id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6515 Crash after swapaa adrian.young@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19042 ChimeraX Version: 1.3rc202112010754 (2021-12-01 07:54:47 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Windows fatal exception: access violation Thread 0x00004c88 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 316 in wait File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 574 in wait File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 1284 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002dbc (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 576 in _handle_results File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000036d4 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 528 in _handle_tasks File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002db0 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\connection.py"", line 816 in _exhaustive_wait File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\connection.py"", line 884 in wait File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 499 in _wait_for_updates File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 519 in _handle_workers File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00000bb8 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x00002c94 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x000013ac (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Thread 0x0000305c (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\multiprocessing\pool.py"", line 114 in worker File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 910 in run File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 973 in _bootstrap_inner File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\threading.py"", line 930 in _bootstrap Current thread 0x00003b98 (most recent call first): File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\chimerax\ui\gui.py"", line 301 in event_loop File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py"", line 867 in init File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py"", line 87 in _run_code File ""C:\Program Files\ChimeraX 1.3rc202112010754\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.3rc202112010754 (2021-12-01) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\Users\alyou\OneDrive - McGill > University\Documents\Liturature\Chantal > Autexier\Telomerase\Structures\PDBs\Telomerase-TPP1 highlighted > interactions.cxs"" format session registering illegal selector name ""Motif 3"" registering illegal selector name ""TEN -B"" registering illegal selector name ""Motif 3-B"" registering illegal selector name ""IFD_B"" opened ChimeraX session > open ""C:\Users\alyou\OneDrive - McGill > University\Documents\Liturature\Chantal > Autexier\Telomerase\Structures\PDBs\Telomerase-TPP1 highlighted > interactions.cxs"" format session registering illegal selector name ""Motif 3"" registering illegal selector name ""TEN -B"" registering illegal selector name ""Motif 3-B"" registering illegal selector name ""IFD_B"" opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select > #3/A:20-23,54-58,101-103,119-121,157-161,167-169,325-327,502-504,561-564,574-577,599-600,617-622,625-626,629-630,633-636,709-712,738-749,755-760,763-765,790-796,800-801,816-820,823-826,862-865,869-873,904-905,920-921,928-930,933-935,942-944 971 atoms, 962 bonds, 118 residues, 1 model selected > select #3/A:621 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:621-625 45 atoms, 46 bonds, 5 residues, 1 model selected > select #3/A:621 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:621-629 73 atoms, 75 bonds, 9 residues, 1 model selected > name frozen ""Motif 1"" sel registering illegal selector name ""Motif 1"" > name frozen Motif1 sel > color (#!3 & sel) #aa557fff > show sel cartoons > select > #3/A:20-23,54-58,101-103,119-121,157-161,167-169,325-327,502-504,561-564,574-577,599-600,617-622,625-626,629-630,633-636,709-712,738-749,755-760,763-765,790-796,800-801,816-820,823-826,862-865,869-873,904-905,920-921,928-930,933-935,942-944 971 atoms, 962 bonds, 118 residues, 1 model selected > select #3/A:630 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:630-634 41 atoms, 41 bonds, 5 residues, 1 model selected > name frozen Motif2 sel > color (#!3 & sel) #ac5681ff > color (#!3 & sel) #ad5682ff > color (#!3 & sel) #af5783ff > color (#!3 & sel) #b45a87ff > color (#!3 & sel) #b55a88ff > color (#!3 & sel) #c56294ff > color (#!3 & sel) #c66394ff > color (#!3 & sel) #c86496ff > color (#!3 & sel) #ce679aff > color (#!3 & sel) #d66ba0ff > color (#!3 & sel) #d86ca2ff > color (#!3 & sel) #d66ba0ff > color (#!3 & sel) #ce679aff > show sel cartoons > select #3/A:635 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:635-653 164 atoms, 165 bonds, 19 residues, 1 model selected > select > #3/A:20-23,54-58,101-103,119-121,157-161,167-169,325-327,502-504,561-564,574-577,599-600,617-622,625-626,629-630,633-636,709-712,738-749,755-760,763-765,790-796,800-801,816-820,823-826,862-865,869-873,904-905,920-921,928-930,933-935,942-944 971 atoms, 962 bonds, 118 residues, 1 model selected > select #3/A:632-635 30 atoms, 30 bonds, 4 residues, 1 model selected > select #3/A:635 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:635-652 153 atoms, 154 bonds, 18 residues, 1 model selected > name frozen Motif2-3linker sel > color (#!3 & sel) black > show sel cartoons > select #3/A:700 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:700-705 47 atoms, 49 bonds, 6 residues, 1 model selected > name frozen Motif3-Alinker sel > color (#!3 & sel) black > show sel cartoons > select #3/A:706 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:706-718 105 atoms, 107 bonds, 13 residues, 1 model selected > name frozen MotifA sel > color (#!3 & sel) hot pink > show sel cartoons > select #3/A:719 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:719-720 15 atoms, 14 bonds, 2 residues, 1 model selected > color (#!3 & sel) black > show sel cartoons > select #3/A:815 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:815-816 20 atoms, 21 bonds, 2 residues, 1 model selected > color (#!3 & sel) black > show sel cartoons > select #3/A:817 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/A:817-852 271 atoms, 273 bonds, 36 residues, 1 model selected > name frozen MotifB sel > color (#!3 & sel) medium blue > show sel cartoons > select #3/A:853-854 19 atoms, 19 bonds, 2 residues, 1 model selected > select #3/A:853-862 78 atoms, 78 bonds, 10 residues, 1 model selected > name frozen MotifB-Clinker sel > color (#!3 & sel) black > show sel cartoons > select #3/A:863 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:863-873 92 atoms, 92 bonds, 11 residues, 1 model selected > name frozen MotifC sel > color (#!3 & sel) cornflower blue > show sel cartoons > select #3/A:874 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:874-876 24 atoms, 25 bonds, 3 residues, 1 model selected > color (#!3 & sel) black > select #3/A:877 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:877-908 255 atoms, 260 bonds, 32 residues, 1 model selected > name frozen MotifD sel > color (#!3 & sel) light sea green > show sel cartoons > select #3/A:908 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:908-926 134 atoms, 137 bonds, 19 residues, 1 model selected > color (#!3 & sel) black > name frozen MotifD-Elinker sel > show sel cartoons > select #3/A:927 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:927-936 82 atoms, 85 bonds, 10 residues, 1 model selected > name frozen MotifE sel > color (#!3 & sel) forest green > show sel cartoons > select #3/A:936 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:683-936 2016 atoms, 2063 bonds, 254 residues, 1 model selected > select #3/A:621-936 2515 atoms, 2571 bonds, 316 residues, 1 model selected > name frozen RTdomain sel > color (#!3 & sel) orange > color (#!3 & sel) light sea green > color (#!3 & sel) #55557fff > select #3/B 5431 atoms, 6055 bonds, 3 pseudobonds, 256 residues, 2 models selected > show sel cartoons > show sel atoms > select TEN 1470 atoms, 1506 bonds, 2 pseudobonds, 189 residues, 2 models selected > select TENS 1447 atoms, 1482 bonds, 2 pseudobonds, 186 residues, 2 models selected > show sel cartoons > select IFDS 760 atoms, 776 bonds, 95 residues, 1 model selected > color (#!3 & sel) purple > select Motif3A 400 atoms, 406 bonds, 49 residues, 1 model selected > color (#!3 & sel) red > select #3/P 2005 atoms, 2048 bonds, 3 pseudobonds, 251 residues, 2 models selected > show sel cartoons > select #3/O 955 atoms, 968 bonds, 3 pseudobonds, 120 residues, 2 models selected > show sel cartoons > select #3/L 643 atoms, 650 bonds, 82 residues, 1 model selected > show sel cartoons > select #3/M 699 atoms, 710 bonds, 90 residues, 1 model selected > show sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #3/B Alignment identifier is 3/B > select #3/B:44 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:44 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:44 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:44-84 875 atoms, 977 bonds, 41 residues, 1 model selected > select #3/B:44 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:44-73 646 atoms, 723 bonds, 30 residues, 1 model selected > name frozen ActivesiteRNA sel > select #3/B 5431 atoms, 6055 bonds, 3 pseudobonds, 256 residues, 2 models selected > hide sel cartoons > hide sel atoms > select ActivesiteRNA 5431 atoms, 723 bonds, 256 residues, 1 model selected > show sel cartoons > show sel atoms > select #3/B:26 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:26-49 510 atoms, 568 bonds, 24 residues, 1 model selected > select ActivesiteRNA 5431 atoms, 723 bonds, 256 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #3/B:26 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:26-53 590 atoms, 656 bonds, 28 residues, 1 model selected > select #3/B:26 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:26-75 1069 atoms, 1194 bonds, 50 residues, 1 model selected > select #3/B:44 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:44-73 646 atoms, 723 bonds, 30 residues, 1 model selected > show sel cartoons > name frozen ActivesiteRNA sel > show sel atoms > select #3/N 461 atoms, 517 bonds, 1 pseudobond, 22 residues, 2 models selected > label (#!3 & sel) attribute label_one_letter_code > label height 2 > select #2/A:976 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:979 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:977 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:973 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byelement > select add #3/N:26 29 atoms, 29 bonds, 2 residues, 2 models selected > view sel > select #2/A:973 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel dashes 6 showDist true interModel false twoColors true intraRes > false select true reveal true retainCurrent true The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 7qxb.cif #2/P PRO 13 N; 7qxb.cif #2/P PRO 34 N; 7qxb.cif #2/P PRO 116 N; 7qxb.cif #2/P PRO 35 N; 7qxb.cif #2/P PRO 70 N; 7qxb.cif #2/P PRO 158 N; 7qxb.cif #2/P PRO 190 N; 7qxb.cif #2/P PRO 192 N; 7qxb.cif #2/P PRO 279 N 2 hydrogen bonds found The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: 7qxb.cif #2/P PRO 13 N; 7qxb.cif #2/P PRO 34 N; 7qxb.cif #2/P PRO 116 N; 7qxb.cif #2/P PRO 35 N; 7qxb.cif #2/P PRO 70 N; 7qxb.cif #2/P PRO 158 N; 7qxb.cif #2/P PRO 190 N; 7qxb.cif #2/P PRO 192 N; 7qxb.cif #2/P PRO 279 N 2 strict hydrogen bonds found > ui tool show H-Bonds > select #3/N:26 20 atoms, 21 bonds, 1 residue, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 20 atom styles > select #3/B:55 22 atoms, 24 bonds, 1 residue, 1 model selected > select #3/B:54 22 atoms, 24 bonds, 1 residue, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 22 atom styles > select #3/N:27 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #3/B:53 41 atoms, 44 bonds, 2 residues, 2 models selected > select add #3/N:28 63 atoms, 68 bonds, 3 residues, 3 models selected > view sel > select subtract #3/N:29 84 atoms, 68 bonds, 6 residues, 3 models selected > select subtract #3/N:30 75 atoms, 68 bonds, 5 residues, 3 models selected > select subtract #3/N:28 59 atoms, 44 bonds, 5 residues, 3 models selected > select add #3/N:28 81 atoms, 68 bonds, 6 residues, 3 models selected > select subtract #3/N:27 60 atoms, 45 bonds, 5 residues, 3 models selected > select add #3/N:27 81 atoms, 68 bonds, 6 residues, 3 models selected > select add #3/N:29 103 atoms, 92 bonds, 7 residues, 3 models selected > select add #3/N:30 125 atoms, 116 bonds, 8 residues, 3 models selected > nucleotides sel atoms > style nucleic & sel stick Changed 125 atom styles > color (#!3 & sel) byelement > select #3/B:52 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #3/B:53 40 atoms, 42 bonds, 2 residues, 2 models selected > select add #3/B:51 60 atoms, 63 bonds, 3 residues, 2 models selected > select add #3/B:50 80 atoms, 84 bonds, 4 residues, 2 models selected > select add #3/N:30 102 atoms, 108 bonds, 5 residues, 2 models selected > select add #3/N:29 124 atoms, 132 bonds, 6 residues, 3 models selected > select add #3/N:28 146 atoms, 156 bonds, 7 residues, 3 models selected > select add #3/N:27 167 atoms, 179 bonds, 8 residues, 3 models selected > color (#!3 & sel) byelement > select RTdomain 7626 atoms, 2571 bonds, 951 residues, 1 model selected > view sel > select #1/A 7649 atoms, 7834 bonds, 3 pseudobonds, 954 residues, 2 models selected > select #2/A 7626 atoms, 7811 bonds, 5 pseudobonds, 951 residues, 3 models selected > hide sel cartoons Drag select of 183 atoms, 12 pseudobonds, 197 bonds, 1090 residues, 123 shapes > ~label (#!2-3 & sel) residues > select #3/A:663 6 atoms, 5 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel dashes 6 showDist true interModel false twoColors true intraRes > false select true reveal true retainCurrent true 3 hydrogen bonds found 2 strict hydrogen bonds found > style sel ball Changed 5 atom styles > select #3/A:663@CA 1 atom, 1 residue, 1 model selected > style sel ball Changed 1 atom style > select #3/A:663@CB 1 atom, 1 residue, 1 model selected > style sel ball Changed 1 atom style > ui tool show H-Bonds > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:445 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:445-558 954 atoms, 980 bonds, 114 residues, 1 model selected > select #3/A:815 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3/A:721-815 760 atoms, 776 bonds, 95 residues, 1 model selected > select Motif3A 400 atoms, 406 bonds, 3 pseudobonds, 49 residues, 2 models selected > ui tool show H-Bonds Drag select of 14 atoms, 2 pseudobonds, 13 bonds Drag select of 10 atoms, 2 pseudobonds, 9 bonds Drag select of 16 atoms, 2 pseudobonds, 14 bonds > hide sel atoms Drag select of 1 atoms > hide sel cartoons > hide sel atoms > select #3/A 7626 atoms, 7811 bonds, 6 pseudobonds, 951 residues, 3 models selected > select #2/A 7626 atoms, 7811 bonds, 5 pseudobonds, 951 residues, 3 models selected > show sel cartoons > color (#!2 & sel) light gray > select clear > select #3/A 7626 atoms, 7811 bonds, 6 pseudobonds, 951 residues, 3 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:1132 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:760-1132 2930 atoms, 2994 bonds, 373 residues, 1 model selected > select #3/A:1107-1132 186 atoms, 189 bonds, 26 residues, 1 model selected > select #3/A:1106-1132 195 atoms, 198 bonds, 27 residues, 1 model selected > select #3/A:1108-1132 178 atoms, 181 bonds, 25 residues, 1 model selected > select #3/A:940-1132 1520 atoms, 1553 bonds, 193 residues, 1 model selected > name frozen MotifEI-III sel > show sel cartoons > color (#!3 & sel) light gray > color (#!3 & sel) dim gray > cd ""C:/Users/alyou/OneDrive - McGill University/Documents/Liturature/Chantal > Autexier/Telomerase/Structures/PDBs"" Current working directory is: C:\Users\alyou\OneDrive - McGill University\Documents\Liturature\Chantal Autexier\Telomerase\Structures\PDBs > save ""C:/Users/alyou/OneDrive - McGill > University/Documents/Liturature/Chantal > Autexier/Telomerase/Structures/PDBs/Telomerase-TPP1 highlighted > interactions.cxs"" > lighting simple Drag select of 2238 residues, 18 pseudobonds, 169 atoms, 185 bonds, 123 shapes > select clear Drag select of 2185 residues, 18 pseudobonds, 169 atoms, 185 bonds, 123 shapes > select clear Drag select of 2238 residues, 18 pseudobonds, 169 atoms, 185 bonds, 123 shapes > hide sel atoms > hide sel cartoons > select Motif3A 400 atoms, 406 bonds, 3 pseudobonds, 49 residues, 2 models selected > show sel cartoons > select IFDS 760 atoms, 776 bonds, 95 residues, 1 model selected > show sel cartoons > select #3/N 461 atoms, 517 bonds, 1 pseudobond, 22 residues, 2 models selected > show sel cartoons > show sel atoms > select #3/O 955 atoms, 968 bonds, 3 pseudobonds, 120 residues, 2 models selected > show sel cartoons > select #3/A:726 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 7 atom styles > color (#!3 & sel) byelement > ui tool show H-Bonds > hbonds sel dashes 6 showDist true interModel false twoColors true intraRes > false select true reveal true retainCurrent true 3 hydrogen bonds found 1 strict hydrogen bonds found > select clear > select #3/A:726 7 atoms, 6 bonds, 1 residue, 1 model selected > label (#!3 & sel) text ""/{0.chain_id} {0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 2 > select clear > select add #3/A:728 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:731 6 atoms, 5 bonds, 1 residue, 1 model selected > ui mousemode right ""move label"" > select clear > hide sel pseudobonds > select clear > select add #3/A:726 7 atoms, 6 bonds, 1 residue, 1 model selected > select subtract #3/A:726 1 model selected > select add #3/A:726 7 atoms, 6 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel ASN rotLib Dunbrack 7qxs.cif #3/A THR 726: phi -69.5, psi -37.6 trans Changed 180 bond radii ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3rc202112010754 (2021-12-01) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 - Build 27.20.100.8682 OpenGL renderer: Intel(R) HD Graphics 615 OpenGL vendor: Intel Manufacturer: Microsoft Corporation Model: Surface Go OS: Microsoft Windows 10 Home (Build 19042) Memory: 8,468,795,392 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Pentium(R) CPU 4415Y @ 1.60GHz OSLanguage: en-US Locale: ('en_CA', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.8 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202112010754 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect feedback normal Structure Editing all ChimeraX