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#6515 feedback defect

Crash after swapaa

Reported by:	adrian.young@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Structure Editing	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Structure Editing
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash after swapaa

comment:2 by Eric Pettersen, 4 years ago

Status:	accepted → feedback

Hi Adrian,

Thanks for reporting this problem. Do you remember what you were doing when this crash occurred? Had you finished applying the rotamers, or was that still going when it crashed?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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