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Opened 4 years ago
Closed 4 years ago
#6080 closed defect (duplicate)
Problem destroying status bar: wrapped C/C++ object of type QScreen has been deleted
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Eric Pettersen, Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I was unable to save a session of three aligneed models as .csx
None of the action tools were open and I did not have any labels.
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_map_model_aligned.cxs
> format session
Opened blur.mrc as #2, grid size 324,324,324, pixel 0.738, shown at level
0.0224, step 1, values float32
Log from Wed Feb 2 22:45:45 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/6SOF_dmIRholo_6PXV.cxs
Opened blur.mrc as #3, grid size 324,324,324, pixel 0.738, shown at level
0.0163, step 2, values float32
Log from Tue Feb 1 10:18:08 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6sof format mmcif fromDatabase pdb
6sof title:
human insulin receptor ectodomain bound by 4 insulin [more info...]
Chain information for 6sof #1
---
Chain | Description
A C | Insulin receptor
B D | Insulin receptor
E G I K | Insulin
F H J L | Insulin
> select /E/F/G/H/I/J/K/L
3048 atoms, 3090 bonds, 204 residues, 1 model selected
> select /A/B/C/D
27285 atoms, 27680 bonds, 1762 residues, 1 model selected
> ui tool show "Model Panel"
> show sel cartoons
> style sel stick
Changed 27285 atom styles
> show sel cartoons
> hide sel atoms
> select clear
> select /C:701
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show "Side View"
> ui mousemode right pivot
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,7.9324,0,1,0,3.5736,0,0,1,1.8035
> view matrix models #1,1,0,0,16.667,0,1,0,4.7833,0,0,1,5.769
> view matrix models #1,1,0,0,16.635,0,1,0,4.7397,0,0,1,5.7806
> select /A:712
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
391 atoms, 395 bonds, 23 residues, 1 model selected
> show sel atoms
> view matrix models #1,1,0,0,14.11,0,1,0,1.1833,0,0,1,0.53925
> view matrix models #1,1,0,0,17.884,0,1,0,-3.8433,0,0,1,11.029
> view matrix models #1,1,0,0,22.215,0,1,0,-4.5873,0,0,1,16.261
> select clear
> select clear
> view orient
> view orient
> view orient
> view orient
> view
> ui tool show "Side View"
> ui tool show "Side View"
> view
> lighting flat
> lighting full
> lighting flat
> set bgColor white
Drag select of 3 residues
> select clear
Drag select of 18 residues
> select up
1214 atoms, 1229 bonds, 83 residues, 1 model selected
> select up
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select down
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> color sel slate blue
> select clear
Drag select of 12 residues
> select up
979 atoms, 989 bonds, 65 residues, 1 model selected
> select up
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> color sel cadet blue
> color sel cadet blue
> color sel medium aquamarine
> color sel dark turquoise
> color sel olive
> color sel dark sea green
> color sel light green
> color sel dark sea green
> select clear
Drag select of 17 residues
> select clear
> save /Users/cristinaviola/MRC_Jan13_Feb22/IRribbons_INSspheres.png width 704
> height 578 supersample 3 transparentBackground true
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
Drag select of 34 residues
> select up
1743 atoms, 1765 bonds, 115 residues, 1 model selected
> select up
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting flat
> cartoon style sel xsection oval modeHelix default
> select clear
Drag select of 51 residues
> select up
4069 atoms, 4126 bonds, 268 residues, 1 model selected
> select up
24777 atoms, 25138 bonds, 1600 residues, 1 model selected
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> select clear
> undo
> undo
> undo
> undo
> select clear
Drag select of 76 residues
> select up
3738 atoms, 3794 bonds, 246 residues, 1 model selected
> select up
24777 atoms, 25138 bonds, 1600 residues, 1 model selected
> cartoon style sel modeHelix tube sides 20
> cartoon style sel xsection oval modeHelix default
> cartoon hide sel
> cartoon sel
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select clear
> set bgColor gray
> set bgColor white
> set bgColor black
> save /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/6SOF.cxs
> save /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/6SOF.cxs
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/dmIRholo_map_model_220121/dIR_01_real_space_refined_008.pdb
> /Users/cristinaviola/MRC_Jan13_Feb22/dmIRholo_map_model_220121/blur.mrc
Chain information for dIR_01_real_space_refined_008.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
Opened blur.mrc as #3, grid size 324,324,324, pixel 0.738, shown at level
0.0163, step 2, values float32
> hide #2 models
> show #2 models
> hide #2 models
> hide #!3 models
> show #2 models
> sequence chain #2/C
Alignment identifier is 2/C
> hide cartoons
> hide cartoons
> show cartoons
> show cartoons
> show atoms
> hide atoms
> show atoms
> hide #1 models
> hide #2 atoms
> show #2 atoms
> color #2 bychain
> mlp #2
Map values for surface "dIR_01_real_space_refined_008.pdb_A SES surface":
minimum -29.03, mean -5.145, maximum 22.9
Map values for surface "dIR_01_real_space_refined_008.pdb_B SES surface":
minimum -28, mean -5.004, maximum 25.77
Map values for surface "dIR_01_real_space_refined_008.pdb_C SES surface":
minimum -30.94, mean -6.35, maximum 21.51
Map values for surface "dIR_01_real_space_refined_008.pdb_D SES surface":
minimum -24.43, mean -4.485, maximum 21.41
Map values for surface "dIR_01_real_space_refined_008.pdb_E SES surface":
minimum -29.4, mean -4.901, maximum 22.81
Map values for surface "dIR_01_real_space_refined_008.pdb_F SES surface":
minimum -22.11, mean -4.829, maximum 19.13
Map values for surface "dIR_01_real_space_refined_008.pdb_G SES surface":
minimum -26.21, mean -5.872, maximum 21.92
Map values for surface "dIR_01_real_space_refined_008.pdb_H SES surface":
minimum -24.52, mean -3.818, maximum 21.93
Map values for surface "dIR_01_real_space_refined_008.pdb_I SES surface":
minimum -22.59, mean -1.662, maximum 22.59
Map values for surface "dIR_01_real_space_refined_008.pdb_J SES surface":
minimum -24.15, mean -2.671, maximum 22.44
To also show corresponding color key, enter the above mlp command and add key
true
> color #!2 bychain
> color #!2 byhetero
> color #!2 bychain
> color #!2 byhetero
> coulombic #!2
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
dIR_01_real_space_refined_008.pdb #2/C VAL 5
dIR_01_real_space_refined_008.pdb #2/C VAL 6
dIR_01_real_space_refined_008.pdb #2/C SER 8
dIR_01_real_space_refined_008.pdb #2/C ARG 11
dIR_01_real_space_refined_008.pdb #2/C ASN 12
dIR_01_real_space_refined_008.pdb #2/C SER 13
dIR_01_real_space_refined_008.pdb #2/C SER 15
dIR_01_real_space_refined_008.pdb #2/D PRO 8
dIR_01_real_space_refined_008.pdb #2/D ALA 9
dIR_01_real_space_refined_008.pdb #2/D ASP 12
dIR_01_real_space_refined_008.pdb #2/D ARG 15
dIR_01_real_space_refined_008.pdb #2/D VAL 16
dIR_01_real_space_refined_008.pdb #2/D ASN 20
dIR_01_real_space_refined_008.pdb #2/E VAL 5
dIR_01_real_space_refined_008.pdb #2/E VAL 6
dIR_01_real_space_refined_008.pdb #2/E SER 8
dIR_01_real_space_refined_008.pdb #2/E ARG 11
dIR_01_real_space_refined_008.pdb #2/E ASN 12
dIR_01_real_space_refined_008.pdb #2/E SER 13
dIR_01_real_space_refined_008.pdb #2/E SER 15
dIR_01_real_space_refined_008.pdb #2/F PRO 8
dIR_01_real_space_refined_008.pdb #2/F ALA 9
dIR_01_real_space_refined_008.pdb #2/F ASP 12
dIR_01_real_space_refined_008.pdb #2/F ARG 15
dIR_01_real_space_refined_008.pdb #2/F VAL 16
dIR_01_real_space_refined_008.pdb #2/F ASN 20
dIR_01_real_space_refined_008.pdb #2/G VAL 5
dIR_01_real_space_refined_008.pdb #2/G VAL 6
dIR_01_real_space_refined_008.pdb #2/G SER 8
dIR_01_real_space_refined_008.pdb #2/G ARG 11
dIR_01_real_space_refined_008.pdb #2/G ASN 12
dIR_01_real_space_refined_008.pdb #2/G SER 13
dIR_01_real_space_refined_008.pdb #2/G SER 15
dIR_01_real_space_refined_008.pdb #2/H PRO 8
dIR_01_real_space_refined_008.pdb #2/H ALA 9
dIR_01_real_space_refined_008.pdb #2/H ASP 12
dIR_01_real_space_refined_008.pdb #2/H ARG 15
dIR_01_real_space_refined_008.pdb #2/H VAL 16
dIR_01_real_space_refined_008.pdb #2/H ASN 20
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for dIR_01_real_space_refined_008.pdb_A SES surface #2.1:
minimum, -24.31, mean -1.21, maximum 14.58
Coulombic values for dIR_01_real_space_refined_008.pdb_B SES surface #2.2:
minimum, -21.19, mean -1.24, maximum 12.47
Coulombic values for dIR_01_real_space_refined_008.pdb_C SES surface #2.3:
minimum, -9.62, mean -0.40, maximum 7.24
Coulombic values for dIR_01_real_space_refined_008.pdb_D SES surface #2.4:
minimum, -9.85, mean 0.02, maximum 8.98
Coulombic values for dIR_01_real_space_refined_008.pdb_E SES surface #2.5:
minimum, -10.18, mean -0.40, maximum 10.51
Coulombic values for dIR_01_real_space_refined_008.pdb_F SES surface #2.6:
minimum, -9.78, mean -0.84, maximum 9.02
Coulombic values for dIR_01_real_space_refined_008.pdb_G SES surface #2.7:
minimum, -16.33, mean -0.77, maximum 8.00
Coulombic values for dIR_01_real_space_refined_008.pdb_H SES surface #2.8:
minimum, -9.55, mean -0.92, maximum 9.28
Coulombic values for dIR_01_real_space_refined_008.pdb_I SES surface #2.9:
minimum, -10.16, mean -0.91, maximum 9.60
Coulombic values for dIR_01_real_space_refined_008.pdb_J SES surface #2.10:
minimum, -12.00, mean -2.36, maximum 9.41
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!2 bychain
> interfaces #!2 & ~solvent
12 buried areas: A B 1464, A J 1006, B I 641, D C 589, B D 494, A H 486, E F
466, G H 398, J H 376, A F 359, D I 329, J G 306
> hide #!2 surfaces
> show #!2 surfaces
> hide #!2 surfaces
> hide #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> show #!2 atoms
> hide #!2 atoms
> hide #!2 cartoons
> hide #!2 surfaces
> show #!2 surfaces
> hide #!2 surfaces
> show #!2 surfaces
> show #!2 atoms
> show #!2 cartoons
> hide #!2 surfaces
> hide #!2 surfaces
> hide #!2 surfaces
> hide #!2 cartoons
> show #!2 cartoons
> show #!2 atoms
> hide #!2 atoms
> hide #!2 atoms
> show #!2 atoms
> hide #!2 atoms
> show #!2 atoms
> hide #!2 atoms
> show #!2 atoms
> hide #!2 atoms
> show #!2 atoms
> hide #!2 surfaces
> show #1 models
> hide #!2 models
> show #1 surfaces
> hide #!1 atoms
> hide #!1 cartoons
> hide #!1 cartoons
> show #!1 cartoons
> show #!1 surfaces
> hide #!1 surfaces
> show #!1 surfaces
> show #!1 cartoons
> hide #!1 cartoons
> show #!1 atoms
> hide #!1 atoms
> style #!1 stick
Changed 30333 atom styles
> hide #!1 atoms
> show #!2 models
> hide cartoons
> show cartoons
> hide atoms
> show atoms
> hide surfaces
> hide surfaces
> show surfaces
> hide surfaces
> show surfaces
> fetch 6SOF
Unknown command: fetch 6SOF
> open 6SOF
6sof title:
human insulin receptor ectodomain bound by 4 insulin [more info...]
Chain information for 6sof #4
---
Chain | Description
A C | Insulin receptor
B D | Insulin receptor
E G I K | Insulin
F H J L | Insulin
> hide #!1 models
> hide #4 models
> show #4 models
> hide #!2 models
> show #!2 models
> hide #4#!2 atoms
> hide #4#!2 atoms
> show #4#!2 atoms
> select #2
14855 atoms, 15183 bonds, 1899 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> hide sel surfaces
> ~select #2
10 models selected
> show #!1 models
> hide #!2 models
> hide #4 models
> select #1
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> show sel surfaces
> show sel surfaces
> show sel surfaces
> show sel atoms
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> color sel bychain
> ~select #1
12 models selected
> hide #!1 models
> show #!2 models
> show #4 models
> ui tool show "Surface Color"
> ui tool show Matchmaker
> matchmaker #4 & sel to #2 & sel
No 'to' model specified
> matchmaker #4 to #2
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 dIR_01_real_space_refined_008.pdb, chain B (#2) with 6sof, chain A
(#4), sequence alignment score = 1139.9
RMSD between 79 pruned atom pairs is 1.156 angstroms; (across all 676 pairs:
20.238)
> hide #4 models
> hide #!2 models
> show #4 models
> show #!2 models
> select #2
14855 atoms, 15183 bonds, 1899 residues, 1 model selected
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> open 7bw7
Summary of feedback from opening 7bw7 fetched from pdb
---
note | Fetching compressed mmCIF 7bw7 from
http://files.rcsb.org/download/7bw7.cif
7bw7 title:
Cryo-EM Structure for the Ectodomain of the Full-length Human Insulin Receptor
in Complex with 1 Insulin. [more info...]
Chain information for 7bw7 #5
---
Chain | Description
A C | Insulin receptor
D | Insulin fusion
> hide #!2 models
> hide #4 models
> show #!5 surfaces
> show #!2 models
> hide #!5 models
> show sel surfaces
> hide #!2 models
> show #4 models
> hide #4 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #4#!5 to #2
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 dIR_01_real_space_refined_008.pdb, chain B (#2) with 6sof, chain A
(#4), sequence alignment score = 1139.9
RMSD between 79 pruned atom pairs is 1.156 angstroms; (across all 676 pairs:
20.238)
Matchmaker dIR_01_real_space_refined_008.pdb, chain B (#2) with 7bw7, chain A
(#5), sequence alignment score = 1112.1
RMSD between 29 pruned atom pairs is 1.357 angstroms; (across all 610 pairs:
12.178)
> show #4 models
> show #!2 models
> ~select #2
10 models selected
> hide #!2 models
> show #!2 models
> hide #4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #4 models
> hide #4 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #4 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #4 models
> show #!5 models
> show #!5 surfaces
> select #5
8824 atoms, 9049 bonds, 10 pseudobonds, 1091 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show sel atoms
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> color sel bychain
> show #!1 models
> hide #!1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> ~select #5
3 models selected
> close #5
> show #!2 models
> hide #!2 models
> open 6pxv
Summary of feedback from opening 6pxv fetched from pdb
---
note | Fetching compressed mmCIF 6pxv from
http://files.rcsb.org/download/6pxv.cif
6pxv title:
Cryo-EM structure of full-length insulin receptor bound to 4 insulin. 3D
refinement was focused on the extracellular region. [more info...]
Chain information for 6pxv #5
---
Chain | Description
A C | Insulin receptor
D E F G | Insulin
> hide #4 models
> ui tool show Matchmaker
> matchmaker #4#!5 to #2
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 dIR_01_real_space_refined_008.pdb, chain B (#2) with 6sof, chain A
(#4), sequence alignment score = 1139.9
RMSD between 79 pruned atom pairs is 1.156 angstroms; (across all 676 pairs:
20.238)
Matchmaker dIR_01_real_space_refined_008.pdb, chain A (#2) with 6pxv, chain A
(#5), sequence alignment score = 1363.4
RMSD between 142 pruned atom pairs is 1.067 angstroms; (across all 758 pairs:
11.948)
> matchmaker #4#!5 to #2
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 dIR_01_real_space_refined_008.pdb, chain B (#2) with 6sof, chain A
(#4), sequence alignment score = 1139.9
RMSD between 79 pruned atom pairs is 1.156 angstroms; (across all 676 pairs:
20.238)
Matchmaker dIR_01_real_space_refined_008.pdb, chain A (#2) with 6pxv, chain A
(#5), sequence alignment score = 1363.4
RMSD between 142 pruned atom pairs is 1.067 angstroms; (across all 758 pairs:
11.948)
> show #4 models
> hide #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
14855 atoms, 15183 bonds, 1899 residues, 1 model selected
> hide #!5 models
> hide sel surfaces
> show sel surfaces
> show sel cartoons
> hide sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> hide sel surfaces
> show sel surfaces
> style sel stick
Changed 14855 atom styles
> show sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> hide sel atoms
> style sel ball
Changed 14855 atom styles
> show sel atoms
> style sel ball
Changed 14855 atom styles
> style sel stick
Changed 14855 atom styles
> hide sel atoms
> show sel surfaces
> show #!5 models
> hide #!5 models
> show #!5 models
> ~select #2
10 models selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show "Model Panel"
> view #2 clip false
> show #!2 models
> hide #4 models
> open 7pg3
Fetching url http://files.rcsb.org/download/7pg3.cif failed: HTTP Error 404:
Not Found
> open 7pg0
Fetching url http://files.rcsb.org/download/7pg0.cif failed: HTTP Error 404:
Not Found
> open 7pg2
Fetching url http://files.rcsb.org/download/7pg2.cif failed: HTTP Error 404:
Not Found
> open 7pg4
Fetching url http://files.rcsb.org/download/7pg4.cif failed: HTTP Error 404:
Not Found
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> hide #5.1 models
> show #5.1 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 2/C
Alignment identifier is 2/D
Alignment identifier is 2/E
Alignment identifier is 2/F
Alignment identifier is 2/G
Alignment identifier is 2/H
Alignment identifier is 2/A
Alignment identifier is 2/B
Alignment identifier is 2/I
Alignment identifier is 2/J
Alignment identifier is 5
Alignment identifier is 6
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!2 models
Drag select of 103 atoms
> select up
262 atoms, 263 bonds, 16 residues, 1 model selected
> select up
698 atoms, 711 bonds, 46 residues, 1 model selected
> select up
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> select down
698 atoms, 711 bonds, 46 residues, 1 model selected
> select up
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select down
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium slate blue
> select clear
Drag select of 71 atoms
> select up
115 atoms, 113 bonds, 8 residues, 1 model selected
> select up
324 atoms, 328 bonds, 22 residues, 1 model selected
> select up
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> color sel medium slate blue
Drag select of 93 atoms
> select up
177 atoms, 173 bonds, 13 residues, 1 model selected
> select up
949 atoms, 956 bonds, 65 residues, 1 model selected
> select up
13659 atoms, 13856 bonds, 881 residues, 1 model selected
> color sel light coral
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 74 atoms
> select up
128 atoms, 129 bonds, 8 residues, 1 model selected
> select up
624 atoms, 633 bonds, 42 residues, 1 model selected
> select up
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select down
2532 atoms, 2565 bonds, 162 residues, 1 model selected
> color sel light pink
Drag select of 230 atoms
> select up
369 atoms, 371 bonds, 24 residues, 1 model selected
> select up
1487 atoms, 1504 bonds, 96 residues, 1 model selected
> select up
11127 atoms, 11290 bonds, 719 residues, 1 model selected
> color sel light pink
Drag select of 138 atoms
> select up
215 atoms, 215 bonds, 14 residues, 1 model selected
> select up
1036 atoms, 1049 bonds, 66 residues, 1 model selected
> select up
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> color sel medium purple
> color sel thistle
> color sel plum
> color sel medium orchid
> color sel dark orchid
> color sel medium purple
> color sel blue violet
> color sel dark slate blue
> color sel cornflower blue
> color sel purple
> color sel medium orchid
> color sel dark orchid
> select clear
Drag select of 230 atoms
> select up
377 atoms, 378 bonds, 28 residues, 1 model selected
> select up
914 atoms, 927 bonds, 66 residues, 1 model selected
> select up
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> select up
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> select down
11118 atoms, 11280 bonds, 719 residues, 1 model selected
> color sel medium purple
> select clear
Drag select of 121 atoms
> select up
194 atoms, 193 bonds, 13 residues, 1 model selected
> select up
569 atoms, 575 bonds, 38 residues, 1 model selected
> select up
2508 atoms, 2541 bonds, 162 residues, 1 model selected
> color sel medium purple
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #!5 models
> hide #4 models
> show #4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #4 models
Drag select of 40 atoms
> select up
79 atoms, 77 bonds, 9 residues, 1 model selected
> select up
339 atoms, 347 bonds, 41 residues, 1 model selected
> select up
6664 atoms, 6844 bonds, 823 residues, 1 model selected
> select up
14774 atoms, 15172 bonds, 1830 residues, 1 model selected
> select down
6664 atoms, 6844 bonds, 823 residues, 1 model selected
> color sel magenta
> color sel deep pink
> color sel hot pink
> select clear
Drag select of 159 atoms
> select up
245 atoms, 247 bonds, 30 residues, 1 model selected
> select up
655 atoms, 673 bonds, 84 residues, 1 model selected
> select up
6664 atoms, 6844 bonds, 823 residues, 1 model selected
> color sel blue
> color sel dark slate blue
> select clear
> show #4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 target m
> hide #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #4 models
> hide #!2 models
> show #4 models
> hide #!5 models
> hide #4 models
> show #4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show Matchmaker
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/088DB95F-58BB-4594-85A7-CD3E5EDC59C1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/088DB95F-58BB-4594-85A7-CD3E5EDC59C1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/088DB95F-58BB-4594-85A7-CD3E5EDC59C1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/088DB95F-58BB-4594-85A7-CD3E5EDC59C1/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> save /Users/cristinaviola/MRC_Jan13_Feb22/superpose_dmIRholo_6sof_6pxv.png
> width 704 height 678 supersample 3 transparentBackground true
> ui tool show "Color Actions"
> color bychain
>
Incomplete command: ui
> undo
> toolshed show
> show #!1 models
> hide #4 models
> hide #!5 models
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> hide #1.4 models
> show #1.4 models
> hide #1.5 models
> show #1.5 models
> hide #1.2 models
> show #1.2 models
> show #!2 models
> show #4 models
> show #!5 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #!2,5 to #4/B pairing bs
Parameters
---
Chain pairing | bs
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 6sof, chain B (#4) with dIR_01_real_space_refined_008.pdb, chain B
(#2), sequence alignment score = 168
RMSD between 19 pruned atom pairs is 1.239 angstroms; (across all 157 pairs:
10.589)
Matchmaker 6sof, chain B (#4) with 6pxv, chain A (#5), sequence alignment
score = 624.7
RMSD between 47 pruned atom pairs is 1.318 angstroms; (across all 155 pairs:
6.951)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #4#!5 surfaces
> hide #4#!5 surfaces
> select #2
14855 atoms, 15183 bonds, 1899 residues, 1 model selected
> select #3
2 models selected
> select #4
30333 atoms, 30770 bonds, 1966 residues, 1 model selected
> hide sel surfaces
> hide sel surfaces
> show sel cartoons
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide #!5 models
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show #!5 models
> select #5
14774 atoms, 15172 bonds, 14 pseudobonds, 1830 residues, 2 models selected
> hide #!4 models
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> hide sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel atoms
> style (#!5 & sel) stick
Changed 14774 atom styles
> style (#!5 & sel) sphere
Changed 14774 atom styles
> ~select #5
6 models selected
> hide #!5 models
> show #!4 models
> hide #!4 surfaces
> show #!4 atoms
> hide #!4 atoms
> hide #!4 cartoons
> show #!4 atoms
> show #!4 cartoons
> hide #!4 models
> show #!2 models
> hide #!2 surfaces
> show #!2 atoms
> style #2 sphere
Changed 14855 atom styles
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!2,5 to #4/D pairing bs
Parameters
---
Chain pairing | bs
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 6sof, chain D (#4) with dIR_01_real_space_refined_008.pdb, chain B
(#2), sequence alignment score = 176.5
RMSD between 33 pruned atom pairs is 1.361 angstroms; (across all 157 pairs:
10.941)
Matchmaker 6sof, chain D (#4) with 6pxv, chain A (#5), sequence alignment
score = 641.5
RMSD between 58 pruned atom pairs is 1.249 angstroms; (across all 155 pairs:
6.513)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> ui tool show "Color Actions"
Drag select of 107 atoms
> select up
154 atoms, 152 bonds, 20 residues, 2 models selected
> select up
535 atoms, 546 bonds, 70 residues, 2 models selected
> select up
6785 atoms, 6937 bonds, 856 residues, 2 models selected
> color sel medium slate blue
> select clear
Drag select of 68 atoms
> select up
79 atoms, 77 bonds, 11 residues, 2 models selected
> select up
358 atoms, 365 bonds, 46 residues, 2 models selected
> select up
6841 atoms, 6994 bonds, 863 residues, 2 models selected
> color sel light coral
> select clear
> show #!4 models
> hide #!2 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4-5 atoms
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!5 cartoons
> show #!4 models
> show #!4-5 atoms
> hide #!4-5 cartoons
> hide #!4 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!2 to #5/C pairing bs
Parameters
---
Chain pairing | bs
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 6pxv, chain C (#5) with dIR_01_real_space_refined_008.pdb, chain A
(#2), sequence alignment score = 1363.4
RMSD between 144 pruned atom pairs is 1.066 angstroms; (across all 758 pairs:
11.991)
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> set bgColor gray
> set bgColor black
> lighting simple
> lighting soft
> lighting simple
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> show #!4 models
> show #!5 models
> lighting flat
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> hide #!2 models
> show #!2 models
> hide #!4 models
> graphics silhouettes true
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/6SOF_dmIRholo_6PXV.cxs
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 1 - updating layer to match.
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 1 - updating layer to match.
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 1 - updating layer to match.
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000695843c0>
contents scale of 1 - updating layer to match.
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/6SOF_dmIRholo_6PXV.cxs
——— End of log from Tue Feb 1 10:18:08 2022 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #2.2
6785 atoms, 856 residues, 1 model selected
> select #2.1
6841 atoms, 863 residues, 1 model selected
> select #2.2
6785 atoms, 856 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #2.1
6841 atoms, 863 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbons_Dilp5_surface.png
> width 1346 height 881 supersample 3 transparentBackground true
> select #2.4
175 atoms, 27 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark salmon
> hide sel atoms
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select #2.3
134 atoms, 21 residues, 1 model selected
> color sel medium slate blue
> hide sel atoms
> show sel cartoons
> select clear
> hide #!2 atoms
> hide #!2 atoms
> show #!2 atoms
>
Incomplete command: ui
> undo
> undo
> undo
> undo
> show sel atoms
> color sel white
> color sel wheat
> color sel silver
> select #2.9
125 atoms, 16 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel dark salmon
> color sel salmon
> select #2.4
175 atoms, 27 residues, 1 model selected
> color sel lime
> select #2.3
134 atoms, 21 residues, 1 model selected
> color sel orange red
> color sel turquoise
> color sel dodger blue
> color sel indigo
> color sel olive
> color sel deep pink
> color sel dark olive green
> color sel magenta
> color sel deep pink
> select #2.4
175 atoms, 27 residues, 1 model selected
> color sel dark olive green
> select #2.5
164 atoms, 24 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel deep pink
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #2.3
134 atoms, 21 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #2.6
118 atoms, 20 residues, 1 model selected
> color sel dark olive green
> select #2.9
125 atoms, 16 residues, 1 model selected
> show sel atoms
> show sel cartoons
> select #2.10
201 atoms, 24 residues, 1 model selected
> color sel medium slate blue
> color sel slate blue
> color sel medium slate blue
> show sel cartoons
> select #2.6
118 atoms, 20 residues, 1 model selected
> color sel deep pink
> select #2.7
170 atoms, 25 residues, 1 model selected
> color sel dark olive green
> select #2.8
142 atoms, 23 residues, 1 model selected
> select #2.6
118 atoms, 20 residues, 1 model selected
> color sel dark olive green
> select #2.7
170 atoms, 25 residues, 1 model selected
> color sel deep pink
> select #2.8
142 atoms, 23 residues, 1 model selected
> color sel dark olive green
> select clear
> select #2.1
6841 atoms, 863 residues, 1 model selected
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting full
> lighting flat
> select clear
> select #2.1
6841 atoms, 863 residues, 1 model selected
> color sel silver
> select clear
> select #2.2
6785 atoms, 856 residues, 1 model selected
> color sel light gray
> color sel light gray
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/6SOF_dmIRholo_6PXV.cxs
> close session
> open
> /Users/cristinaviola/MRC_Jan13_Feb22/dmIRholo_map_model_220121/dIR_01_real_space_refined_008.pdb
> /Users/cristinaviola/MRC_Jan13_Feb22/dmIRholo_map_model_220121/blur.mrc
Chain information for dIR_01_real_space_refined_008.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
Opened blur.mrc as #2, grid size 324,324,324, pixel 0.738, shown at level
0.0163, step 2, values float32
> ui tool show "Show Sequence Viewer"
> select /A
6841 atoms, 6994 bonds, 863 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> volume #2 step 1
> volume #2 color #b2b2b263
> volume #2 style mesh
> volume #2 style image
> volume #2 style mesh
> volume #2 style surface
> volume #2 color #b2b2b23b
> volume #2 color #b2b2b237
> select /B
6785 atoms, 6937 bonds, 856 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> volume #2 level 0.02164
> select /C
134 atoms, 136 bonds, 21 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel magenta
> select /D
175 atoms, 177 bonds, 27 residues, 1 model selected
> color sel pale green
> color sel pale green
> hide sel atoms
> show sel cartoons
> color sel medium spring green
> color sel medium spring green
> color sel spring green
> color sel coral
> color sel chartreuse
> select /E
164 atoms, 167 bonds, 24 residues, 1 model selected
> color sel magenta
> hide sel atoms
> show sel cartoons
> select /F
118 atoms, 119 bonds, 20 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel chartreuse
> select /G
170 atoms, 173 bonds, 25 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel magenta
> select /H
142 atoms, 144 bonds, 23 residues, 1 model selected
> color sel chartreuse
> hide sel atoms
> show sel cartoons
> select /I
125 atoms, 128 bonds, 16 residues, 1 model selected
> color sel medium slate blue
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select /J
201 atoms, 205 bonds, 24 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> color sel dark salmon
> select clear
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_map_model_aligned.cxs
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon.png
> width 1346 height 881 supersample 3 transparentBackground true
> volume #2 color #b2b2b259
> volume #2 color #b2b2b255
> volume #2 color #b2b2b254
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon2.png
> width 1346 height 881 supersample 3
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon2.png
> width 1346 height 881 supersample 3 transparentBackground true
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> select /A
6841 atoms, 6994 bonds, 863 residues, 1 model selected
> cartoon style sel xsection oval modeHelix default
> cartoon style sel modeHelix tube sides 20
> cartoon style sel xsection oval modeHelix default
> select clear
> hide #!2 models
> show #!2 models
> lighting flat
> lighting flat
> set bgColor white
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting flat
> graphics silhouettes false
> lighting flat
> lighting full
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting simple
> lighting soft
> lighting soft
> lighting soft
> lighting soft
> lighting soft
> lighting soft
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> lighting soft
> lighting soft
> lighting full
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon.png
> width 1346 height 881 supersample 3 transparentBackground true
> volume #2 color #b2b2b26b
> volume #2 color #b2b2b26c
> volume #2 color #b2b2b270
> volume #2 color #919191
> volume #2 color #91919156
> volume #2 color #91919157
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon2.png
> width 1346 height 881 supersample 3 transparentBackground true
> volume #2 color #005493
> volume #2 color #00549336
> volume #2 color #9437ff
> volume #2 color #9437ff3b
> volume #2 color #005493
> volume #2 color #00549325
> volume #2 color #00549326
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon3.png
> width 1346 height 881 supersample 3
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon3.png
> width 1346 height 881 supersample 3 transparentBackground true
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon3.png
> width 1346 height 881 supersample 3 transparentBackground true
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon3.png
> width 1125 height 881 supersample 3 transparentBackground true
> hide #!2 models
> show #!2 models
> ui tool show "Side View"
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon3.png
> width 1125 height 881 supersample 3 transparentBackground true
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_ribbon_Dilps_ribbon4.png
> width 1125 height 881 supersample 3 transparentBackground true
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.02451
> volume #2 level 0.02235
> save /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/zoom1.png width 1125
> height 881 supersample 3 transparentBackground true
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/6SOF_chimera/dmIR_map_model_aligned.cxs
> includeMaps true
——— End of log from Wed Feb 2 22:45:45 2022 ———
opened ChimeraX session
> set bgColor black
> open /Users/cristinaviola/Desktop/7pg0.pdb
7pg0.pdb title:
Low resolution cryo-em structure of full-length insulin receptor bound to 3
insulin with visible DDM micelle, conf 1 [more info...]
Chain information for 7pg0.pdb #3
---
Chain | Description
A B | IR
C E I | insulin
D F J | insulin
> ui tool show Matchmaker
> matchmaker #3/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 dIR_01_real_space_refined_008.pdb, chain A (#1) with 7pg0.pdb,
chain B (#3), sequence alignment score = 1314.5
RMSD between 104 pruned atom pairs is 1.326 angstroms; (across all 748 pairs:
37.522)
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #3/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 dIR_01_real_space_refined_008.pdb, chain B (#1) with 7pg0.pdb,
chain B (#3), sequence alignment score = 1339.9
RMSD between 83 pruned atom pairs is 1.339 angstroms; (across all 745 pairs:
16.162)
> ui tool show "Side View"
> hide atoms
> show cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> select #1
14855 atoms, 15183 bonds, 1899 residues, 1 model selected
> select #3
14030 atoms, 14414 bonds, 10 pseudobonds, 1742 residues, 2 models selected
> select #1
14855 atoms, 15183 bonds, 1899 residues, 1 model selected
> select #1/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:335-628
2321 atoms, 2369 bonds, 294 residues, 1 model selected
> select #1/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:335-734
3134 atoms, 3199 bonds, 400 residues, 1 model selected
> select #1/B:734
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/B:731-734
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:335-675
2673 atoms, 2728 bonds, 341 residues, 1 model selected
> select #1/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:335-534
1604 atoms, 1632 bonds, 200 residues, 1 model selected
> select #1/B:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:335-469
1092 atoms, 1113 bonds, 135 residues, 1 model selected
> select #1/B:470
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:470-591
945 atoms, 963 bonds, 122 residues, 1 model selected
> hide #1 models
> show #1 models
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B
Alignment identifier is 1
> select #3/A-B:1
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A-B:1-468
7278 atoms, 7465 bonds, 5 pseudobonds, 911 residues, 2 models selected
> select #3/A-B:1
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A-B:1-647
10190 atoms, 10476 bonds, 6 pseudobonds, 1263 residues, 2 models selected
> select #3/A-B:1
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/A-B:1-601
9434 atoms, 9696 bonds, 6 pseudobonds, 1171 residues, 2 models selected
> color (#!3 & sel) light gray
> select clear
> hide #1 models
> hide #!3 models
> show #!3 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 #!3 models
> show #!2 models
> ui tool show "Volume Viewer"
> volume #2 level 0.01624
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> open /Users/cristinaviola/MRC_Jan13_Feb22/chimera_compare6SOF/6SOFcolor.pdb
6SOFcolor.pdb title:
Human insulin receptor ectodomain bound by 4 insulin [more info...]
Chain information for 6SOFcolor.pdb #4
---
Chain | Description
A C | IR
B D | IR
E G I K | insulin
F H J L | insulin
> show #1,4 atoms
> hide #1,4 atoms
> show #1,4 cartoons
> ui tool show Matchmaker
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x600017006dc0>
contents scale of 1 - updating layer to match.
> matchmaker #4/A to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 dIR_01_real_space_refined_008.pdb, chain B (#1) with 6SOFcolor.pdb,
chain A (#4), sequence alignment score = 1139.9
RMSD between 79 pruned atom pairs is 1.156 angstroms; (across all 676 pairs:
20.238)
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request
tool_instance.delete()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete
ToolInstance.delete(self)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool
tw._destroy()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy
sbar.destroy()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy
v.delete()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete
self.make_current()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current
qc = self._initialize_context()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> show #!3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/C
Alignment identifier is 1
> select #4/A,C:466
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/A,C:466-605
4410 atoms, 4485 bonds, 280 residues, 1 model selected
> select #4/A,C:466
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/A,C:466-523
1904 atoms, 1938 bonds, 116 residues, 1 model selected
> select #4/A,C:466
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/A,C:466-571
3408 atoms, 3471 bonds, 212 residues, 1 model selected
> hide #1 models
> show #1 models
> matchmaker #1/B to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with dIR_01_real_space_refined_008.pdb,
chain B (#1), sequence alignment score = 107.9
RMSD between 57 pruned atom pairs is 1.086 angstroms; (across all 92 pairs:
7.427)
> matchmaker #1/B to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with dIR_01_real_space_refined_008.pdb,
chain B (#1), sequence alignment score = 107.9
RMSD between 57 pruned atom pairs is 1.086 angstroms; (across all 92 pairs:
7.427)
> matchmaker #1/B to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with dIR_01_real_space_refined_008.pdb,
chain B (#1), sequence alignment score = 107.9
RMSD between 57 pruned atom pairs is 1.086 angstroms; (across all 92 pairs:
7.427)
> matchmaker #3/B to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with 7pg0.pdb, chain B (#3), sequence
alignment score = 517.7
RMSD between 80 pruned atom pairs is 1.136 angstroms; (across all 100 pairs:
2.555)
> matchmaker #3/B to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with 7pg0.pdb, chain B (#3), sequence
alignment score = 517.7
RMSD between 80 pruned atom pairs is 1.136 angstroms; (across all 100 pairs:
2.555)
> hide #1 models
> hide #!3 models
> show #!3 models
> hide #4 models
> show #4 models
> matchmaker #3/A to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with 7pg0.pdb, chain A (#3), sequence
alignment score = 483.5
RMSD between 74 pruned atom pairs is 1.095 angstroms; (across all 106 pairs:
2.797)
> show #1 models
> hide #4 models
> hide #!3 models
> hide #1 models
> show #!3 models
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #4 models
> matchmaker #3/B to #4/C & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain C (#4) with 7pg0.pdb, chain B (#3), sequence
alignment score = 512.3
RMSD between 77 pruned atom pairs is 1.078 angstroms; (across all 100 pairs:
2.635)
> show #4 models
> hide #!3 models
> hide #4 models
> show #4 models
> show #!3 models
> show #1 models
> hide #!3 models
> hide #4 models
> matchmaker #1/A to #4/C & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain C (#4) with dIR_01_real_space_refined_008.pdb,
chain A (#1), sequence alignment score = 118.6
RMSD between 56 pruned atom pairs is 0.908 angstroms; (across all 92 pairs:
6.864)
> show #!3 models
> show #4 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #!3 models
> show #!3 models
> hide #4 models
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #4 models
> matchmaker #3/A to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with 7pg0.pdb, chain A (#3), sequence
alignment score = 483.5
RMSD between 74 pruned atom pairs is 1.095 angstroms; (across all 106 pairs:
2.797)
> show #4 models
> hide #4 models
> hide #!3 models
> show #1 models
> show #4 models
> hide #4 models
> matchmaker #1/A to #4/A & sel pairing ss
Parameters
---
Chain pairing | ss
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 6SOFcolor.pdb, chain A (#4) with dIR_01_real_space_refined_008.pdb,
chain A (#1), sequence alignment score = 107.9
RMSD between 52 pruned atom pairs is 1.021 angstroms; (across all 92 pairs:
7.317)
> show #!3 models
> show #4 models
> hide #1 models
> hide #4 models
> show #1 models
> show #4 models
> hide #!3 models
> hide #1 models
> show #1 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 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
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #4 models
> hide #!2 models
> show #!3 models
> show #4 models
No model chosen to save relative to
No model chosen to save relative to
No model chosen to save relative to
No model chosen to save relative to
> save /Users/cristinaviola/MRC_Jan13_Feb22/dIR.pdb models #1 relModel #1
> save /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/dIR.pdb
> models #1 relModel #1
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/Novo_7PG0.pdb
> models #3 relModel #1
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/Coskun)6SOF.pdb
> models #4 relModel #1
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/IRviews_align_Fn1.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f861a954070>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f861a954070>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 /Users/cristinaviola/Desktop/IRviews.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f861a954070>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f861a954070>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f861a954070>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request
tool_instance.delete()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete
ToolInstance.delete(self)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool
tw._destroy()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy
sbar.destroy()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy
v.delete()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete
self.make_current()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current
qc = self._initialize_context()
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> select clear
> save /Users/cristinaviola/Desktop/test.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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.
> show #!2 models
> hide #!2 models
> close #2
> save /Users/cristinaviola/Desktop/test.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 /Users/cristinaviola/Desktop/test.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 162, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/IRviews.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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.
> ui tool show "Cage Builder"
No model chosen to save relative to
> save
> /Users/cristinaviola/MRC_Jan13_Feb22/Marek_IRviews_super_220203/test.cxs
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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
0x7f8661168be0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7f8645a81e80>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7f8661168be0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7f8645a81e80>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/private/var/folders/xc/lg35tphs29g02w0l0mf_t3vw0000gn/T/AppTranslocation/B6EE9CEE-F86A-4143-AFF4-22ED808C02AB/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/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: 4.1 INTEL-14.7.18
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H1323)
Kernel Version: Darwin 19.6.0
Time since boot: 25 days 18:19
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
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: 1.13.2
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: 1.2.5
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: 1.1.3
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: 1.7.6
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: 5.0.9
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: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
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
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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: 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: 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
Change History (3)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem destroying status bar: wrapped C/C++ object of type QScreen has been deleted |
follow-up: 2 comment:2 by , 4 years ago
Dear Eric, Many thanks for getting back to me and looking into the problem - I will try and save sessions more frequently. Kind regards, Cristina On Fri, 4 Feb 2022 at 17:32, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:3 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This was fixed long ago and our current ChimeraX 1.3 does not have this problem which was caused by using two screens and disconnecting one of them.
Note:
See TracTickets
for help on using tickets.
Hi Cristina,
--Eric