![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7423 closed defect (can't reproduce)
Crash deleting structures
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1160.42.2.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007f91d6c8a740 (most recent call first):
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 773 in delete
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/std_commands/delete.py", line 39 in delete_atoms
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/std_commands/delete.py", line 22 in delete
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 297 in execute
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 134 in keyPressEvent
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/brittanydrummond/Documents/AtDDD/7AUG22_4pm_DDD.pdb format pdb
7AUG22_4pm_DDD.pdb title:
Alphafold monomer V2.0 prediction for light-mediated development protein DET1
(P48732) [more info...]
Chain information for 7AUG22_4pm_DDD.pdb #1
---
Chain | Description | UniProt
A | light-mediated development protein DET1 | DET1_ARATH
D | No description available |
F | No description available |
G | No description available |
> color bychain
> set bgColor white
> open /home/brittanydrummond/Downloads/DET1_AF.pdb
DET1_AF.pdb title:
Alphafold monomer V2.0 prediction for light-mediated development protein DET1
(P48732) [more info...]
Chain information for DET1_AF.pdb #2
---
Chain | Description | UniProt
A | light-mediated development protein DET1 | DET1_ARATH
> ui mousemode right select
> select #2/A:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:445
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2
4418 atoms, 4535 bonds, 543 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,151.1,0,1,0,73.121,0,0,1,104.4
> view matrix models #2,1,0,0,194.78,0,1,0,99.113,0,0,1,37.529
> view matrix models #2,1,0,0,188.26,0,1,0,96.21,0,0,1,20.968
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,179.78,0,1,0,97.276,0,0,1,17.253
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.48709,0.36503,0.79341,169.78,-0.35925,0.91179,-0.19894,94.602,-0.79604,-0.18813,0.57526,11.236
> view matrix models
> #2,0.28026,0.77466,-0.56688,174.1,0.55403,0.35172,0.75455,100.07,0.7839,-0.52554,-0.33061,33.097
> view matrix models
> #2,-0.96119,-0.0043256,-0.27587,160.4,-0.097613,0.94054,0.32536,94.634,0.25806,0.33966,-0.90446,29.401
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> sequence chain #1/F
Alignment identifier is 1/F
> sequence chain #1/G
Alignment identifier is 1/G
> sequence chain #2/A
Alignment identifier is 2/A
> ~select #2
Nothing selected
> select #1/G:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/G:1-47
720 atoms, 735 bonds, 47 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/D
Alignment identifier is 1/D
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/D:2
22 atoms, 22 bonds, 1 residue, 1 model selected
> select #1/D:2-58
903 atoms, 917 bonds, 57 residues, 1 model selected
> color sel purple
> select
> #2/A:39-41,49-54,61-65,70-76,105-112,126-128,133-139,162-169,175-182,194-197,200-205,210-216,222-228,329-335,340-346,361-367,372-378,480-483,491-495,510-516,522-529,536-541
1163 atoms, 1175 bonds, 137 residues, 1 model selected
> select #2
4418 atoms, 4535 bonds, 543 residues, 1 model selected
> view matrix models
> #2,-0.94278,0.27788,-0.18427,159.77,0.11514,0.78997,0.60224,95.65,0.31292,0.54656,-0.77676,29.065
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.94278,0.27788,-0.18427,113.82,0.11514,0.78997,0.60224,147.83,0.31292,0.54656,-0.77676,181.13
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select #2/A:381
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:340-381
327 atoms, 336 bonds, 42 residues, 1 model selected
> select #2/A:381
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:329-381
429 atoms, 441 bonds, 53 residues, 1 model selected
> color sel red
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.94278,0.27788,-0.18427,134.46,0.11514,0.78997,0.60224,157.9,0.31292,0.54656,-0.77676,146.37
> view matrix models
> #2,-0.94278,0.27788,-0.18427,147.81,0.11514,0.78997,0.60224,158.6,0.31292,0.54656,-0.77676,155.14
> view matrix models
> #2,-0.94278,0.27788,-0.18427,144,0.11514,0.78997,0.60224,157.59,0.31292,0.54656,-0.77676,138.72
> view matrix models
> #2,-0.94278,0.27788,-0.18427,141.84,0.11514,0.78997,0.60224,157.82,0.31292,0.54656,-0.77676,138.67
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.94364,0.2945,-0.15108,141.64,0.13288,0.75511,0.64199,157.85,0.30314,0.58573,-0.75168,138.38
> undo
> view matrix models
> #2,-0.94187,0.25864,-0.21443,142.03,0.082577,0.79688,0.59847,157.49,0.32566,0.54597,-0.77192,138.78
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.94187,0.25864,-0.21443,141.1,0.082577,0.79688,0.59847,158.26,0.32566,0.54597,-0.77192,137.69
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.95231,0.25609,-0.16592,140.74,0.083532,0.74176,0.66545,157.99,0.29348,0.61985,-0.72777,137.03
> view matrix models
> #2,-0.9674,0.22658,0.1131,139.18,0.25023,0.92392,0.28941,161.47,-0.038923,0.30828,-0.9505,135.04
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.9674,0.22658,0.1131,145.94,0.25023,0.92392,0.28941,165.15,-0.038923,0.30828,-0.9505,180.76
> select #2/A:382
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:382-413
265 atoms, 273 bonds, 32 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.9674,0.22658,0.1131,129.49,0.25023,0.92392,0.28941,176.95,-0.038923,0.30828,-0.9505,149.3
> view matrix models
> #2,-0.9674,0.22658,0.1131,134.83,0.25023,0.92392,0.28941,168.22,-0.038923,0.30828,-0.9505,139.23
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.95468,0.2738,0.11669,134.88,0.2975,0.88966,0.3464,168.47,-0.0089667,0.36542,-0.9308,139.37
> view matrix models
> #2,-0.93185,0.31084,0.18716,134.72,0.36007,0.85581,0.37139,169.04,-0.044727,0.41347,-0.90942,138.82
> view matrix models
> #2,-0.97895,-0.16376,0.12184,135.15,-0.0099718,0.63457,0.7728,163.32,-0.20387,0.75532,-0.62284,135.22
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.97895,-0.16376,0.12184,130.63,-0.0099718,0.63457,0.7728,157.89,-0.20387,0.75532,-0.62284,136.64
> view matrix models
> #2,-0.97895,-0.16376,0.12184,131.96,-0.0099718,0.63457,0.7728,159.12,-0.20387,0.75532,-0.62284,140.39
> view matrix models
> #2,-0.97895,-0.16376,0.12184,132.91,-0.0099718,0.63457,0.7728,158.74,-0.20387,0.75532,-0.62284,141.56
> view matrix models
> #2,-0.97895,-0.16376,0.12184,133.49,-0.0099718,0.63457,0.7728,156.94,-0.20387,0.75532,-0.62284,139.58
> open /home/brittanydrummond/Downloads/P60_J361_1.96A.mrc
Opened P60_J361_1.96A.mrc as #3, grid size 400,400,400, pixel 0.66, shown at
level 0.0153, step 2, values float32
> volume #3 step 1
> volume #3 level 0.04161
> volume #3 level 0.06265
> transparency 50
> hide #1 models
> show #1 models
> hide #!3 models
> ui mousemode right select
> select clear
> select #1/F
12293 atoms, 12411 bonds, 782 residues, 1 model selected
> color sel blue
> show #!3 models
> color #3 #40abbf models transparency 0
> color #3 #40abbf74 models
> color #3 #40abbf8c models
> lighting simple
> lighting soft
> lighting full
> hide #2 models
> select #1
16554 atoms, 16739 bonds, 1048 residues, 1 model selected
> ui mousemode right select
> select clear
> select #1/A:387
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A
2638 atoms, 2676 bonds, 162 residues, 1 model selected
> hide #!3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #!3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> ui mousemode right select
> select clear
> select #2/A:471
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:466-471
43 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A:381
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:340-381
327 atoms, 336 bonds, 42 residues, 1 model selected
> select #2/A:381
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:329-381
429 atoms, 441 bonds, 53 residues, 1 model selected
> save det1.329_381 selectedOnly true
No known data format for file suffix '.329_381'
> save det1.329_381.pdb selectedOnly true
> open /home/brittanydrummond/Documents/AtDDD/det1.329_381.pdb
Chain information for det1.329_381.pdb #4
---
Chain | Description
A | No description available
> hide #2 models
> color #4 #ef2929 transparency 0
> select #1/A:383
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:383-390
140 atoms, 141 bonds, 8 residues, 1 model selected
> select #1/A:382
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:382-391
175 atoms, 177 bonds, 10 residues, 1 model selected
> color sel red
> hide #4 models
> show #4 models
> ui mousemode right select
> select clear
> hide #4 models
> show #4 models
> ui mousemode right "rotate selected models"
> select #4
429 atoms, 441 bonds, 53 residues, 1 model selected
> view matrix models
> #4,0.9966,0.081203,-0.013639,-11.407,-0.081305,0.99666,-0.0070879,13.048,0.013018,0.0081728,0.99988,-3.2115
> view matrix models
> #4,0.8012,0.53016,0.27752,-98.073,-0.58347,0.79508,0.16559,95.427,-0.13286,-0.29459,0.94634,75.692
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.8012,0.53016,0.27752,-98.607,-0.58347,0.79508,0.16559,95.423,-0.13286,-0.29459,0.94634,75.277
> view matrix models
> #4,0.8012,0.53016,0.27752,-99.21,-0.58347,0.79508,0.16559,95.565,-0.13286,-0.29459,0.94634,74.354
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.79939,0.53055,0.28193,-99.606,-0.58414,0.79611,0.15811,96.48,-0.14057,-0.29108,0.94632,74.859
> view matrix models
> #4,0.82145,0.47312,0.3184,-97.891,-0.49823,0.86704,-0.0029676,93.705,-0.27747,-0.1562,0.94795,71.324
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.82145,0.47312,0.3184,-97.145,-0.49823,0.86704,-0.0029676,93.732,-0.27747,-0.1562,0.94795,71.391
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.82145,0.47312,0.3184,-97.869,-0.49823,0.86704,-0.0029676,93.344,-0.27747,-0.1562,0.94795,71.272
> view matrix models
> #4,0.82145,0.47312,0.3184,-98.624,-0.49823,0.86704,-0.0029676,93.31,-0.27747,-0.1562,0.94795,71.07
> view matrix models
> #4,0.82145,0.47312,0.3184,-98.938,-0.49823,0.86704,-0.0029676,93.331,-0.27747,-0.1562,0.94795,71.115
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.81337,0.47748,0.33232,-100.38,-0.50162,0.86496,-0.015045,95.769,-0.29463,-0.15446,0.94305,73.911
> view matrix models
> #4,0.80887,0.46515,0.35967,-101.29,-0.48385,0.87413,-0.04236,95.325,-0.3341,-0.13976,0.93212,78.484
> ~select #4
Nothing selected
> select #4
429 atoms, 441 bonds, 53 residues, 1 model selected
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.80887,0.46515,0.35967,-100.72,-0.48385,0.87413,-0.04236,93.654,-0.3341,-0.13976,0.93212,77.4
> hide #!3 models
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.80887,0.46515,0.35967,-101.49,-0.48385,0.87413,-0.04236,94.035,-0.3341,-0.13976,0.93212,75.978
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.84206,0.41903,0.33964,-95.764,-0.44911,0.89341,0.011232,78.733,-0.29873,-0.16199,0.94049,73.596
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.84206,0.41903,0.33964,-94.817,-0.44911,0.89341,0.011232,78.293,-0.29873,-0.16199,0.94049,73.962
> undo
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.85116,0.4057,0.33306,-93.935,-0.42051,0.90679,-0.029914,77.879,-0.31416,-0.1146,0.94243,67.532
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85116,0.4057,0.33306,-92.818,-0.42051,0.90679,-0.029914,77.778,-0.31416,-0.1146,0.94243,67.675
> view matrix models
> #4,0.85116,0.4057,0.33306,-92.782,-0.42051,0.90679,-0.029914,77.623,-0.31416,-0.1146,0.94243,67.832
> ~select #4
Nothing selected
> select #4
429 atoms, 441 bonds, 53 residues, 1 model selected
> show #!3 models
> hide #4 models
> show #4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.041619,0.96978,0.24042,-48.886,-0.99606,-0.059141,0.066127,309.56,0.078348,-0.23672,0.96841,29.256
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.041619,0.96978,0.24042,-58.737,-0.99606,-0.059141,0.066127,314.92,0.078348,-0.23672,0.96841,32.755
> view matrix models
> #4,-0.041619,0.96978,0.24042,-58.396,-0.99606,-0.059141,0.066127,313.92,0.078348,-0.23672,0.96841,31.558
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.12576,0.76504,0.63158,-63.853,-0.97559,0.020169,-0.21869,335.46,-0.18005,-0.64366,0.74383,166.73
> view matrix models
> #4,0.21035,0.7397,0.63921,-108.31,-0.92312,0.36556,-0.11925,256.53,-0.32188,-0.56498,0.75973,171.48
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.21035,0.7397,0.63921,-100.82,-0.92312,0.36556,-0.11925,253.22,-0.32188,-0.56498,0.75973,170
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.43811,0.79374,0.42194,-113.42,-0.88637,0.4596,0.055739,208.9,-0.14968,-0.39842,0.90491,98.17
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.43811,0.79374,0.42194,-115.52,-0.88637,0.4596,0.055739,209.91,-0.14968,-0.39842,0.90491,98.574
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.47897,0.76868,0.42393,-117.36,-0.8493,0.5279,0.0023704,200.21,-0.22197,-0.36118,0.90569,102.45
> view matrix models
> #4,0.39899,0.79344,0.45963,-114.92,-0.89928,0.43653,0.027085,219.44,-0.17915,-0.42415,0.8877,109.38
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.39899,0.79344,0.45963,-113.43,-0.89928,0.43653,0.027085,218.5,-0.17915,-0.42415,0.8877,109.83
> undo
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.041619,0.96978,0.24042,-55.575,-0.99606,-0.059141,0.066127,315.28,0.078348,-0.23672,0.96841,28.721
> view matrix models
> #4,-0.041619,0.96978,0.24042,-58.598,-0.99606,-0.059141,0.066127,311.16,0.078348,-0.23672,0.96841,28.592
> view matrix models
> #4,-0.041619,0.96978,0.24042,-57.612,-0.99606,-0.059141,0.066127,313.25,0.078348,-0.23672,0.96841,31.053
> hide #1 models
> show #1 models
> show #2 models
> hide #2 models
> show #2 models
> delete #4
> hide #2 models
> open /home/brittanydrummond/Documents/AtDDD/det1.329_381.pdb
Chain information for det1.329_381.pdb #4
---
Chain | Description
A | No description available
> ui mousemode right "translate selected models"
> select #4
429 atoms, 441 bonds, 53 residues, 1 model selected
> view matrix models #4,1,0,0,-2.7326,0,1,0,1.5486,0,0,1,-0.38902
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99643,0.083381,0.013126,-18.037,-0.083647,0.99627,0.021223,11.236,-0.011308,-0.022245,0.99969,5.0109
> hide #!3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> volume #3 level 0.09841
> volume gaussian #3 bfactor 200
Opened P60_J361_1.96A.mrc gaussian as #5, grid size 400,400,400, pixel 0.66,
shown at step 1, values float32
> volume #5 level 0.06301
> volume #5 color #8cbf40
> volume #5 color #40bf60
> volume #5 color #40bf6054
> volume #5 level 0.03414
> volume #5 level 0.01799
> volume #5 level 0.04148
> volume #5 color #729fcf
> volume #5 color #bf404075
> volume #5 color #bf404035
> volume #5 color #4058bf35
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting full
> graphics silhouettes true
> select #1/F
12293 atoms, 12411 bonds, 782 residues, 1 model selected
> color sel light gray
> ui mousemode right select
> select clear
> volume #5 level 0.0312
> ui mousemode right translate
> show #4 models
> volume #5 level -0.003546
> volume #5 level 0.003794
> ui mousemode right "rotate selected models"
> select #4
429 atoms, 441 bonds, 53 residues, 1 model selected
> volume #5 level 0.01945
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99277,0.11047,0.04697,-26.582,-0.1123,0.99294,0.038113,13.622,-0.042428,-0.043112,0.99817,13.152
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99277,0.11047,0.04697,-23.518,-0.1123,0.99294,0.038113,15.661,-0.042428,-0.043112,0.99817,13.457
> view matrix models
> #4,0.99277,0.11047,0.04697,-21.63,-0.1123,0.99294,0.038113,13.571,-0.042428,-0.043112,0.99817,14.068
> view matrix models
> #4,0.99277,0.11047,0.04697,-23.552,-0.1123,0.99294,0.038113,14.332,-0.042428,-0.043112,0.99817,12.522
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99408,0.083892,0.069032,-22.184,-0.087072,0.99521,0.044418,9.5304,-0.064975,-0.050165,0.99663,17.119
> view matrix models
> #4,0.975,-0.082659,0.20628,-9.6004,0.065452,0.99389,0.088899,-17.81,-0.21236,-0.073175,0.97445,44.873
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.97378,-0.082797,0.21189,-10.15,0.066607,0.99437,0.082448,-17.198,-0.21753,-0.066173,0.97381,44.509
> view matrix models
> #4,0.97778,-0.090693,0.18899,-6.3446,0.070686,0.99141,0.11005,-20.943,-0.19734,-0.094243,0.97579,46.116
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97778,-0.090693,0.18899,-5.2557,0.070686,0.99141,0.11005,-21.421,-0.19734,-0.094243,0.97579,44.373
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.96476,-0.11052,0.23881,-6.6769,0.085352,0.98989,0.11332,-23.681,-0.24892,-0.088941,0.96443,52.31
> ui mousemode right translate
> ui mousemode right select
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:379
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:375-379
45 atoms, 46 bonds, 5 residues, 1 model selected
> select #4/A:360
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:359-360
17 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/A:356
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:356-358
23 atoms, 23 bonds, 3 residues, 1 model selected
> select #4/A:347
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:347-360
100 atoms, 102 bonds, 14 residues, 1 model selected
> ui mousemode right select
> select clear
> select #4/A:831@C #1/A:382@N
1 atom, 1 residue, 1 model selected
> select #4/A:831@C #4/A:382@N
Nothing selected
> select #4/A:831@C #1/A:382@N
1 atom, 1 residue, 1 model selected
> select #4/A:381@C #1/A:382@N
2 atoms, 2 residues, 2 models selected
> ui tool show "Build Structure"
> bond sel
Cannot bond atoms in different molecules
> combine #4, 1
Remapping chain ID 'A' in 7AUG22_4pm_DDD.pdb #1 to 'B'
> hide #4 models
> hide #1 models
> select #1
16554 atoms, 16739 bonds, 1048 residues, 1 model selected
> ~select #1
Nothing selected
> select #6/A:381@C #6/B:382@N
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> save /home/brittanydrummond/Documents/AtDDD/8AUG22_4pm_DDD.pdb models #6
> relModel #3
> open /home/brittanydrummond/Documents/AtDDD/8AUG22_4pm_DDD.pdb
8AUG22_4pm_DDD.pdb title:
Alphafold monomer V2.0 prediction for light-mediated development protein DET1
(P48732) [more info...]
Chain information for 8AUG22_4pm_DDD.pdb #7
---
Chain | Description | UniProt
A | light-mediated development protein DET1 | DET1_ARATH
D | No description available |
F | No description available |
G | No description available |
> delete #6,1,2,4
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce GTX 1070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Red Hat Enterprise Linux Server 7.9 Maipo
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-5820K CPU @ 3.30GHz
Cache Size: 15360 KB
Memory:
total used free shared buff/cache available
Mem: 27G 13G 4.5G 1.4G 9.6G 12G
Swap: 15G 3.5M 15G
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070 Ti] [10de:1b82] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:119d]
Kernel driver in use: nvidia
Locale: ('en_NZ', 'UTF-8')
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: 2.0.9
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-Clipper: 0.17.0
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: 1.3
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-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
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
line-profiler: 3.3.0
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
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
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash deleting structures |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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