 11063 atom styles  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select #1.7/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1.7/A

Alignment identifier is 1.7/A  

> select #1.7/A:13

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.7/A:13

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.7/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> select intersect C

834 atoms, 660 bonds, 167 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel orange target apf

> select #1.7/A:17

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.7/A:1-17

268 atoms, 272 bonds, 17 residues, 1 model selected  

> select #1.7/A:1-17

268 atoms, 272 bonds, 17 residues, 1 model selected  

> style sel stick

Changed 268 atom styles  

> select #1.7/A:14

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1.7/A:14

15 atoms, 14 bonds, 1 residue, 1 model selected  

> isolde sim start #1.7

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for temp.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/O | No description available  
2.2/Q | No description available  
  
ISOLDE: started sim  

> isolde sim pause

> select intersect #2.2/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> style sel sphere

Changed 8016 atom styles  

> style sel sphere

Changed 8016 atom styles  

> style sel sphere

Changed 8016 atom styles  

> select intersect #2.2/Q

Nothing selected  

> select #2.2/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> style sel sphere

Changed 2664 atom styles  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #2.2/A

Alignment identifier is 2.2/A  

> sequence chain #2.2/O

Alignment identifier is 2.2/O  

> sequence chain #2.2/Q

Alignment identifier is 2.2/Q  

> select #2.2/Q:166

18 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:1-166

2619 atoms, 2638 bonds, 166 residues, 1 model selected  

> select clear

> select #2.2/Q:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:46

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:40-46

135 atoms, 135 bonds, 7 residues, 1 model selected  

> style sel stick

Changed 135 atom styles  

> select clear

> hide #!2.2 models

> show #!2.2 models

> select #2.2/A:15

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2.2/A:15

14 atoms, 13 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 14 atom styles  

> style sel sphere

Changed 14 atom styles  

> select #2.2/A:19-20

48 atoms, 49 bonds, 2 residues, 1 model selected  

> select #2.2/A:18-20

70 atoms, 71 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 70 atom styles  

> select #2.2/A:15

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2.2/A:15

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2.2/A:11

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2.2/A:11

20 atoms, 20 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug selection"

> isolde sim resume

> select #2.2/A:8

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2.2/A:8

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2.2/A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #2.2/A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> 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 #1.7

No atoms selected!  

> isolde sim start #2

ISOLDE: started sim  

> show sel atoms

> select #2.2/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> style sel sphere

Changed 8016 atom styles  

> select #2.2/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> style sel sphere

Changed 2664 atom styles  

> select clear

> select #2.2/Q:46

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:40-46

135 atoms, 135 bonds, 7 residues, 1 model selected  

> style sel stick

Changed 135 atom styles  

> select #2.2/A:18

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2.2/A:18-23

115 atoms, 116 bonds, 6 residues, 1 model selected  

> style sel sphere

Changed 115 atom styles  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug selection"

> select #2.2/A:11

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2.2/A:1-11

189 atoms, 192 bonds, 11 residues, 1 model selected  

> roll y -90 1

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:5

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2.2/A:1-5

80 atoms, 79 bonds, 5 residues, 1 model selected  

> select #2.2/A:8

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2.2/A:8

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:5

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2.2/A:1-5

80 atoms, 79 bonds, 5 residues, 1 model selected  

> select #2.2/A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #2.2/A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> ui mousemode right "isolde tug atom"

> select #2.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #2.2/A:18-20

70 atoms, 71 bonds, 3 residues, 1 model selected  

> style sel stick

Changed 70 atom styles  

> style sel sphere

Changed 70 atom styles  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select #2.2/Q:113

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:62-113

846 atoms, 853 bonds, 52 residues, 1 model selected  

> select clear

> select #2.2/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> show sel atoms

> select #2.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #2.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #2.2/A:9

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:9

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> style sel sphere

Changed 8016 atom styles  

> style sel sphere

Changed 8016 atom styles  

> select #2.2/A:9

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:9

15 atoms, 14 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 15 atom styles  

> select #2.2/Q:49

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/Q:35-49

240 atoms, 240 bonds, 15 residues, 1 model selected  

> select #2.2/A:15-16

24 atoms, 23 bonds, 2 residues, 1 model selected  

> select #2.2/A:1-16

254 atoms, 257 bonds, 16 residues, 1 model selected  

> select intersect backbone

97 atoms, 96 bonds, 16 residues, 1 model selected  

> style sel sphere

Changed 97 atom styles  

> select #2.2/Q:38

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2.2/Q:38-40

44 atoms, 44 bonds, 3 residues, 1 model selected  

> select #2.2/Q:46

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/Q:39-46

146 atoms, 146 bonds, 8 residues, 1 model selected  

> style sel sphere

Changed 146 atom styles  

> style sel stick

Changed 146 atom styles  

> select intersect backbone

48 atoms, 47 bonds, 8 residues, 1 model selected  

> style sel sphere

Changed 48 atom styles  

> select #2.2/Q:48-49

22 atoms, 21 bonds, 2 residues, 1 model selected  

> select #2.2/Q:49-56

128 atoms, 127 bonds, 8 residues, 1 model selected  

> select #2.2/Q:39

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2.2/Q:39-56

293 atoms, 293 bonds, 18 residues, 1 model selected  

> select intersect sideonly

184 atoms, 168 bonds, 17 residues, 1 model selected  

> style sel stick

Changed 184 atom styles  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 10 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #2.2/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #2.2/A:18-23

115 atoms, 116 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 115 atom styles  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/temp.pdb"

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/temp.cxs"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/temp.pdb" format pdb

Chain information for temp.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.7/A | No description available  
1.4/B | No description available  
1.5/C | No description available  
1.6/D | No description available  
1.7/O | No description available  
1.7/Q | No description available  
1.2/R | No description available  
  

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #1.2 models

> hide #1.4 models

> hide #1.5 models

> hide #1.6 models

> hide #1.3 models

> show #1.3 models

> show sel atoms

> ui tool show "Show Sequence Viewer"

> hide #1.3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1.7/A

Alignment identifier is 1.7/A  

> sequence chain #1.7/O

Alignment identifier is 1.7/O  

> sequence chain #1.7/Q

Alignment identifier is 1.7/Q  

> select #1.7/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #1.7/A:18-20

70 atoms, 71 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 70 atom styles  

> select #1.7/O:868

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #1.7/O:868-911

699 atoms, 706 bonds, 44 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 699 atom styles  

> select ::name="GTP"

44 atoms, 46 bonds, 1 residue, 1 model selected  

> select add ::name="MG"

45 atoms, 46 bonds, 2 residues, 1 model selected  

> select add sel : select #1.7/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> isolde sim start #1.7

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for temp.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/O | No description available  
2.2/Q | No description available  
  
ISOLDE: started sim  

> isolde sim pause

> select #2.2/A:13

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:11-13

46 atoms, 46 bonds, 3 residues, 1 model selected  

> isolde sim resume

> ui mousemode right "isolde tug selection"

> select

37393 atoms, 37789 bonds, 4 pseudobonds, 2287 residues, 25 models selected  

> show sel & #!2.2 cartoons

> hide sel & #!2.2 atoms

> select #2.2/A:3

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #2.2/A:2-3

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select #2.2/A:7

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:1-7

113 atoms, 113 bonds, 7 residues, 1 model selected  

> select #2.2/A:20

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #2.2/A:18-20

70 atoms, 71 bonds, 3 residues, 1 model selected  

> select sel : isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 10 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> dssp

> select #2.2/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> select sel : select #2.2/A:14

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2.2/A:13-14

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select sel : select #2.2/A:11

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #2.2/A:10-11

40 atoms, 41 bonds, 2 residues, 1 model selected  

> select sel : show sel & #!2.2 atoms

> select #2.2/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> select sel : save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH a.pdb"

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH a.pdb" models #2

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH a.pdb" format pdb

Chain information for RacGEF HH a.pdb #1  
---  
Chain | Description  
A | No description available  
O | No description available  
Q | No description available  
  

> ui tool show H-Bonds

> hbonds radius 0.2 dashes 0 reveal true

Skipping possible acceptor with bad geometry: /O GLU 565 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 OXT  
  
Skipping possible acceptor with bad geometry: /O GLU 565 O  
Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 O  
  
Skipping possible acceptor with bad geometry: /O GLU 565 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 OXT  
  
Skipping possible acceptor with bad geometry: /O GLU 565 O  
Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 O  
  
Skipping possible acceptor with bad geometry: /O GLU 565 OXT  
Wrong number of grandchild atoms for phi/psi acceptor /O GLU 565 OXT  
  

Skipped 8 atom(s) with bad connectivities; see log for details  

684 hydrogen bonds found  

> select /A

383 atoms, 389 bonds, 6 pseudobonds, 23 residues, 2 models selected  

> show sel atoms

> select

11063 atoms, 11188 bonds, 688 pseudobonds, 674 residues, 3 models selected  

> show sel atoms

> select clear

> select /O

8016 atoms, 8115 bonds, 497 pseudobonds, 483 residues, 2 models selected  

> hide sel atoms

> select clear

> select /A

383 atoms, 389 bonds, 6 pseudobonds, 23 residues, 2 models selected  

> select intersect C

128 atoms, 107 bonds, 23 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel forest green target acpf

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> interfaces #1

3 buried areas: O Q 1230, Q A 890, O A 301  

> select /Q:46

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /Q:25-46

364 atoms, 368 bonds, 5 pseudobonds, 22 residues, 2 models selected  

> show sel atoms

> hide sel cartoons

> style sel sphere

Changed 364 atom styles  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod2i.pdb

1NVV-REDmod2i.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod2i.pdb #2  
---  
Chain | Description | UniProt  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod2i.pdb #2  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> select clear

> select add #2

13102 atoms, 13235 bonds, 6 pseudobonds, 803 residues, 3 models selected  

> select #2/R

2619 atoms, 2638 bonds, 166 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/Q

Alignment identifier is 2/Q  

> ui tool show Matchmaker

> matchmaker #2/Q to #1/Q 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 RacGEF HH a.pdb, chain Q (#1) with 1NVV-REDmod2i.pdb, chain Q (#2),
sequence alignment score = 748.3  
RMSD between 89 pruned atom pairs is 1.332 angstroms; (across all 166 pairs:
3.051)  
  

> select #2/Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> select ~sel & ##selected

10437 atoms, 10550 bonds, 2 pseudobonds, 635 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select #1/Q

2664 atoms, 2684 bonds, 160 pseudobonds, 168 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> select add #1

11063 atoms, 11188 bonds, 688 pseudobonds, 674 residues, 3 models selected  

> select #1/O

8016 atoms, 8115 bonds, 497 pseudobonds, 483 residues, 2 models selected  

> select sel : combine #1,2 close true name "RacGEF HH"

Remapping chain ID 'Q' in 1NVV-REDmod2i.pdb #2 to 'R'  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in   
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in   
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "add models":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 391, in _items_change  
prev_value = self.get_value()  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 350, in get_value  
return self.item_map[text]  
~~~~~~~~~~~~~^^^^^^  
KeyError: '1NVV-REDmod2i.pdb #2/Q'  
  
Error processing trigger "add models":  
KeyError: '1NVV-REDmod2i.pdb #2/Q'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 350, in get_value  
return self.item_map[text]  
~~~~~~~~~~~~~^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 391, in _items_change  
prev_value = self.get_value()  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 350, in get_value  
return self.item_map[text]  
~~~~~~~~~~~~~^^^^^^  
KeyError: '1NVV-REDmod2i.pdb #2/Q'  
  
Error processing trigger "changes":  
KeyError: '1NVV-REDmod2i.pdb #2/Q'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 350, in get_value  
return self.item_map[text]  
~~~~~~~~~~~~~^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim start #1

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> 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

> close #1.3

> hide sel atoms

> show sel cartoons

> isolde sim resume

> 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  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH a.pdb" format pdb

Chain information for RacGEF HH a.pdb #1  
---  
Chain | Description  
A | No description available  
O | No description available  
Q | No description available  
  

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod2i.pdb

1NVV-REDmod2i.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod2i.pdb #2  
---  
Chain | Description | UniProt  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod2i.pdb #2  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> ui tool show Matchmaker

> matchmaker #2/Q to #1/Q 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 RacGEF HH a.pdb, chain Q (#1) with 1NVV-REDmod2i.pdb, chain Q (#2),
sequence alignment score = 748.3  
RMSD between 89 pruned atom pairs is 1.332 angstroms; (across all 166 pairs:
3.051)  
  

> select add #2

13102 atoms, 13235 bonds, 6 pseudobonds, 803 residues, 3 models selected  

> select subtract #2/Q

10437 atoms, 10550 bonds, 2 pseudobonds, 635 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> close #2

> open /Users/tmckeithan/Downloads/Chimera/PDB/1NVV-REDmod2i.pdb

1NVV-REDmod2i.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for 1NVV-REDmod2i.pdb #2  
---  
Chain | Description | UniProt  
Q R | C-H-RAS | RASH_HUMAN 1-166  
S | SOS-1 | SOS1_HUMAN 566-1046  
  
Non-standard residues in 1NVV-REDmod2i.pdb #2  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/Q

Alignment identifier is 2/Q  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/S

Alignment identifier is 2/S  

> select #2/S:864

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2/S:819-864

786 atoms, 791 bonds, 46 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2/Q to #1/O 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 RacGEF HH a.pdb, chain O (#1) with 1NVV-REDmod2i.pdb, chain Q (#2),
sequence alignment score = 15.7  
RMSD between 6 pruned atom pairs is 1.283 angstroms; (across all 97 pairs:
20.094)  
  

> select add #2

13102 atoms, 13235 bonds, 6 pseudobonds, 803 residues, 3 models selected  

> select subtract #2/Q

10437 atoms, 10550 bonds, 2 pseudobonds, 635 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> ui tool show Matchmaker

> matchmaker #2/Q to #1/Q 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 RacGEF HH a.pdb, chain Q (#1) with 1NVV-REDmod2i.pdb, chain Q (#2),
sequence alignment score = 748.3  
RMSD between 89 pruned atom pairs is 1.332 angstroms; (across all 166 pairs:
3.051)  
  

> select #1/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> select sel : ui tool show Matchmaker

> select up

9852 atoms, 9968 bonds, 596 residues, 2 models selected  

> select down

8746 atoms, 8834 bonds, 527 residues, 2 models selected  

> matchmaker #2/Q to #1/Q & 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 RacGEF HH a.pdb, chain Q (#1) with 1NVV-REDmod2i.pdb, chain Q (#2),
sequence alignment score = 112.6  
RMSD between 13 pruned atom pairs is 0.874 angstroms; (across all 23 pairs:
4.221)  
  

> select #1/Q

2664 atoms, 2684 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> delete atoms (#!1 & sel)

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 392, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in   
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in   
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 518, in  
filter_func=lambda c, ref=chain: c.structure != ref.structure)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> delete bonds (#!1 & sel)

> combine #1,2 close true name "RacGEF HH"

> interfaces #1

3 buried areas: O Q 1374, Q A 927, O A 301  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> select /A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:2-23

364 atoms, 370 bonds, 22 residues, 1 model selected  

> select /A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> select /Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> show sel atoms

> select clear

> isolde sim start #1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: started sim  

> isolde sim pause

> hide #1.3 models

> hide sel atoms

> isolde sim resume

> select /A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> show sel atoms

> select /Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> show sel atoms

> select clear

> select /A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug selection"

> 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 #1

ISOLDE: started sim  

> select clear

> select /A:11

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:11

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:10

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:8-10

56 atoms, 57 bonds, 3 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> ui mousemode right "isolde tug atom"

> select /A:2

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:1-2

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select /A:2

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:2

17 atoms, 16 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug selection"

> select /A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:5

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:4-5

34 atoms, 33 bonds, 2 residues, 1 model selected  

> select /A:5

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:5

17 atoms, 16 bonds, 1 residue, 1 model selected  

> ui mousemode right "isolde tug atom"

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:17-19

60 atoms, 62 bonds, 3 residues, 1 model selected  

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 24 atom styles  

> select sel : 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  

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:18-19

46 atoms, 47 bonds, 2 residues, 1 model selected  

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> show sel cartoons

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:19

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select sel : show sel atoms

> style sel sphere

Changed 227 atom styles  

> show sel atoms

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH b.pdb"

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH b.pdb" format pdb

RacGEF HH b.pdb title:  
Structural evidence for feedback activation by rasgtp of the ras- specific
nucleotide exchange factor sos [more info...]  
  
Chain information for RacGEF HH b.pdb #1  
---  
Chain | Description | UniProt  
A | No description available |  
O | No description available |  
Q | C-H-RAS | RASH_HUMAN 1-166  
  
Non-standard residues in RacGEF HH b.pdb #1  
---  
GTP — (GTP)  
MG — magnesium ion  
  

> interfaces #1

3 buried areas: O Q 1374, Q A 927, O A 301  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> show sel atoms

> select clear

> open /Users/tmckeithan/Downloads/Chimera/PDB/2II0.pdb

2II0.pdb title:  
Crystal structure of catalytic domain of son of sevenless (rem-CDC25) In the
absence of ras [more info...]  
  
Chain information for 2II0.pdb #2  
---  
Chain | Description | UniProt  
A | SOS-1 | SOS1_HUMAN 564-1049  
  

> select #1/O:819

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/O:819-864

786 atoms, 791 bonds, 46 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/O 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 RacGEF HH b.pdb, chain O (#1) with 2II0.pdb, chain A (#2), sequence
alignment score = 2403.4  
RMSD between 187 pruned atom pairs is 1.261 angstroms; (across all 463 pairs:
4.953)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/O & 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 RacGEF HH b.pdb, chain O (#1) with 2II0.pdb, chain A (#2), sequence
alignment score = 239.8  
RMSD between 46 pruned atom pairs is 0.568 angstroms; (across all 46 pairs:
0.568)  
  

> select add #1

11064 atoms, 11189 bonds, 4 pseudobonds, 674 residues, 2 models selected  

> select subtract #1

Nothing selected  

> hide #!2 models

> show #!2 models

> select #1/Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> select sel : select up

6164 atoms, 6224 bonds, 4 pseudobonds, 456 residues, 3 models selected  

> select down

3747 atoms, 3732 bonds, 4 pseudobonds, 262 residues, 3 models selected  

> ui tool show Matchmaker

> matchmaker #2/A to #1/O & 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 RacGEF HH b.pdb, chain O (#1) with 2II0.pdb, chain A (#2), sequence
alignment score = 155.8  
RMSD between 18 pruned atom pairs is 0.842 angstroms; (across all 32 pairs:
4.649)  
  

> select clear

> select #1/O:992

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/O:781-992

3522 atoms, 3556 bonds, 212 residues, 1 model selected  

> cartoon hide sel

> select #1/O:745

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/O:565-745

3046 atoms, 3081 bonds, 181 residues, 1 model selected  

> cartoon hide sel

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select #2/A:994

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:994-1045

426 atoms, 441 bonds, 52 residues, 1 model selected  

> hide sel cartoons

> select #2/A:754

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/A:754-779

213 atoms, 221 bonds, 26 residues, 1 model selected  

> cartoon hide sel

> select #1/O:744

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #1/O:744-745

36 atoms, 35 bonds, 2 residues, 1 model selected  

> show sel cartoons

> select #1/O:600

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/O:589-600

183 atoms, 184 bonds, 12 residues, 1 model selected  

> cartoon sel

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Alphafold models/SOS1-AF-split.pdb"

Summary of feedback from opening /Users/tmckeithan/Desktop/Cell biology and
also early evolution/Chimera models/Alphafold models/SOS1-AF-split.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 176 UNP Q07889 SOS1_HUMAN 1 1333  
  
SOS1-AF-split.pdb title:  
Alphafold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889)
[more info...]  
  
Chain information for SOS1-AF-split.pdb #3  
---  
Chain | Description  
A | son of sevenless homolog 1  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> select clear

> select add #3

10740 atoms, 11011 bonds, 1333 residues, 1 model selected  

> select subtract #3/A

9314 atoms, 9556 bonds, 1157 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:20-23

69 atoms, 68 bonds, 4 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> matchmaker #3/A to #1/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 RacGEF HH b.pdb, chain A (#1) with SOS1-AF-split.pdb, chain A (#3),
sequence alignment score = 18.1  
RMSD between 4 pruned atom pairs is 0.431 angstroms; (across all 4 pairs:
0.431)  
  

> select clear

> hide atoms

> show cartoons

> select #1/O:992

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/O:781-992

3522 atoms, 3556 bonds, 212 residues, 1 model selected  

> hide sel cartoons

> select #1/O:743

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #1/O:602-743

2423 atoms, 2451 bonds, 142 residues, 1 model selected  

> select #1/O:742-743

29 atoms, 28 bonds, 2 residues, 1 model selected  

> select #1/O:601-743

2442 atoms, 2470 bonds, 143 residues, 1 model selected  

> hide sel cartoons

> select #1/O:588

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #1/O:565-588

385 atoms, 389 bonds, 24 residues, 1 model selected  

> hide sel cartoons

> select #2/A:779

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:754-779

213 atoms, 221 bonds, 26 residues, 1 model selected  

> hide sel cartoons

> select #2/A:994

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:994-1045

426 atoms, 441 bonds, 52 residues, 1 model selected  

> hide sel cartoons

> select #1/O:993

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/O:993

14 atoms, 13 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> hide #3 models

> show #3 models

> select #3/A:20

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:1-20

176 atoms, 182 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> select #3/A:22

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:21-22

12 atoms, 11 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 12 atom styles  

> show sel atoms

> select #1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:21-22

26 atoms, 25 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 26 atom styles  

> style sel sphere

Changed 26 atom styles  

> select clear

> select add #3

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> select #3/A:20

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:2-20

168 atoms, 174 bonds, 19 residues, 1 model selected  

> select sel : select sel & #3/A:23-176

51 atoms, 45 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 51 atom styles  

> hide #3 models

> select #2/A:1001

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:1001-1022

191 atoms, 195 bonds, 22 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 191 atom styles  

> select #2/A:892

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:888-892

46 atoms, 47 bonds, 5 residues, 1 model selected  

> select #2/A:885

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:885-894

88 atoms, 90 bonds, 10 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 88 atom styles  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select #1/O:1013-1014

30 atoms, 29 bonds, 2 residues, 1 model selected  

> select #1/O:1014-1022

156 atoms, 157 bonds, 9 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 156 atom styles  

> hide sel cartoons

> hide #!1 models

> show #!1 models

> select #1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:22

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> select #1/A:21

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:18-21

77 atoms, 78 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 77 atom styles  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:18-23

115 atoms, 116 bonds, 6 residues, 1 model selected  

> style sel sphere

Changed 115 atom styles  

> show sel atoms

> hide #!1 models

> hide #!2 models

> show #3 models

> select #3/A:19-20

25 atoms, 26 bonds, 2 residues, 1 model selected  

> select #3/A:1-20

176 atoms, 182 bonds, 20 residues, 1 model selected  

> select #3/A:24

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:24-176

1230 atoms, 1252 bonds, 153 residues, 1 model selected  

> show sel atoms

> select #3/A:22-23

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #3/A:18-23

54 atoms, 55 bonds, 6 residues, 1 model selected  

> select #3/A:21

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:21-23

20 atoms, 19 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 20 atom styles  

> show sel atoms

> select #3/A:21

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:21

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> select #3/A:22

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:22-176

1246 atoms, 1268 bonds, 155 residues, 1 model selected  

> hide sel cartoons

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select intersect backbone

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel black target apf

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> color sel white target apf

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> style #3 stick

Changed 1426 atom styles  

> style #3 sphere

Changed 1426 atom styles  

> select clear

> select #3/A:22

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:22

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show #!2 models

> select #3/A:21-22

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #3/A:1-22

188 atoms, 194 bonds, 22 residues, 1 model selected  

> select add #3

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #3/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-23

196 atoms, 202 bonds, 23 residues, 1 model selected  

> show #!1 models

> hide sel cartoons

> select sel : select intersect #3/A

283 atoms, 283 bonds, 34 residues, 1 model selected  

> select sel & #3/A:23-176

95 atoms, 88 bonds, 12 residues, 1 model selected  

> show sel atoms

> select #2/A:1022

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #2/A:1018-1022

42 atoms, 43 bonds, 5 residues, 1 model selected  

> select clear

> select #2/A:995-1045

418 atoms, 433 bonds, 51 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select clear

> select add #3

1426 atoms, 1455 bonds, 176 residues, 1 model selected  

> hide #!1 models

> hide #!2 models

> select #3/A:176

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:24-176

1230 atoms, 1252 bonds, 153 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> show #!2 models

> select #3/A:22

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:1-22

188 atoms, 194 bonds, 22 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #3

1238 atoms, 1260 bonds, 154 residues, 1 model selected  

> cofr sel

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.29481,-0.2251,-0.92866,316.97,-0.86946,0.33996,-0.35842,353.71,0.39639,0.9131,-0.095495,337.35

> view matrix models
> #3,0.47953,0.28169,-0.83108,325.63,-0.83206,0.44684,-0.32864,355.43,0.27879,0.84911,0.44866,330

> view matrix models
> #3,0.58507,0.76332,-0.27392,328.96,-0.79928,0.48558,-0.35406,356.93,-0.13725,0.42609,0.89421,310.63

> view matrix models
> #3,0.67515,0.62261,-0.39563,332.14,-0.72553,0.4635,-0.5087,360.28,-0.13334,0.63049,0.76466,312.44

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #3 models

> show #!2 models

> show #3 models

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.67515,0.62261,-0.39563,339.6,-0.72553,0.4635,-0.5087,356.48,-0.13334,0.63049,0.76466,328.24

> show sel surfaces

> hide sel atoms

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
SOS1-AF-split.pdb #3/A PHE 176 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for SOS1-AF-split.pdb_A SES surface #3.1: minimum, -14.02,
mean -1.69, maximum 10.51  
To also show corresponding color key, enter the above coulombic command and
add key true  

> view matrix models
> #3,0.67515,0.62261,-0.39563,339.9,-0.72553,0.4635,-0.5087,353.9,-0.13334,0.63049,0.76466,328.04

> view matrix models
> #3,0.67515,0.62261,-0.39563,339.95,-0.72553,0.4635,-0.5087,353.1,-0.13334,0.63049,0.76466,327.7

> view matrix models
> #3,0.67515,0.62261,-0.39563,339.07,-0.72553,0.4635,-0.5087,353.26,-0.13334,0.63049,0.76466,328.1

> view matrix models
> #3,0.67515,0.62261,-0.39563,339.58,-0.72553,0.4635,-0.5087,351.91,-0.13334,0.63049,0.76466,330.33

> select add #3

1238 atoms, 1260 bonds, 154 residues, 3 models selected  

> view matrix models
> #3,0.67515,0.62261,-0.39563,330.17,-0.72553,0.4635,-0.5087,354.42,-0.13334,0.63049,0.76466,333.14

> hide sel surfaces

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:21-23

45 atoms, 44 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> select add #3

1283 atoms, 1304 bonds, 157 residues, 3 models selected  

> show sel cartoons

> show sel atoms

> view matrix models
> #1,1,0,0,-4.1424,0,1,0,0.6663,0,0,1,2.2396,#3,0.67515,0.62261,-0.39563,326.03,-0.72553,0.4635,-0.5087,355.08,-0.13334,0.63049,0.76466,335.38

> undo

> select clear

> select add #3

1238 atoms, 1260 bonds, 154 residues, 2 models selected  

> view matrix models
> #3,0.67515,0.62261,-0.39563,331.15,-0.72553,0.4635,-0.5087,360.35,-0.13334,0.63049,0.76466,334.44

> view matrix models
> #3,0.67515,0.62261,-0.39563,330.95,-0.72553,0.4635,-0.5087,360.05,-0.13334,0.63049,0.76466,334.46

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select add #1

12302 atoms, 12449 bonds, 4 pseudobonds, 828 residues, 5 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> select #2/A:994-1045

426 atoms, 441 bonds, 52 residues, 1 model selected  

> select #1/O:948-993

796 atoms, 802 bonds, 46 residues, 1 model selected  

> select #1/O:781-993

3536 atoms, 3570 bonds, 213 residues, 1 model selected  

> hide sel cartoons

> select

16391 atoms, 16384 bonds, 6 pseudobonds, 1538 residues, 6 models selected  

> hide sel atoms

> select #1/O:1017

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/O:1017-1022

103 atoms, 104 bonds, 6 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> select clear

> select add #3

1238 atoms, 1260 bonds, 154 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.58003,0.65564,-0.48342,327.96,-0.8113,0.41165,-0.41514,356.23,-0.073184,0.633,0.77069,336.67

> view matrix models
> #3,0.045811,0.84055,-0.5398,309.55,-0.99622,0.078348,0.037453,345.75,0.073773,0.53604,0.84096,341.26

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.045811,0.84055,-0.5398,309.17,-0.99622,0.078348,0.037453,345.14,0.073773,0.53604,0.84096,341.47

> view matrix models
> #3,0.045811,0.84055,-0.5398,308.93,-0.99622,0.078348,0.037453,344.67,0.073773,0.53604,0.84096,341.81

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:23

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> view matrix models
> #3,0.045811,0.84055,-0.5398,308.66,-0.99622,0.078348,0.037453,343.86,0.073773,0.53604,0.84096,342.12

> view matrix models
> #3,0.045811,0.84055,-0.5398,308.66,-0.99622,0.078348,0.037453,342.46,0.073773,0.53604,0.84096,342.35

> view matrix models
> #3,0.045811,0.84055,-0.5398,309.52,-0.99622,0.078348,0.037453,343.17,0.073773,0.53604,0.84096,344.02

> view matrix models
> #3,0.045811,0.84055,-0.5398,309.8,-0.99622,0.078348,0.037453,342.8,0.073773,0.53604,0.84096,344.27

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.11828,0.85805,-0.49976,312.42,-0.99107,0.13325,-0.0057718,343.47,0.061639,0.49597,0.86615,343.5

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.11828,0.85805,-0.49976,313.63,-0.99107,0.13325,-0.0057718,342.58,0.061639,0.49597,0.86615,343.3

> view matrix models
> #3,0.11828,0.85805,-0.49976,314.29,-0.99107,0.13325,-0.0057718,342.17,0.061639,0.49597,0.86615,343.01

> view matrix models
> #3,0.11828,0.85805,-0.49976,316.21,-0.99107,0.13325,-0.0057718,342.28,0.061639,0.49597,0.86615,343.05

> view matrix models
> #3,0.11828,0.85805,-0.49976,316.91,-0.99107,0.13325,-0.0057718,341.04,0.061639,0.49597,0.86615,343.26

> view matrix models
> #3,0.11828,0.85805,-0.49976,318.1,-0.99107,0.13325,-0.0057718,340.62,0.061639,0.49597,0.86615,342.75

> select #1/O

8016 atoms, 8115 bonds, 483 residues, 1 model selected  

> select #1/Q

2665 atoms, 2685 bonds, 4 pseudobonds, 168 residues, 2 models selected  

> show sel atoms

> style sel sphere

Changed 2665 atom styles  

> hide sel cartoons

> select #3/A

1238 atoms, 1260 bonds, 154 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> select #3/A:176

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:175-176

19 atoms, 19 bonds, 2 residues, 1 model selected  

> view matrix models
> #3,0.11828,0.85805,-0.49976,319.85,-0.99107,0.13325,-0.0057718,338.86,0.061639,0.49597,0.86615,342.67

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select add #3

1238 atoms, 1260 bonds, 154 residues, 3 models selected  

> show sel atoms

> hide sel atoms

> view matrix models
> #3,0.11828,0.85805,-0.49976,320.65,-0.99107,0.13325,-0.0057718,338.68,0.061639,0.49597,0.86615,342.16

> view matrix models
> #3,0.11828,0.85805,-0.49976,321.27,-0.99107,0.13325,-0.0057718,339.09,0.061639,0.49597,0.86615,342.74

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.052168,0.85403,-0.51759,318.87,-0.99733,0.071036,0.016689,338.41,0.051021,0.51534,0.85546,342.5

> view matrix models
> #3,-0.090191,0.84598,-0.52554,313.61,-0.98965,-0.017003,0.14247,337.71,0.11159,0.53295,0.83876,344.9

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.090191,0.84598,-0.52554,309.52,-0.98965,-0.017003,0.14247,335.27,0.11159,0.53295,0.83876,345.14

> view matrix models
> #3,-0.090191,0.84598,-0.52554,311.1,-0.98965,-0.017003,0.14247,335.55,0.11159,0.53295,0.83876,346.95

> view matrix models
> #3,-0.090191,0.84598,-0.52554,312.72,-0.98965,-0.017003,0.14247,334.56,0.11159,0.53295,0.83876,346.93

> show sel atoms

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 383 atom styles  

> select clear

> select #3/A:85@CZ2

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.092137,0.84689,-0.52373,312.65,-0.99282,-0.037807,0.11353,334.49,0.076343,0.53043,0.84429,345.61

> undo

> view matrix models
> #3,-0.15846,0.85265,-0.49788,310.15,-0.98035,-0.075867,0.18209,334.4,0.11749,0.51695,0.84792,347.01

> roll x -90 1

> select clear

> select add #2

4089 atoms, 3935 bonds, 2 pseudobonds, 710 residues, 2 models selected  

> show sel atoms

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH c.pdb"

> combine #1-3 name working

Remapping chain ID 'A' in 2II0.pdb #2 to 'B'  
Remapping chain ID 'A' in SOS1-AF-split.pdb #3 to 'C'  

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH c.pdb" models #4

> close #4

> save "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH c.cxs"

> select clear

> select add #3

1238 atoms, 1260 bonds, 154 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> select #2/A:994

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:994-1045

426 atoms, 441 bonds, 52 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/A:779

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:754-779

213 atoms, 221 bonds, 26 residues, 1 model selected  

> cartoon hide sel

> hide sel target a

> select clear

> select #1/A

383 atoms, 389 bonds, 23 residues, 1 model selected  

> select #3/A

1238 atoms, 1260 bonds, 154 residues, 1 model selected  

> show sel atoms

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1g.pdb" format pdb

Chain information for RacGEF working1g.pdb #1  
---  
Chain | Description  
A | No description available  
C F H I J L M N | No description available  
D | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> select P

25 atoms, 12 residues, 1 model selected  

> select sel : select intersect O

126 atoms, 14 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel red target apf

> select /C:325@CG

1 atom, 1 residue, 1 model selected  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1h.cxs" format session

opened ChimeraX session  

> close session

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF working1i.pdb"

Chain information for RacGEF working1i.pdb #1  
---  
Chain | Description  
C D F H I J L M | No description available  
E | No description available  
G | No description available  
K | No description available  
O | No description available  
Q | No description available  
R | No description available  
  

> color N cornflowerblue atoms

> color O hotpink atoms

> color :arg,hic,his,lys & sidechain & N blue atoms

> color :asp,glu & sidechain & O red atoms

> color S yellow atoms

> color P purple atoms

> hide H atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /R

Alignment identifier is 1/R  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> select /R:176

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /R:176-200

371 atoms, 373 bonds, 25 residues, 1 model selected  

> isolde sim start /R

> set selectionWidth 4

Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for RacGEF working1i.pdb  
---  
Chain | Description  
1.2/C 1.2/D 1.2/F 1.2/H 1.2/I 1.2/J 1.2/L 1.2/M | No description available  
1.2/E | No description available  
1.2/G | No description available  
1.2/K | No description available  
1.2/O | No description available  
1.2/Q | No description available  
1.2/R | 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

> select clear

> select /R:176

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /R:176-200

371 atoms, 373 bonds, 25 residues, 1 model selected  

> ui mousemode right "isolde tug selection"

> isolde sim resume

> select clear

> isolde sim pause

> select /R:176-177

37 atoms, 38 bonds, 2 residues, 1 model selected  

> select /R:176-199

357 atoms, 359 bonds, 24 residues, 1 model selected  

> select sel : ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1.2/E  

> sequence chain /F

Alignment identifier is 1.2/F  

> sequence chain /G

Alignment identifier is 1.2/G  

> select /G:32

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select /G:31-32

36 atoms, 36 bonds, 2 residues, 1 model selected  

> select sel : interfaces #1

28 buried areas: R O 2460, R G 2313, F K 1867, C J 1315, F D 1285, F M 1219, C
H 1216, R Q 1210, H L 1210, O Q 1179, I D 1131, F C 766, O K 746, D K 672, F J
587, C D 585, O D 534, H D 533, J M 525, O E 525, O F 495, H I 491, C K 438, F
E 433, R D 366, I L 355, E K 348, C E 331  

> ui tool show "Show Sequence Viewer"

> sequence chain /O

Alignment identifier is 1.2/O  

> select /O:1046

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /O:1024-1046

392 atoms, 400 bonds, 23 residues, 1 model selected  

> show sel atoms

> close session

Sim termination reason: model deleted  
ISOLDE: model deleted during running simulation.  

> open "/Users/tmckeithan/Desktop/Cell biology and also early
> evolution/Chimera models/Working models/RacGEF HH c.cxs" format session

opened ChimeraX session  

> select ::name="HOH"

247 atoms, 247 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/A:600

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:597-600

27 atoms, 27 bonds, 4 residues, 1 model selected  

> select #2/A:599

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:597-599

19 atoms, 19 bonds, 3 residues, 1 model selected  

> select clear

> select #1/O:588-589

35 atoms, 35 bonds, 2 residues, 1 model selected  

> select #1/O:565-589

400 atoms, 404 bonds, 25 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/O:597

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/O:597-743

2501 atoms, 2530 bonds, 147 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/O:781

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/O:781-872

1520 atoms, 1531 bonds, 92 residues, 1 model selected  

> select #1/O:781

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/O:781-992

3522 atoms, 3556 bonds, 212 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/A:780

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:754-780

223 atoms, 232 bonds, 27 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #1/A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select

9498 atoms, 9656 bonds, 8 pseudobonds, 880 residues, 7 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> combine #1,2,3 close true name HHc

Remapping chain ID 'A' in 2II0.pdb #2 to 'B'  
Remapping chain ID 'A' in SOS1-AF-split.pdb #3 to 'C'  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /B

Alignment identifier is 1/B  

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /O

Alignment identifier is 1/O  

> select /A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:23

19 atoms, 18 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /A:22@C/C:23@N

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select /A:22@C/A:23@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> select /B:589@C/O:590@N

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> bond sel reasonable false

Created 0 bonds  

> select /B:589@C/:590@N

Expected an objects specifier or a keyword  

> select /B:589@C/B:590@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> select /B:596@C/B:597@N

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /B:596@C/B:597@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> select /B:743@C/B:744@N

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /B:743@C/B:744@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> select /B:780@C/B:781@N

2 atoms, 2 residues, 1 model selected  

> select /B:780@C/B:781@N

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /B:780@C/B:781@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> select /B:993-994

49 atoms, 47 bonds, 4 residues, 1 model selected  

> select /B:993-1045

1304 atoms, 1334 bonds, 106 residues, 1 model selected  

> select /B:993

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /B:993

22 atoms, 20 bonds, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel


===== 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: 1.7.1 (2024-01-23)  
© 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: 12 days, 9 hours, 2 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: 0.7.16
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 1.7.1
    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: 1.7.1
    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: 2.6.1
    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: 1.5.14
    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: 1.0.4
    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: 1.12.4
    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: 1.33.3
    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: 0.2.1
    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: 4.47.2
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    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: 10.2.0
    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: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    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: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9