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Opened 4 years ago
Closed 4 years ago
#4755 closed defect (duplicate)
wrapped C/C++ object of type QScreen has been deleted
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
Model could not be saved.
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für
> Chimera/ChimeraX/X AD169 und Towne model 1 mit bekannten Epitopen
> markiert.cxs"
Log from Tue Jun 8 15:54:48 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"
Log from Tue Jun 8 14:57:22 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Rebec\Studium Humanmedizin\Doktorarbeit\PDB für Chimera\X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs" format session
Log from Sat May 29 17:00:55 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Rebec\Studium Humanmedizin\Doktorarbeit\PDB für Chimera\X
> AD169 und Towne model 1 markiert.cxs" format session
Log from Sat May 15 17:11:12 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 markiert.cxs"
Log from Sat May 15 17:06:07 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\Rebec\Studium Humanmedizin\Doktorarbeit\PDB für Chimera\X
> AD169 und Towne model 1.cxs" format session
Log from Sat May 15 16:24:00 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/I-Tasser/AD169
> model1.pdb" "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/I-Tasser/Towne
> model1.pdb"
Chain information for AD169 model1.pdb #1
---
Chain | Description
A | No description available
Chain information for Towne model1.pdb #2
---
Chain | Description
A | No description available
> select #1
11845 atoms, 11989 bonds, 743 residues, 1 model selected
Drag select of 93 residues
> select #2
11848 atoms, 11988 bonds, 742 residues, 1 model selected
> select #1
11845 atoms, 11989 bonds, 743 residues, 1 model selected
> cofr sel
> view sel
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select #2
11848 atoms, 11988 bonds, 742 residues, 1 model selected
> ~select #2
Nothing selected
> select #1
11845 atoms, 11989 bonds, 743 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,77.884,0,1,0,30.214,0,0,1,-69.692
> ~select #1
Nothing selected
> ui mousemode right pivot
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AD169 model1.pdb_A SES surface #1.1: minimum, -15.48,
mean -1.40, maximum 9.68
Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23,
mean -1.37, maximum 12.36
To also show corresponding color key, enter the above coulombic command and
add key true
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1.cxs"
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AD169 model1.pdb, chain A (#1) with Towne model1.pdb, chain A (#2),
sequence alignment score = 3543
RMSD between 671 pruned atom pairs is 0.327 angstroms; (across all 742 pairs:
3.210)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1
11845 atoms, 11989 bonds, 743 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> select #2
11848 atoms, 11988 bonds, 742 residues, 2 models selected
> ~select #2
1 model selected
> select #1
11845 atoms, 11989 bonds, 743 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-15.19,0,1,0,30.823,0,0,1,-95.799
> ~select #1
1 model selected
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1.cxs"
——— End of log from Sat May 15 16:24:00 2021 ———
opened ChimeraX session
> ui mousemode right "rotate selected models"
> ui mousemode right pivot
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:7
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 7
> select #1/A:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:10-11
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #1/A:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 10
> select #1/A:12
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/A:12-13
34 atoms, 34 bonds, 2 residues, 1 model selected
> select #1/A:12
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/A:12
20 atoms, 20 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 12
> select #1/A:15
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:15
21 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 15
> select #1/A:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 21
> select #1/A:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 33
> select #1/A:36
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:36
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 36
> select #1/A:151
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:151
17 atoms, 16 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 151
> select #1/A:177
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:177
12 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 177
> select #1/A:179
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:179-180
29 atoms, 28 bonds, 2 residues, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 179,180
> select #1/A:220
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:220
17 atoms, 16 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 220
> select #1/A:285
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:285
10 atoms, 9 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 285
> select #1/A:296
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:296
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 296
> select #1/A:360
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:360
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 360
> select #1/A:361
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:361-362
34 atoms, 33 bonds, 2 residues, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 360,361
> select #1/A:364
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:364
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 364
> select #1/A:412
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:412
12 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 412
> select #1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:450
17 atoms, 16 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 450
> select #1/A:547
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:547-548
24 atoms, 23 bonds, 2 residues, 1 model selected
> select #1/A:547
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:547
10 atoms, 9 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> label (#!1 & sel) text 547
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 markiert.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:7
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:7
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 7
> select #2/A:10
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:10
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 10
> select #2/A:12
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:12
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 12
> select #2/A:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:15
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 15
> select #2/A:21
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:21
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 21
> select #2/A:33
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:33
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 33
> select #2/A:36
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:36-37
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #2/A:36
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:36
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 36
> select #2/A:150
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:150
15 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 150
> select #2/A:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 176
> select #2/A:178
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:178
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 178
> select #2/A:179
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:179
15 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> view sel
> label (#!2 & sel) text 179
> select #2/A:219
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:219
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 219
> select #2/A:295
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:295
14 atoms, 14 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 295
> select #2/A:284
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:284
12 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 284
> select #2/A:359
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:359
10 atoms, 9 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 359
> select #2/A:360
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:360
17 atoms, 16 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 360
> select #2/A:361
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:361
16 atoms, 15 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 361
> select #2/A:363
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #2/A:363
16 atoms, 15 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 363
> select #2/A:411
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:411
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 411
> select #2/A:449
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:449
22 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text 449
> select #2/A:546
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:546
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> label (#!2 & sel) text "546 bei Merlin ein A"
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 markiert.cxs"
——— End of log from Sat May 15 17:06:07 2021 ———
opened ChimeraX session
> ui mousemode right pivot
> ui mousemode right "rotate selected models"
> coulombic sel
Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23,
mean -1.37, maximum 12.36
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23,
mean -1.37, maximum 12.36
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow sel
> mlp sel
Map values for surface "Towne model1.pdb_A SES surface": minimum -28.54, mean
-2.275, maximum 25.31
To also show corresponding color key, enter the above mlp command and add key
true
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> coulombic sel
Coulombic values for AD169 model1.pdb_A SES surface #1.1: minimum, -15.48,
mean -1.40, maximum 9.68
To also show corresponding color key, enter the above coulombic command and
add key true
> select #2
11848 atoms, 11988 bonds, 742 residues, 3 models selected
> ~select #2
Nothing selected
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> select #2
11848 atoms, 11988 bonds, 742 residues, 3 models selected
> mlp sel
Map values for surface "Towne model1.pdb_A SES surface": minimum -28.54, mean
-2.275, maximum 25.31
To also show corresponding color key, enter the above mlp command and add key
true
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> mlp sel
Map values for surface "AD169 model1.pdb_A SES surface": minimum -29.15, mean
-2.437, maximum 24.45
To also show corresponding color key, enter the above mlp command and add key
true
> select #2
11848 atoms, 11988 bonds, 742 residues, 3 models selected
> coulombic sel
Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23,
mean -1.37, maximum 12.36
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> ~select #1
Nothing selected
> hide surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:546
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:546-547
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #2/A:546
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:546
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 markiert.cxs"
——— End of log from Sat May 15 17:11:12 2021 ———
opened ChimeraX session
> select clear
> select #2/A:677
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/A:677-684
125 atoms, 127 bonds, 8 residues, 1 model selected
> color (#!2 & sel) purple
> label (#!2 & sel) text "3G11 AS 677-684"
> select #2/A:705
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:705-708
57 atoms, 56 bonds, 4 residues, 1 model selected
> color (#!2 & sel) purple
> label (#!2 & sel) text "3G11 AS 705-708"
> select #2/A:238-239
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #2/A:238-247
146 atoms, 146 bonds, 10 residues, 1 model selected
> color (#!2 & sel) orange
> label (#!2 & sel) text "13H11 AS 238-247"
> select #2/A:442
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:442-446
78 atoms, 78 bonds, 5 residues, 1 model selected
> color (#!2 & sel) forest green
> label (#!2 & sel) text "MSL-109 AS 442-446"
> select #2/A:403
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:403-419
276 atoms, 278 bonds, 17 residues, 1 model selected
> select #2/A:410-411
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #2/A:410-411
28 atoms, 28 bonds, 2 residues, 1 model selected
> select #2/A:403
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:403-410
137 atoms, 139 bonds, 8 residues, 1 model selected
> color (#!2 & sel) forest green
> label (#!2 & sel) text "MSL-109 AS 403-410"
> select #2/A:412
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:412-419
125 atoms, 124 bonds, 8 residues, 1 model selected
> color (#!2 & sel) forest green
> label (#!2 & sel) text "MSL-109 AS 412-419"
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select #1/A:678
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/A:678-684
110 atoms, 112 bonds, 7 residues, 1 model selected
> view sel
> color (#!1 & sel) forest green
> color (#!1 & sel) purple
> undo
> undo
> select #1/A:678
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/A:678-685
125 atoms, 127 bonds, 8 residues, 1 model selected
> color (#!1 & sel) purple
> label (#!1 & sel) text "3G16 AS 678-685"
> select #1/A:706-707
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1/A:706-709
57 atoms, 56 bonds, 4 residues, 1 model selected
> color (#!1 & sel) purple
> label (#!1 & sel) text "3G16 AS706-709"
> select #1/A:239
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1/A:239-248
146 atoms, 146 bonds, 10 residues, 1 model selected
> view sel
> color (#!1 & sel) orange
> label (#!1 & sel) text "13H11 AS 239-248"
> select #1/A:443
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:443-447
78 atoms, 78 bonds, 5 residues, 1 model selected
> view sel
> color (#!1 & sel) forest green
> label (#!1 & sel) text "MSL-109 AS 443-447"
> select #1/A:403
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:403
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:404
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1/A:404-410
123 atoms, 124 bonds, 7 residues, 1 model selected
> view sel
> select #1/A:404-407
66 atoms, 65 bonds, 4 residues, 1 model selected
> select #1/A:404-411
137 atoms, 139 bonds, 8 residues, 1 model selected
> color (#!1 & sel) forest green
> label (#!1 & sel) text "MSL-109 AS404-411"
> select #1/A:413
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:413-420
125 atoms, 124 bonds, 8 residues, 1 model selected
> color (#!1 & sel) forest green
> label (#!1 & sel) text "MSL-109 AS 413-420"
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"
——— End of log from Sat May 29 17:00:55 2021 ———
opened ChimeraX session
> select
23693 atoms, 23977 bonds, 1485 residues, 7 models selected
> view sel
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"
——— End of log from Tue Jun 8 14:57:22 2021 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> select ~sel
11848 atoms, 11988 bonds, 742 residues, 3 models selected
> select #1/A:34
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:34-43
166 atoms, 169 bonds, 10 residues, 1 model selected
> select #1/A:34
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:34-36
45 atoms, 45 bonds, 3 residues, 1 model selected
> select #1/A:34
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/A:34-35
31 atoms, 30 bonds, 2 residues, 1 model selected
> color (#!1 & sel) yellow
> label (#!1 & sel) text "AP86 AS34-35"
> select #1/A:37
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1/A:37-43
121 atoms, 123 bonds, 7 residues, 1 model selected
> color (#!1 & sel) yellow
> label (#!1 & sel) text "AP86 AS37-43"
> select #2/A:34
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:34-35
31 atoms, 30 bonds, 2 residues, 1 model selected
> color (#!2 & sel) yellow
> label (#!2 & sel) text "AP86 AS34-35"
> select #2/A:37
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:37-42
104 atoms, 105 bonds, 6 residues, 1 model selected
> color (#!2 & sel) yellow
> label (#!2 & sel) text "AP86 AS37-42"
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"
> select
23693 atoms, 23977 bonds, 1485 residues, 7 models selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AD169 model1.pdb, chain A (#1) with Towne model1.pdb, chain A (#2),
sequence alignment score = 3543
RMSD between 671 pruned atom pairs is 0.327 angstroms; (across all 742 pairs:
3.210)
> select
23693 atoms, 23977 bonds, 1485 residues, 7 models selected
> select clear
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1
11845 atoms, 11989 bonds, 743 residues, 4 models selected
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,-43.571,0,1,0,-31.003,0,0,1,-98.711
> ~select #1
1 model selected
> ui mousemode right rotate
> ui mousemode right clip
> ui mousemode right "rotate selected models"
> view
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für Chimera/X
> AD169 und Towne model 1 mit bekannten Epitopen markiert.cxs"
——— End of log from Tue Jun 8 15:54:48 2021 ———
opened ChimeraX session
> hide surfaces
> show surfaces
> select
23693 atoms, 23977 bonds, 1485 residues, 6 models selected
> coulombic sel
Coulombic values for AD169 model1.pdb_A SES surface #1.1: minimum, -15.48,
mean -1.40, maximum 9.68
Coulombic values for Towne model1.pdb_A SES surface #2.1: minimum, -19.23,
mean -1.37, maximum 12.36
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
> hide #!1 models
> select #2/A:359
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:359-363
70 atoms, 69 bonds, 5 residues, 1 model selected
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 932, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 652, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 529, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 252, in reset_state
alignment._destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 603, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 474, in alignment_notification
self.delete()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 512, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 725, in remove_tool
tw._destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 2189, in destroy
sbar.destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 51, in destroy
v.delete()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 438, in delete
self.make_current()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 99, in make_current
qc = self._initialize_context()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 635, in _mmap_mod_cb
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 392, in disassociate
self.session.alignments.destroy_alignment(self)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 108, in destroy_alignment
alignment._destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 603, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 474, in alignment_notification
self.delete()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 512, in delete
ToolInstance.delete(self)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 725, in remove_tool
tw._destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\gui.py", line 2189, in destroy
sbar.destroy()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\ui\statusbar.py", line 51, in destroy
v.delete()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 438, in delete
self.make_current()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 99, in make_current
qc = self._initialize_context()
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
Error processing trigger "modified":
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> open "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/I-Tasser/Models/AD169
> model1.pdb"
Chain information for AD169 model1.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select /A:678
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:678-685
125 atoms, 127 bonds, 8 residues, 1 model selected
> color sel purple
> label sel atoms text 3G16
> open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup
> show sel atoms
> hide sel atoms
> label sel text 3G16
> select /A:706
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:706-709
57 atoms, 56 bonds, 4 residues, 1 model selected
> color sel purple
> label sel text 3G16
> select /A:239
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:239-248
146 atoms, 146 bonds, 10 residues, 1 model selected
> color sel orange
> label sel text 13H11
> select /A:443
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:443-447
78 atoms, 78 bonds, 5 residues, 1 model selected
> color sel lime
> label sel text MSL-109
> select /A:407-408
29 atoms, 28 bonds, 2 residues, 1 model selected
> select /A:407-409
53 atoms, 54 bonds, 3 residues, 1 model selected
> select
> /A:20-23,95-98,103-109,116-123,129-132,265-268,285-288,291-294,300-303,310-328,336-353,357-359,364-385,389-392,398-408,417-429,433-435,438-455,462-476,482-495,498-508,516-519,522-524,533-538,548-559,646-648,673-680,708-714
3825 atoms, 3830 bonds, 237 residues, 1 model selected
> select /A:404
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:404-420
274 atoms, 276 bonds, 17 residues, 1 model selected
> color sel lime
> label sel text MSL-109
> select /A:34
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:34-43
166 atoms, 169 bonds, 10 residues, 1 model selected
> color sel yellow
> label sel text AP86
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für
> Chimera/ChimeraX/AD169 model 1 markiert.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
RuntimeError: Access violation - no RTTI data!
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000254766E62B0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000025416D70B80> -> <chimerax.atomic.molobject.StructureSeq object at
0x0000025416D14700> 'chain A': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving
session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
RuntimeError: Access violation - no RTTI data!
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000254766E62B0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000025416D70B80> -> <chimerax.atomic.molobject.StructureSeq object at
0x0000025416D14700> 'chain A': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving
session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> select clear
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für
> Chimera/ChimeraX/AD169 model 1 markiert.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
RuntimeError: Access violation - no RTTI data!
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000254766E62B0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000025416D70B80> -> <chimerax.atomic.molobject.StructureSeq object at
0x0000025416D14700> 'chain A': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving
session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
RuntimeError: Access violation - no RTTI data!
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000254766E62B0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000025416D70B80> -> <chimerax.atomic.molobject.StructureSeq object at
0x0000025416D14700> 'chain A': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving
session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "C:/Users/Rebec/Studium Humanmedizin/Doktorarbeit/PDB für
> Chimera/ChimeraX/AD169 model 1 markiert.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
RuntimeError: Access violation - no RTTI data!
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000254766E62B0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000025416D70B80> -> <chimerax.atomic.molobject.StructureSeq object at
0x0000025416D14700> 'chain A': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving
session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\atomic\molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
RuntimeError: Access violation - no RTTI data!
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 45, in run_provider
what(session)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\toolbar\providers.py", line 27, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 607, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x00000254766E62B0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x0000025416D70B80> -> <chimerax.atomic.molobject.StructureSeq object at
0x0000025416D14700> 'chain A': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x00000254766E62B0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x0000025416D70B80> ->
<chimerax.atomic.molobject.StructureSeq object at 0x0000025416D14700> 'chain
A'
ValueError: error processing: 'tools' -> -> -> 'chain A': Error while saving
session data for 'tools' -> -> -> 'chain A'
File "C:\Program Files\ChimeraX 1.2.2\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 21.20.16.4727
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Manufacturer: HP
Model: HP Spectre x360 Convertible
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 8,496,566,272
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
OSLanguage: de-DE
Locale: ('de_DE', '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: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type QScreen has been deleted |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
I fixed this about a month ago, bug #4583. The fix is in the ChimeraX daily build but was too late to make it into ChimeraX 1.2.
The error happens when ChimeraX is used on a computer with two screens, a Sequence panel is shown while ChimeraX is on an external screen, then that external screen is disconnected, then the user tries to close the Sequence panel. The trouble is that the status line in the sequence panel remembered the screen the panel was created on and tries to use that screen when closing the sequence panel. It takes a pretty convoluted set of steps to hit this problem.
Note:
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for help on using tickets.
This error occurred as a sequence viewer in-window status bar was being deleted. Likely led to the later session-saving error since a should-be-dead sequence viewer was still in the tools list.