Crash getting secondary structure IDs after deleting residues

[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)


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  "procLaunch" : "2024-03-29 00:29:11.0360 -0700",
  "procStartAbsTime" : 11613163313908,
  "procExitAbsTime" : 15272794284039,
  "procName" : "ChimeraX",
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  "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},
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[deleted to fit within ticket limits]

> 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

[pett]

Hi Tim,

Thanks for reporting this problem. The information you was provided was enlightening, though not quite enough for me to get over the hump to actually reproduce the problem. Also there's been a lot of changes in the structure-editing code between 1.7.1 and the current daily build, so it's not clear I'd be able to reproduce the problem even with an exact recipe. Thanks for taking the time to describe what happened.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab