id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15311 Crash deleting part of structure tmckeith@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-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 delete several amino acids when it crashed. The pdf, generated by ChimeraX previously, had inconsistencies between the actual atoms and positions and the putative sequence. Fatal Python error: Segmentation fault Current thread 0x0000000205278240 (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 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""/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 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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/Downloads/Chimera/PDB/4ZG4 Myo5c PPS.pdb"" format pdb 4ZG4 Myo5c PPS.pdb title: Myosin VC pre-powerstroke [more info...] Chain information for 4ZG4 Myo5c PPS.pdb #1 --- Chain | Description | UniProt B E | myosin-VC | MYO5C_HUMAN 1-755 Non-standard residues in 4ZG4 Myo5c PPS.pdb #1 --- ADP — adenosine-5'-diphosphate EDO — 1,2-ethanediol (ethylene glycol) MG — magnesium ion VO4 — vanadate ion > select /E 10904 atoms, 10774 bonds, 14 pseudobonds, 952 residues, 3 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:571 21 atoms, 21 bonds, 1 residue, 1 model selected > select /B:571-593 382 atoms, 386 bonds, 23 residues, 1 model selected > select sel @ select clear > select /B:351 12 atoms, 11 bonds, 1 residue, 1 model selected > select /B:351-375 388 atoms, 391 bonds, 25 residues, 1 model selected > select /B:570-571 37 atoms, 37 bonds, 2 residues, 1 model selected > select /B:571-593 382 atoms, 386 bonds, 23 residues, 1 model selected > close session > open /Users/tmckeithan/Downloads/Chimera/PDB/1MMD.pdb 1MMD.pdb title: Truncated head of myosin from dictyostelium discoideum complexed with mgadp- BEF3 [more info...] Chain information for 1MMD.pdb #1 --- Chain | Description | UniProt A | myosin | MYS2_DICDI 1-759 Non-standard residues in 1MMD.pdb #1 --- ADP — adenosine-5'-diphosphate BEF — beryllium trifluoride ion MG — magnesium ion > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select ::name=""ADP""::name=""BEF""::name=""HOH""::name=""MG"" 407 atoms, 32 bonds, 5 pseudobonds, 378 residues, 2 models selected > select subtract ::name=""HOH"" 32 atoms, 32 bonds, 3 pseudobonds, 3 residues, 2 models selected > select sel @ select /A:237 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:233-237 36 atoms, 35 bonds, 5 residues, 1 model selected > select sel @ close session > open /Users/tmckeithan/Downloads/Chimera/PDB/6FSA.pdb 6FSA.pdb title: Beta-cardiac myosin post-rigor [more info...] Chain information for 6FSA.pdb #1 --- Chain | Description | UniProt A B | myosin-7 | MYH7_BOVIN 1-1935 D H | myosin light chain 3 | MYL3_BOVIN 1-199 Non-standard residues in 6FSA.pdb #1 --- ADP — adenosine-5'-diphosphate EDO — 1,2-ethanediol (ethylene glycol) FMT — formic acid MG — magnesium ion > select /B 6336 atoms, 6139 bonds, 8 pseudobonds, 1076 residues, 3 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) Drag select of 43 residues > select up 521 atoms, 530 bonds, 64 residues, 1 model selected > select up 1178 atoms, 1197 bonds, 150 residues, 1 model selected > delete atoms sel > delete bonds sel > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /D Alignment identifier is 1/D > select ::name=""ADP"" 27 atoms, 29 bonds, 1 residue, 1 model selected > select add ::name=""MG"" 28 atoms, 29 bonds, 2 residues, 1 model selected > select add sel @ select /A:242 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:238-242 36 atoms, 35 bonds, 5 residues, 1 model selected > select /A:242 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:241-242 12 atoms, 11 bonds, 2 residues, 1 model selected > style sel sphere Changed 12 atom styles > hide sel cartoons > show sel atoms > select add ::name=""ADP"" 39 atoms, 40 bonds, 3 residues, 1 model selected > select add ::name=""MG"" 40 atoms, 40 bonds, 4 residues, 1 model selected > select add sel @ select clear > select add ::name=""ADP"" 27 atoms, 29 bonds, 1 residue, 1 model selected > select add ::name=""MG"" 28 atoms, 29 bonds, 2 residues, 1 model selected > select add sel @ select clear > select add ::name=""ADP"" 27 atoms, 29 bonds, 1 residue, 1 model selected > select add sel @ select /A:34 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:2-34 257 atoms, 261 bonds, 33 residues, 1 model selected > hide sel cartoons > select add > ::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=""MLY""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 7425 atoms, 7572 bonds, 2 pseudobonds, 937 residues, 2 models selected > hide sel atoms > select add ::name=""ADP"" 7452 atoms, 7601 bonds, 2 pseudobonds, 938 residues, 2 models selected > style sel sphere Changed 7452 atom styles > select add ::name=""MG"" 7453 atoms, 7601 bonds, 2 pseudobonds, 939 residues, 2 models selected > style sel sphere Changed 7453 atom styles > select clear > select add ::name=""HOH"" 460 atoms, 460 residues, 1 model selected > show sel atoms > style sel sphere Changed 460 atom styles > hide sel target a > select add ::name=""ADP"" 487 atoms, 29 bonds, 461 residues, 1 model selected > select add ::name=""MG"" 488 atoms, 29 bonds, 462 residues, 1 model selected > select add sel @ select clear > select add ::name=""ADP"" 27 atoms, 29 bonds, 1 residue, 1 model selected > select add ::name=""MG"" 28 atoms, 29 bonds, 2 residues, 1 model selected > select add sel @ select intersect ::name=""ADP""::name=""EDO""::name=""FMT""::name=""HOH""::name=""MG"" 39 atoms, 29 bonds, 1 pseudobond, 13 residues, 2 models selected > show sel atoms > select intersect sel @ select sel @ select /A:461 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:461 8 atoms, 7 bonds, 1 residue, 1 model selected > select sel @ close session > open 8P94 fromDatabase pdb format mmcif Summary of feedback from opening 8P94 fetched from pdb --- warnings | Atom H1 is not in the residue template for MET /B:1 Atom H1 is not in the residue template for MET /C:1 Atom H1 is not in the residue template for MET /D:1 Atom H1 is not in the residue template for MET /E:1 Atom H1 is not in the residue template for MET /V:1 note | Fetching compressed mmCIF 8p94 from http://files.rcsb.org/download/8p94.cif 8p94 title: Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches [more info...] Chain information for 8p94 #1 --- Chain | Description | UniProt A | Actin-related protein 3 | ARP3_HUMAN 1-418 B | Actin-related protein 2 | ARP2_HUMAN 1-394 C | Actin-related protein 2/3 complex subunit 1B | ARC1B_HUMAN 1-372 D | Actin-related protein 2/3 complex subunit 2 | ARPC2_HUMAN 1-300 E | Actin-related protein 2/3 complex subunit 3 | ARPC3_HUMAN 1-178 F | Actin-related protein 2/3 complex subunit 4 | ARPC4_HUMAN 1-168 G | Actin-related protein 2/3 complex subunit 5-like protein | ARP5L_HUMAN 1-153 H J K N O P Q R S W | Actin, cytoplasmic 1 | ACTB_PIG 1-375 I | Src substrate cortactin | SRC8_MOUSE 1-546 U | F-actin-capping protein subunit alpha-1 | CAZA1_MOUSE 1-286 V | Isoform 2 of F-actin-capping protein subunit beta | CAPZB_MOUSE 1-272 a b c d h i j k l m | Phalloidin | Non-standard residues in 8p94 #1 --- ADP — adenosine-5'-diphosphate DTH — D-threonine EEP — (2S,4R)-2-amino-4,5-dihydroxy-4-methylpentanoic acid MG — magnesium ion > set bgColor white > ui tool show ""Show Sequence Viewer"" > sequence chain /I Alignment identifier is 1/I Drag select of 1483 atoms, 95 bonds > select up 1488 atoms, 1348 bonds, 174 residues, 1 model selected > select up 2844 atoms, 2830 bonds, 174 residues, 1 model selected > select up 6129 atoms, 6176 bonds, 382 residues, 1 model selected > select up 24421 atoms, 24704 bonds, 1551 residues, 1 model selected Drag select of 376 atoms, 3 bonds > select up 378 atoms, 223 bonds, 88 residues, 1 model selected > select up 1492 atoms, 1467 bonds, 88 residues, 1 model selected > select up 4866 atoms, 4911 bonds, 304 residues, 1 model selected > select up 30144 atoms, 30488 bonds, 1922 residues, 1 model selected > select up 30304 atoms, 30652 bonds, 1930 residues, 1 model selected > select sel @ 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 > close session > open ""/Users/tmckeithan/Desktop/Cell biology and also early > evolution/Chimera models/Working models/RacGEF cat-Ras 1a.pdb"" format pdb Chain information for RacGEF cat-Ras 1a.pdb #1 --- Chain | Description A | No description available D | No description available E | No description available F | No description available G | No description available H | No description available Q | No description available > select /Q 2728 atoms, 2750 bonds, 4 pseudobonds, 171 residues, 2 models 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 > hide H atoms > select clear > hide atoms > show cartoons > graphics silhouettes true > select clear Drag select of 1 residues > show sel atoms > hide sel cartoons > select /G:992@OXT 1 atom, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select /F:993 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > select /F:993@n 1 atom, 1 residue, 1 model selected > style sel stick Changed 1 atom style > style sel sphere Changed 1 atom style > view sel > show sel atoms > hide sel cartoons > ui tool show ""Side View"" > select add /G:992@C 2 atoms, 2 residues, 1 model selected > ui tool show ""Build Structure"" > bond sel Created 0 bonds > bond sel reasonable false Created 1 bond > select clear > select /G:992@C 1 atom, 1 residue, 1 model selected > select add /G:993@N 2 atoms, 2 residues, 1 model selected > ui tool show ""Selection Inspector"" > style sel stick Changed 2 atom styles Drag select of 29 atoms, 69 residues, 5 bonds > hide sel atoms > show sel cartoons > select /G:781 16 atoms, 16 bonds, 1 residue, 1 model selected > select add /E:780 34 atoms, 34 bonds, 2 residues, 1 model selected > show sel atoms > hide sel cartoons > select intersect sideonly 20 atoms, 19 bonds, 2 residues, 1 model selected > style sel stick Changed 20 atom styles > select clear > select /G:781@N 1 atom, 1 residue, 1 model selected > select add /E:780@C 2 atoms, 2 residues, 1 model selected > bond sel reasonable false Created 1 bond > select /E:781@N 1 atom, 1 residue, 1 model selected > select add /E:780@C 2 atoms, 2 residues, 1 model selected > show sel cartoons > hide sel atoms > select /E:781@CA 1 atom, 1 residue, 1 model selected > hide sel atoms > select /Q:80 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 103 atoms, 104 bonds, 7 residues, 1 model selected > select up 2683 atoms, 2704 bonds, 169 residues, 1 model selected > show sel atoms > hide sel cartoons > combine #1 name 2xHP > select clear > select add #2 13714 atoms, 13864 bonds, 4 pseudobonds, 863 residues, 2 models selected > select subtract #2/D 13390 atoms, 13534 bonds, 4 pseudobonds, 822 residues, 2 models selected > select subtract #2/H 13275 atoms, 13418 bonds, 4 pseudobonds, 808 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #1/D 324 atoms, 330 bonds, 41 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/H 115 atoms, 116 bonds, 14 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/H 115 atoms, 116 bonds, 14 residues, 1 model selected > show sel atoms > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.73597,-0.35836,0.57439,52.128,0.18313,0.92217,0.3407,-143.26,-0.65178,-0.14555,0.74431,371.23 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.73597,-0.35836,0.57439,47.934,0.18313,0.92217,0.3407,-136.7,-0.65178,-0.14555,0.74431,368.43 > view matrix models > #2,0.73597,-0.35836,0.57439,47.573,0.18313,0.92217,0.3407,-135.73,-0.65178,-0.14555,0.74431,367.43 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.79768,-0.4219,0.43093,95.347,0.1561,0.83465,0.5282,-151.34,-0.58253,-0.35407,0.73164,427.36 > view matrix models > #2,0.65989,-0.63653,0.39922,238.05,0.34627,0.72917,0.59026,-198.35,-0.66682,-0.25127,0.70158,427.28 > view matrix models > #2,0.83012,-0.55167,0.080973,244.6,0.49727,0.79818,0.34003,-200.25,-0.25222,-0.242,0.93692,200.47 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.83012,-0.55167,0.080973,244.27,0.49727,0.79818,0.34003,-197.77,-0.25222,-0.242,0.93692,203.02 > view matrix models > #2,0.83012,-0.55167,0.080973,243.63,0.49727,0.79818,0.34003,-195.55,-0.25222,-0.242,0.93692,201.05 > view matrix models > #2,0.83012,-0.55167,0.080973,244.26,0.49727,0.79818,0.34003,-195.19,-0.25222,-0.242,0.93692,201.56 > view matrix models > #2,0.83012,-0.55167,0.080973,244.33,0.49727,0.79818,0.34003,-194.97,-0.25222,-0.242,0.93692,201.72 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.81482,-0.5794,-0.019352,292.3,0.56927,0.79337,0.21563,-179.61,-0.10958,-0.18672,0.97628,116.64 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.81482,-0.5794,-0.019352,291.26,0.56927,0.79337,0.21563,-180.8,-0.10958,-0.18672,0.97628,117.2 > view matrix models > #2,0.81482,-0.5794,-0.019352,291.34,0.56927,0.79337,0.21563,-180.47,-0.10958,-0.18672,0.97628,116.94 > undo > view matrix models > #2,0.81482,-0.5794,-0.019352,292.41,0.56927,0.79337,0.21563,-179.76,-0.10958,-0.18672,0.97628,116.54 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.88642,-0.44755,-0.11812,246.84,0.44409,0.75032,0.48971,-204.78,-0.13054,-0.48654,0.86385,275.8 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.88642,-0.44755,-0.11812,251.34,0.44409,0.75032,0.48971,-211.99,-0.13054,-0.48654,0.86385,273.56 > view matrix models > #2,0.88642,-0.44755,-0.11812,251.2,0.44409,0.75032,0.48971,-211.86,-0.13054,-0.48654,0.86385,273.76 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.80787,-0.50591,-0.30233,360.3,0.58872,0.66879,0.45401,-221.01,-0.027491,-0.54477,0.83813,267.38 > view matrix models > #2,0.87968,-0.32084,-0.35103,278.2,0.47171,0.49494,0.72974,-198.8,-0.060393,-0.80752,0.58673,460.47 > view matrix models > #2,0.99935,0.018066,-0.03135,2.8191,0.0091345,0.7124,0.70171,-107.83,0.035011,-0.70154,0.71177,345.58 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/E Alignment identifier is 1/E > sequence chain #1/Q Alignment identifier is 1/Q > sequence chain #2/D Alignment identifier is 2/D > sequence chain #2/H Alignment identifier is 2/H > select #2/H:950@CD 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > style sel stick Changed 11 atom styles > ui tool show Rotamers > swapaa interactive sel ARG rotLib Dunbrack 2xHP #2/H ARG 950: phi -138.2, psi 130.4 trans Changed 600 bond radii > style sel sphere Changed 11 atom styles > view matrix models > #2,0.91937,0.35995,-0.15874,-60.64,-0.24004,0.83297,0.49854,-0.78149,0.31167,-0.42024,0.85221,92.76 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.91937,0.35995,-0.15874,-62.343,-0.24004,0.83297,0.49854,-1.7767,0.31167,-0.42024,0.85221,92.321 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.93098,0.28121,-0.2328,-12.611,-0.14745,0.87301,0.46489,-39.942,0.33397,-0.39847,0.85421,75.236 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.93098,0.28121,-0.2328,-13.593,-0.14745,0.87301,0.46489,-39.833,0.33397,-0.39847,0.85421,75.454 > select add #2 439 atoms, 446 bonds, 55 residues, 1 model selected > show sel atoms > select #1/E:813 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 64 atoms, 63 bonds, 4 residues, 1 model selected > show sel atoms > select #2/H:949@CD 1 atom, 1 residue, 1 model selected > select add #2 439 atoms, 446 bonds, 55 residues, 1 model selected > hide sel atoms > show sel cartoons > select clear > select #1/Q 2728 atoms, 2750 bonds, 4 pseudobonds, 171 residues, 2 models selected > select sel @ select clear > select #1/E:815@CG 1 atom, 1 residue, 1 model selected > select up 15 atoms, 14 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > sequence chain #1/E Destroying pre-existing alignment with identifier 1/E Alignment identifier is 1/E > sequence chain #1/Q Destroying pre-existing alignment with identifier 1/Q Alignment identifier is 1/Q > sequence chain #2/D Destroying pre-existing alignment with identifier 2/D Alignment identifier is 2/D > sequence chain #2/H Destroying pre-existing alignment with identifier 2/H Alignment identifier is 2/H > select #1/Q 2728 atoms, 2750 bonds, 4 pseudobonds, 171 residues, 2 models selected > select sel @ ui tool show ""Show Sequence Viewer"" > sequence chain #1/E Destroying pre-existing alignment with identifier 1/E Alignment identifier is 1/E > select #1/E:642 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 211 atoms, 212 bonds, 12 residues, 1 model selected > select up 8022 atoms, 8121 bonds, 483 residues, 1 model selected > select down 211 atoms, 212 bonds, 12 residues, 1 model selected > show sel atoms > select #1/E:628 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 169 atoms, 171 bonds, 10 residues, 1 model selected > show sel atoms > select clear > select #1/E:607 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 153 atoms, 152 bonds, 8 residues, 1 model selected > show sel atoms > select #2/H 115 atoms, 116 bonds, 14 residues, 1 model selected > show sel atoms > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.9922,0.1076,-0.063023,-21.995,-0.049226,0.80234,0.59483,-88.839,0.11457,-0.58709,0.80138,244.11 > view matrix models > #2,0.99911,0.0033059,0.041952,-17.249,-0.031526,0.71915,0.69414,-94.348,-0.027875,-0.69484,0.71862,363.18 Drag select of 129 atoms, 161 residues > select up 2448 atoms, 2219 bonds, 163 residues, 2 models selected > select up 3552 atoms, 3578 bonds, 234 residues, 2 models selected > select up 10986 atoms, 11114 bonds, 692 residues, 2 models selected > select down 3552 atoms, 3578 bonds, 234 residues, 2 models selected > hide sel atoms > show sel cartoons > select clear > select #2/H:951@CA 1 atom, 1 residue, 1 model selected > select up 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 2 residues, 1 model selected > select up 115 atoms, 116 bonds, 14 residues, 1 model selected > show sel atoms > select #2/D:605 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/D:580-605 198 atoms, 201 bonds, 26 residues, 1 model selected > show sel atoms > select #1/E:939 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 188 atoms, 189 bonds, 11 residues, 1 model selected > show sel atoms > select #1/E:942 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 37 atoms, 36 bonds, 3 residues, 1 model selected > show sel atoms > select clear > hide atoms > show cartoons > select #1/E:944 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/E:944-956 223 atoms, 224 bonds, 13 residues, 1 model selected > select #1/E:957 14 atoms, 13 bonds, 1 residue, 1 model selected > select #1/E:944-957 237 atoms, 238 bonds, 14 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/H:957 8 atoms, 7 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > select clear > select #1/E:958 20 atoms, 20 bonds, 1 residue, 1 model selected > select #2/H:957 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel atoms > hide sel cartoons > select add #1/E:958 28 atoms, 27 bonds, 2 residues, 2 models selected > hide sel cartoons > show sel atoms > select intersect sideonly 18 atoms, 17 bonds, 2 residues, 2 models selected > style sel stick Changed 18 atom styles > select #2/H:957@C 1 atom, 1 residue, 1 model selected > select add #1/E:958@N 2 atoms, 2 residues, 2 models selected > ui tool show ""Build Structure"" > bond sel reasonable false Cannot bond atoms in different molecules > combine #1,2 close true name RacGEF > ui tool show ""Build Structure"" > bond sel reasonable false Must specify two or more atoms > select /E:958@N 1 atom, 1 residue, 1 model selected > select add /H:957@C 2 atoms, 2 residues, 1 model selected > bond sel reasonable false Created 1 bond > hide sel atoms > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /D Alignment identifier is 1/D > sequence chain /H Alignment identifier is 1/H > sequence chain /Q Alignment identifier is 1/Q > select add /H:944 10 atoms, 7 bonds, 3 residues, 1 model selected > select add /H:945 17 atoms, 14 bonds, 4 residues, 1 model selected > select add /H:947 24 atoms, 20 bonds, 5 residues, 1 model selected > select subtract /H:947 17 atoms, 14 bonds, 4 residues, 1 model selected > select /H:946 9 atoms, 8 bonds, 1 residue, 1 model selected > select /H:944 8 atoms, 7 bonds, 1 residue, 1 model selected > select /H:945 7 atoms, 7 bonds, 1 residue, 1 model selected > select /H:944 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel atoms > hide sel cartoons > select /H:945 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel atoms > hide sel cartoons > select /H:945@CG 1 atom, 1 residue, 1 model selected > select add /H:944@CA 2 atoms, 2 residues, 1 model selected > select up 15 atoms, 15 bonds, 2 residues, 1 model selected > select intersect sideonly 7 atoms, 5 bonds, 2 residues, 1 model selected > style sel stick Changed 7 atom styles > select /H:944@C 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select /H:944@C 1 atom, 1 residue, 1 model selected > select add /H:945@N 2 atoms, 2 residues, 1 model selected > bond sel reasonable false Created 0 bonds > select up 15 atoms, 15 bonds, 2 residues, 1 model selected > show sel cartoons > hide sel atoms > select /H:944 8 atoms, 7 bonds, 1 residue, 1 model selected > select /H:944 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /H:943 15 atoms, 13 bonds, 2 residues, 1 model selected > hide sel cartoons > show sel atoms > select /H:943@C 1 atom, 1 residue, 1 model selected > select add /H:944@N 2 atoms, 2 residues, 1 model selected > ui tool show ""Build Structure"" > bond sel reasonable false Created 1 bond > select up 15 atoms, 14 bonds, 2 residues, 1 model selected > hide sel atoms > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > sequence chain /D Destroying pre-existing alignment with identifier 1/D Alignment identifier is 1/D > sequence chain /H Destroying pre-existing alignment with identifier 1/H Alignment identifier is 1/H > sequence chain /Q Destroying pre-existing alignment with identifier 1/Q Alignment identifier is 1/Q > select clear > select /H:607 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 153 atoms, 152 bonds, 8 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /H Alignment identifier is 1/H > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /D Alignment identifier is 1/D > sequence chain /H Alignment identifier is 1/H > sequence chain /Q Alignment identifier is 1/Q > select /H:587 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 58 atoms, 58 bonds, 3 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: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 33 days, 29 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 closed normal Core can't reproduce all ChimeraX