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Opened 2 years ago
Closed 2 years ago
#9197 closed defect (limitation)
Session close, bond rotations: 'list' object has no attribute 'values'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here) Does not restore session
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:/Users/sohai/OneDrive/Documents/2023/Raymond Work/Chimera
> Files/GPD2-Dimer-Ribbon2.cxs"
Log from Fri Jun 16 15:21:05 2023UCSF ChimeraX version: 1.7.dev202306142048
(2023-06-14)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "H:\My documents\2023\AlphaFold Structure_G3PDh2\Chimera X
> Structures\GPD2-Dimer-Ribbon2.cxs" format session
Log from Fri Jun 16 12:32:02 2023 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.dev202306142048 (2023-06-14)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-dimer with Signal Peptide.pdb"
Chain information for GPD2-dimer with Signal Peptide.pdb #1
---
Chain | Description
A B | No description available
> open "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/Ecoli-GPD2_2r4e.pdb"
Ecoli-GPD2_2r4e.pdb title:
Crystal structure of escherichia coli glycerol-3-phosphate dehydrogenase In
complex with dhap [more info...]
Chain information for Ecoli-GPD2_2r4e.pdb #2
---
Chain | Description | UniProt
A B | aerobic glycerol-3-phosphate dehydrogenase | GLPD_ECOLI 1-501
Non-standard residues in Ecoli-GPD2_2r4e.pdb #2
---
13P — 1,3-dihydroxyacetonephosphate
BOG — octyl β-D-glucopyranoside
EDO — 1,2-ethanediol (ethylene glycol)
FAD — flavin-adenine dinucleotide
IMD — imidazole
PO4 — phosphate ion
T3A — N-(tris(hydroxymethyl)methyl)-3-aminopropanesulfonicacid
> select #2/A#2/B
8532 atoms, 8447 bonds, 1283 residues, 1 model selected
> show target m
> log metadata #1
The model has no metadata
> log chains #1
Chain information for GPD2-dimer with Signal Peptide.pdb #1
---
Chain | Description
A B | No description available
> log metadata #2
Metadata for Ecoli-GPD2_2r4e.pdb #2
---
Title | Crystal structure of escherichia coli glycerol-3-phosphate
dehydrogenase In complex with dhap
Citation | Structure of glycerol-3-phosphate dehydrogenase, anessential
monotopic membrane enzyme involved In respirationand metabolism. PMID:
18296637
Non-standard residues | 13P — 1,3-dihydroxyacetonephosphate
BOG — octyl β-D-glucopyranoside
EDO — 1,2-ethanediol (ethylene glycol)
FAD — flavin-adenine dinucleotide
IMD — imidazole
PO4 — phosphate ion
T3A — N-(tris(hydroxymethyl)methyl)-3-aminopropanesulfonicacid
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.10Å
> log chains #2
Chain information for Ecoli-GPD2_2r4e.pdb #2
---
Chain | Description | UniProt
A B | aerobic glycerol-3-phosphate dehydrogenase | GLPD_ECOLI 1-501
> log metadata #1
The model has no metadata
> log chains #1
Chain information for GPD2-dimer with Signal Peptide.pdb #1
---
Chain | Description
A B | No description available
> log metadata #2
Metadata for Ecoli-GPD2_2r4e.pdb #2
---
Title | Crystal structure of escherichia coli glycerol-3-phosphate
dehydrogenase In complex with dhap
Citation | Structure of glycerol-3-phosphate dehydrogenase, anessential
monotopic membrane enzyme involved In respirationand metabolism. PMID:
18296637
Non-standard residues | 13P — 1,3-dihydroxyacetonephosphate
BOG — octyl β-D-glucopyranoside
EDO — 1,2-ethanediol (ethylene glycol)
FAD — flavin-adenine dinucleotide
IMD — imidazole
PO4 — phosphate ion
T3A — N-(tris(hydroxymethyl)methyl)-3-aminopropanesulfonicacid
Gene source | Escherichia coli
Experimental method | X-ray diffraction
Resolution | 2.10Å
> log chains #2
Chain information for Ecoli-GPD2_2r4e.pdb #2
---
Chain | Description | UniProt
A B | aerobic glycerol-3-phosphate dehydrogenase | GLPD_ECOLI 1-501
> hide target m
> show target m
> select subtract #2
Nothing selected
> select #1/A
11411 atoms, 11518 bonds, 727 residues, 1 model selected
> select add #1
22822 atoms, 23036 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select #1/B
11411 atoms, 11518 bonds, 727 residues, 1 model selected
> select add #1
22822 atoms, 23036 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
22822 atoms, 23036 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
8532 atoms, 8447 bonds, 1283 residues, 1 model selected
> select subtract #2
Nothing selected
> help help:user/tools/modelpanel.html
> show #2 target m
> view #2 clip false
[Repeated 1 time(s)]
> show #2 target m
> view #2 clip false
> color #1 #d26fcaff
> hide #1 models
> show #1 models
> color #1 #d272c8ff
> color #1 #ffaa00ff
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
ID must be one or more integers separated by '.' characters
[Repeated 2 time(s)]
> select add #1
22822 atoms, 23036 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
22822 atoms, 23036 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> ui autostart false "Model Panel"
> ui autostart true "Model Panel"
> ui tool show Matchmaker
> matchmaker #1 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 Ecoli-GPD2_2r4e.pdb, chain B (#2) with GPD2-dimer with Signal
Peptide.pdb, chain B (#1), sequence alignment score = 905.7
RMSD between 310 pruned atom pairs is 0.993 angstroms; (across all 476 pairs:
3.892)
> matchmaker #1 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 Ecoli-GPD2_2r4e.pdb, chain B (#2) with GPD2-dimer with Signal
Peptide.pdb, chain B (#1), sequence alignment score = 905.7
RMSD between 310 pruned atom pairs is 0.993 angstroms; (across all 476 pairs:
3.892)
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select #1/B
11411 atoms, 11518 bonds, 727 residues, 1 model selected
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select #2/B
4251 atoms, 4207 bonds, 642 residues, 1 model selected
> hide #1 target m
[Repeated 1 time(s)]
> show #1 target m
> hide sel cartoons
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> hide #2 models
> show #2 models
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> select #2/A
4281 atoms, 4240 bonds, 641 residues, 1 model selected
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> select clear
> select #2/A
4281 atoms, 4240 bonds, 641 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #2/B
4251 atoms, 4207 bonds, 642 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2/B
4251 atoms, 4207 bonds, 642 residues, 1 model selected
> select ::name="13P"
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 20 atom styles
> select ::name="BOG"
120 atoms, 120 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 120 atom styles
> color sel orange
> select add #2
8532 atoms, 8447 bonds, 1283 residues, 1 model selected
> select subtract #2
Nothing selected
> select ::name="13P"
20 atoms, 18 bonds, 2 residues, 1 model selected
> select clear
> select ::name="BOG"
120 atoms, 120 bonds, 6 residues, 1 model selected
> color sel purple
> select clear
> select ::name="13P"
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel forest green
> select clear
[Repeated 2 time(s)]
> select #2/A:1955@C2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:1952@O1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
4281 atoms, 4240 bonds, 641 residues, 1 model selected
> hide sel atoms
> select clear
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 106 atom styles
> color sel yellow
> select clear
> select #2/A:600@C10
1 atom, 1 residue, 1 model selected
> select up
53 atoms, 58 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui tool show Rotamers
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B
Alignment identifier is 1
> select #1/A-B:78
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A-B:78
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A-B:76
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A-B:76-78
42 atoms, 40 bonds, 6 residues, 1 model selected
> select #1/A-B:78
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A-B:78
14 atoms, 12 bonds, 2 residues, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel GLU rotLib Dunbrack
GPD2-dimer with Signal Peptide.pdb #1/A GLY 78: phi -80.4, psi 174.5 trans
Changed 324 bond radii
GPD2-dimer with Signal Peptide.pdb #!1/B GLY 78: phi -81.4, psi 173.0 trans
Changed 324 bond radii
> clashes #!1 & ~#!1/B:78 & ~solvent radius 0.075 reveal true restrict #1.2 &
> ~@c,ca,n
263 clashes
> clashes #!1 & ~#!1/A:78 & ~solvent radius 0.075 reveal true restrict #1.1 &
> ~@c,ca,n
266 clashes
No rotamers selected
> swapaa #!1/A:78 GLU criteria 1 rotLib Dunbrack
Using Dunbrack library
GPD2-dimer with Signal Peptide.pdb #!1/A GLY 78: phi -80.4, psi 174.5 trans
Applying GLU rotamer (chi angles: -63.8 -66.6 -31.8) to GPD2-dimer with Signal
Peptide.pdb #!1/A GLU 78
> swapaa #!1/B:78 GLU criteria 1 rotLib Dunbrack
Using Dunbrack library
GPD2-dimer with Signal Peptide.pdb #!1/B GLY 78: phi -81.4, psi 173.0 trans
Applying GLU rotamer (chi angles: -63.8 -66.6 -31.8) to GPD2-dimer with Signal
Peptide.pdb #!1/B GLU 78
> swapaa interactive sel GLU rotLib Dunbrack
GPD2-dimer with Signal Peptide.pdb #1/A GLU 78: phi -80.4, psi 174.5 trans
Changed 324 bond radii
GPD2-dimer with Signal Peptide.pdb #!1/B GLU 78: phi -81.4, psi 173.0 trans
Changed 324 bond radii
> swapaa #!1/B:78 GLU criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
GPD2-dimer with Signal Peptide.pdb #!1/B GLU 78: phi -81.4, psi 173.0 trans
Applying GLU rotamer (chi angles: -63.8 -66.6 -31.8) to GPD2-dimer with Signal
Peptide.pdb #!1/B GLU 78
> swapaa #!1/A:78 GLU criteria 1 rotLib Dunbrack retain false
Using Dunbrack library
GPD2-dimer with Signal Peptide.pdb #!1/A GLU 78: phi -80.4, psi 174.5 trans
Applying GLU rotamer (chi angles: -63.8 -66.6 -31.8) to GPD2-dimer with Signal
Peptide.pdb #!1/A GLU 78
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/B:80@HG1
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:80
28 atoms, 26 bonds, 2 residues, 1 model selected
> select #1/A-B:80
28 atoms, 26 bonds, 2 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> style sel ball
Changed 24 atom styles
> color sel red
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select clear
> select #1/B:104@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> hide sel atoms
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #1/B:79@HB1
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A-B:42
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/A-B:1-42
1316 atoms, 1324 bonds, 84 residues, 1 model selected
> color sel white
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> save "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-Dimer-Ribbon.cxs"
> color bychain
> select ::name="13P"
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel forest green
> select clear
> select ::name="BOG"
120 atoms, 120 bonds, 6 residues, 1 model selected
> color sel purple
> select clear
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> select #1/A-B:43
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/A-B:40-43
116 atoms, 114 bonds, 8 residues, 1 model selected
> select #1/A-B:42-43
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #1/A-B:41-43
84 atoms, 82 bonds, 6 residues, 1 model selected
> select #1/A-B:1
38 atoms, 36 bonds, 2 residues, 1 model selected
> select #1/A-B:1-41
1296 atoms, 1304 bonds, 82 residues, 1 model selected
> select #1/A-B:42-43
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #1/A-B:41-43
84 atoms, 82 bonds, 6 residues, 1 model selected
> select #1/A-B:1
38 atoms, 36 bonds, 2 residues, 1 model selected
> select #1/A-B:1-42
1316 atoms, 1324 bonds, 84 residues, 1 model selected
> color sel white
> select clear
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> color sel red
> select clear
> save "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-Dimer-Ribbon2.cxs" includeMaps true
——— End of log from Fri Jun 16 12:32:02 2023 ———
opened ChimeraX session
> select #1/A-B:402
48 atoms, 46 bonds, 2 residues, 1 model selected
> select #1/A-B:402
48 atoms, 46 bonds, 2 residues, 1 model selected
> color sel blue
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #3
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #3 models
> select subtract #3
Nothing selected
> select #1/A-B:402
48 atoms, 46 bonds, 2 residues, 1 model selected
> select #1/A-B:402
48 atoms, 46 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select subtract #3
Nothing selected
> save "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-Dimer-Ribbon2.cxs"
> save "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-Dimer-Ribbon3.tif" width 1341 height 788 supersample 3
> select #1/A
11416 atoms, 11523 bonds, 727 residues, 1 model selected
> color sel hot pink
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> save "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-Dimer-Ribbon3.tif" width 1341 height 788 supersample 3
> save "H:/My documents/2023/AlphaFold Structure_G3PDh2/Chimera X
> Structures/GPD2-Dimer-Ribbon2.cxs"
——— End of log from Fri Jun 16 15:21:05 2023 ———
opened ChimeraX session
> select subtract #3
Nothing selected
> select ::name="BOG"
120 atoms, 120 bonds, 6 residues, 1 model selected
> style sel sphere
Changed 120 atom styles
> select subtract #3
120 atoms, 120 bonds, 6 residues, 1 model selected
> select add #2
8532 atoms, 8447 bonds, 1283 residues, 1 model selected
> select subtract #2
Nothing selected
> select subtract #3
Nothing selected
> select #1/B
11416 atoms, 11523 bonds, 727 residues, 1 model selected
> color sel light gray
> color sel gray
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select #1/A-B:42-43
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #1/A-B:42-43
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #1/A-B:1
38 atoms, 36 bonds, 2 residues, 1 model selected
> select #1/A-B:1-42
1316 atoms, 1324 bonds, 84 residues, 1 model selected
> color sel white
> select clear
> select #1/A
11416 atoms, 11523 bonds, 727 residues, 1 model selected
> color sel dark gray
> select clear
> select #1/A
11416 atoms, 11523 bonds, 727 residues, 1 model selected
> color sel cyan
> select clear
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #1/A-B:78
24 atoms, 22 bonds, 2 residues, 1 model selected
> color sel red
> select clear
> select #1/A-B:1
38 atoms, 36 bonds, 2 residues, 1 model selected
> select #1/A-B:1-42
1316 atoms, 1324 bonds, 84 residues, 1 model selected
> color sel white
> select clear
> select #1/A-B:402
48 atoms, 46 bonds, 2 residues, 1 model selected
> select #1/A-B:402
48 atoms, 46 bonds, 2 residues, 1 model selected
> color sel blue
> select clear
> save C:\Users\Public\Desktop\image1.png supersample 3
Permission denied writing file C:\Users\Public\Desktop\image1.png
> save "C:/Users/sohai/OneDrive/Documents/2023/Raymond Work/Chimera
> Files/GPD2_Ribbon_Raymond colors1.cxs"
> save "C:/Users/sohai/OneDrive/Documents/2023/Raymond Work/Chimera
> Files/GPD2_Ribbon_Raymond colors1.tif" width 1343 height 819 supersample 3
> select subtract #3
Nothing selected
> select add #1
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> hide sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:1950@C8'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/B:1949@C3'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #1/A:402@NH2
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
36 atoms, 35 bonds, 3 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:78@CB
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select up
14 atoms, 12 bonds, 2 residues, 1 model selected
> select up
23 atoms, 21 bonds, 2 residues, 1 model selected
> select up
138 atoms, 137 bonds, 11 residues, 1 model selected
> select up
11416 atoms, 11523 bonds, 727 residues, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> save "C:/Users/sohai/OneDrive/Documents/2023/Raymond Work/Chimera
> Files/Acive-site with GE mutation 1.tif" width 1343 height 819 supersample 3
> save "C:/Users/sohai/OneDrive/Documents/2023/Raymond Work/Chimera
> Files/GPD2-catalytic site_GE mutation 1.cxs"
> select sel @< 5
188 atoms, 166 bonds, 32 residues, 2 models selected
> select clear
> select #1/B:78@O
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:402@HA
1 atom, 1 residue, 1 model selected
> select clear
> select add #1/B:78@O
1 atom, 1 residue, 1 model selected
> select add #1/B:402@HA
2 atoms, 2 residues, 1 model selected
> select up
36 atoms, 34 bonds, 2 residues, 1 model selected
> select sel @< 5
462 atoms, 423 bonds, 79 residues, 2 models selected
> select sel @< 5
1620 atoms, 1495 bonds, 230 residues, 2 models selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
30738 atoms, 31142 bonds, 2442 residues, 2 models selected
> select add #2
31364 atoms, 31493 bonds, 2737 residues, 2 models selected
> select subtract #2
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #3
22832 atoms, 23046 bonds, 1454 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1/B:78@O
1 atom, 1 residue, 1 model selected
> select add #1/B:402@HA
2 atoms, 2 residues, 1 model selected
> select up
36 atoms, 34 bonds, 2 residues, 1 model selected
> select sel :< 5
795 atoms, 780 bonds, 79 residues, 2 models selected
> select sel :< 5
3625 atoms, 3587 bonds, 348 residues, 2 models selected
> show sel atoms
> undo
> select subtract #3
3625 atoms, 3587 bonds, 348 residues, 2 models selected
> select add #2
10846 atoms, 10758 bonds, 1438 residues, 2 models selected
> select subtract #2
2314 atoms, 2311 bonds, 155 residues, 1 model selected
> select subtract #3
2314 atoms, 2311 bonds, 155 residues, 1 model selected
> show sel target ab
> undo
> select sel :< 5
7864 atoms, 7819 bonds, 735 residues, 2 models selected
> select sel :< 5
12007 atoms, 12010 bonds, 1097 residues, 2 models selected
> select subtract #3
12007 atoms, 12010 bonds, 1097 residues, 2 models selected
> hide #* target a
> show sel target ab
> undo
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 1018, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 669, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
AttributeError: 'list' object has no attribute 'values'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
See log for complete Python traceback.
> open "C:\Users\sohai\OneDrive\Documents\2023\Raymond Work\Chimera
> Files\GPD2-catalytic site_GE mutation 1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore
self.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore
self.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 368, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1004, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 742, in restore
self.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
AttributeError: 'list' object has no attribute 'values'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
See log for complete Python traceback.
> open "C:\Users\sohai\OneDrive\Documents\2023\Raymond Work\Chimera
> Files\GPD2-catalytic site_GE mutation 1.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore
self.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore
self.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 368, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1004, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 742, in restore
self.reset()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
AttributeError: 'list' object has no attribute 'values'
AttributeError: 'list' object has no attribute 'values'
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 45, in delete_all_rotations
for rotater in self.bond_rotaters.values():
See log for complete Python traceback.
OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.40 27.20.14040.4
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: en_AU.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: LENOVO
Model: F0FY0002AU
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 7,929,311,232
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Session close, bond rotations: 'list' object has no attribute 'values' |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
You can't restore the session saved from the 1.7 daily build in the 1.6.1 release. Session files are not backwards compatible.