id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14858 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, 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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 }}} " defect new normal Unassigned