![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9450 closed defect (duplicate)
Session restore: 'list' object has no attribute 'values'
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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-10-10.0.22621
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
trying to restore a saved *.cxs file....
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21b.cxs" format session
Log from Fri Jul 21 12:47:56 2023UCSF ChimeraX version: 1.7.dev202307052255
(2023-07-05)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for
> nanome\july-21a.cxs" format session
Log from Fri Jul 21 12:11:30 2023UCSF ChimeraX version: 1.7.dev202307052255
(2023-07-05)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic
> open
> L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/klk5-spink9(6qfe-6kbrspink2).pdb
> format pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/klk5-spink9(6qfe-6kbrspink2).pdb
---
warnings | Ignored bad PDB record found on line 26
HELIX 1 1 GLN A 165 ALA A 173 1 Generated by MOE 7
Ignored bad PDB record found on line 27
HELIX 2 2 LEU A 231 PHE A 234 5 Generated by MOE 4
Ignored bad PDB record found on line 28
HELIX 3 3 THR A 235 ALA A 244 1 Generated by MOE 10
Ignored bad PDB record found on line 29
HELIX 4 4 ASP B 64 THR B 74 1 Generated by MOE 11
Ignored bad PDB record found on line 30
SHEET 1 SER A 20 ASP A 21 Generated by MOE
17 messages similar to the above omitted
Chain information for klk5-spink9(6qfe-6kbrspink2).pdb #1
---
Chain | Description
A | No description available
B | No description available
> split
Split klk5-spink9(6qfe-6kbrspink2).pdb (#1) into 2 models
Chain information for klk5-spink9(6qfe-6kbrspink2).pdb A #1.1
---
Chain | Description
A | No description available
Chain information for klk5-spink9(6qfe-6kbrspink2).pdb B #1.2
---
Chain | Description
B | No description available
> color #1.2 #ff55ffff
> open L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/babu-
> jun28-21-spink9-klk5.pptx
Unrecognized file suffix '.pptx'
> select add #1.2/B:47
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel target ab
> select add #1.2/B:48
34 atoms, 34 bonds, 2 residues, 1 model selected
> show sel target ab
> open
> L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/jun24_spink9_all_seven.pdb
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/jun24_spink9_all_seven.pdb
---
warnings | Ignored bad PDB record found on line 8
HELIX 1 1 ASP A 64 THR A 74 1 Generated by MOE 11
Ignored bad PDB record found on line 9
SHEET 1 ILE A 53 GLY A 55 Generated by MOE
Ignored bad PDB record found on line 10
SHEET 2 THR A 60 TYR A 61 Generated by MOE
Ignored bad PDB record found on line 11
SHEET 3 PHE A 80 PHE A 83 Generated by MOE
Chain information for jun24_spink9_all_seven.pdb #2
---
Chain | Description
A | No description available
> hide #1.2 models
> select add #2/A:48
58 atoms, 57 bonds, 3 residues, 2 models selected
> show (#2 & sel) target ab
> select clear
> delete H
> show #1.2 models
> save
> L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/klk5-spink9_jul20.cxs.pdb
> hide #1.2 models
> hide #2 models
> show #1.2 models
> help help:user
> interfaces #1.1 contacting #1.2
Expected a keyword
> interfaces #1.1 #1.2 probeRadius 3.8
1 buried areas: #1.1/A #1.2/B 1475
> interfaces #1.1 #1.2
1 buried areas: #1.1/A #1.2/B 1017
> interfaces #1.1 #2
1 buried areas: #1.1/A #2/A 1015
> show #2 models
> hide #1.2 models
> color (#1.1 &protein) & ((#2 & protein) <3.8) red target ars
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color (#1.1 & protein) & ((#2 & protein) <3.8) red target ars
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color (#1.1 & protein) & ((#2 & protein) @<3.8) red target ars
> color (#1.1 & protein) & ((#1.2 & protein) @<3.8) red target ars
> color (#1.1 & protein) & ((#2 & protein) @<3.8) red target ars
> select (#1.1 & protein) & ((#2 & protein) @<3.8) red target ars
Expected a keyword
> select (/#1.1 & protein) & ((/#2 & protein) @<3.8)
Expected an objects specifier or a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8)
79 atoms, 45 bonds, 26 residues, 1 model selected
> show sel target ab
> select residues (#1.1 & protein) & ((#2 & protein) @<3.8)
Invalid "residues" argument: Expected true or false (or 1 or 0)
> save L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/*.cxs.pdb
Cannot save 'L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/*.cxs.pdb':
Unable to open file
'L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/*.cxs.pdb' for writing
> select residues (#1.1 & protein) & ((#2 & protein) @<3.8)
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select residues true (#1.1 & protein) & ((#2 & protein) @<3.8)
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 residue tru
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 residue true
Expected a keyword
> help help:user
> select residues true (#1.1 & protein) & ((#2 & protein) @<3.8 residue true
Expected a keyword
> select residues true (#1.1 & protein) & ((#2 & protein) @<3.8
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 residues true
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 color blue
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 ) color blue
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 ) target ars
Expected a keyword
> select (#1.1 & protein) & ((#2 & protein) @<3.8 )
79 atoms, 45 bonds, 26 residues, 1 model selected
> select (#1.1 & protein) & ((#2 & protein) @<3.8 ) residues true
210 atoms, 207 bonds, 26 residues, 1 model selected
> show sel target ab
> select (#1.1 & protein) & ((#1.2 & protein) @<3.8 ) residues true
198 atoms, 194 bonds, 23 residues, 1 model selected
> select (#1.1 & protein) & ((#1.2 & protein) @<3.0 ) residues true
131 atoms, 126 bonds, 14 residues, 1 model selected
> select (#1.1 & protein) & ((#2 & protein) @<3.0 ) residues true
95 atoms, 90 bonds, 11 residues, 1 model selected
> tile
2 models tiled
> close session
> save L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/jul20.cxs
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5__KLK5_6qfe_A.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5__KLK5_6qfe_A.pdb
---
warnings | Ignored bad PDB record found on line 22
HELIX 1 1 GLN A 165 ALA A 173 1 Generated by MOE 7
Ignored bad PDB record found on line 23
HELIX 2 2 LEU A 231 PHE A 234 5 Generated by MOE 4
Ignored bad PDB record found on line 24
HELIX 3 3 THR A 235 ALA A 244 1 Generated by MOE 10
Ignored bad PDB record found on line 25
SHEET 1 SER A 20 ASP A 21 Generated by MOE
Ignored bad PDB record found on line 26
SHEET 2 GLN A 30 LEU A 37 Generated by MOE
12 messages similar to the above omitted
Chain information for klk5__KLK5_6qfe_A.pdb #1
---
Chain | Description
A | No description available
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5__spink9_all_seven.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5__spink9_all_seven.pdb
---
warnings | Ignored bad PDB record found on line 8
HELIX 1 1 ASP A 64 THR A 74 1 Generated by MOE 11
Ignored bad PDB record found on line 9
SHEET 1 ILE A 53 GLY A 55 Generated by MOE
Ignored bad PDB record found on line 10
SHEET 2 THR A 60 TYR A 61 Generated by MOE
Ignored bad PDB record found on line 11
SHEET 3 PHE A 80 PHE A 83 Generated by MOE
Chain information for klk5__spink9_all_seven.pdb #2
---
Chain | Description
A | No description available
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5__spink9_His48Arg.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5__spink9_His48Arg.pdb
---
warnings | Ignored bad PDB record found on line 8
HELIX 1 1 ASP A 64 THR A 74 1 Generated by MOE 11
Ignored bad PDB record found on line 9
SHEET 1 ILE A 53 GLY A 55 Generated by MOE
Ignored bad PDB record found on line 10
SHEET 2 THR A 60 TYR A 61 Generated by MOE
Ignored bad PDB record found on line 11
SHEET 3 PHE A 80 PHE A 83 Generated by MOE
Chain information for klk5__spink9_His48Arg.pdb #3
---
Chain | Description
A | No description available
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5__spink9_Native_B.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5__spink9_Native_B.pdb
---
warnings | Ignored bad PDB record found on line 8
HELIX 1 1 ASP B 64 THR B 74 1 Generated by MOE 11
Ignored bad PDB record found on line 9
SHEET 1 ILE B 53 GLY B 55 Generated by MOE
Ignored bad PDB record found on line 10
SHEET 2 THR B 60 TYR B 61 Generated by MOE
Ignored bad PDB record found on line 11
SHEET 3 PHE B 80 PHE B 83 Generated by MOE
Chain information for klk5__spink9_Native_B.pdb #4
---
Chain | Description
B | No description available
> hide #3 models
> hide #2 models
> show #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> tile
3 models tiled
> stop tile
Expected fewer arguments
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/bcx13616_A.pdb"
> hide #5 models
> show #5 models
> hide #3 models
> hide #4 models
> tile off
> delete H
> tile
2 models tiled
> hide #5
> show #5
> show #4 models
> tile off
> select #5
38 atoms, 43 bonds, 1 residue, 1 model selected
> focus
Unknown command: focus
> select #5
38 atoms, 43 bonds, 1 residue, 1 model selected
> view
> zoom
Pixel size at center of rotation is 0.171
> zoom #5
Expected a number > 0 or a keyword
> zoom 120
> zoom -50
Missing or invalid "factor" argument: Must be greater than 0
> zoom 1
> tile off
> hide #4 models
> show sel cartoons
> hide sel cartoons
> ui mousemode right zoom
> zoom 10
> zoom 8
> zoom -1
Missing or invalid "factor" argument: Must be greater than 0
> ui mousemode right pivot
> pivot
Unknown command: pivot
> cofr sel
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5__spink9_17725.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5__spink9_17725.pdb
---
warning | Ignored bad PDB record found on line 6
HELIX 1 1 ASP A 64 CYS A 68 1 Generated by MOE 5
Chain information for klk5__spink9_17725.pdb #6
---
Chain | Description
A | No description available
> hide #6.1 models
> show #6.1 models
> select add #6/A:66
58 atoms, 63 bonds, 2 residues, 2 models selected
> select up
111 atoms, 117 bonds, 6 residues, 2 models selected
> select up
368 atoms, 378 bonds, 22 residues, 2 models selected
> close #6
> show #4 models
> hide #4 models
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5__spink9_17725.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5__spink9_17725.pdb
---
warnings | Ignored bad PDB record found on line 8
HELIX 1 1 ASP A 64 THR A 74 1 Generated by MOE 11
Ignored bad PDB record found on line 9
SHEET 1 ILE A 53 GLY A 55 Generated by MOE
Ignored bad PDB record found on line 10
SHEET 2 THR A 60 TYR A 61 Generated by MOE
Ignored bad PDB record found on line 11
SHEET 3 PHE A 80 PHE A 83 Generated by MOE
Chain information for klk5__spink9_17725.pdb #6
---
Chain | Description
A | No description available
> hide #5 models
> show #5 models
> show #4 models
> ui tool show Matchmaker
> matchmaker #6 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 klk5__spink9_all_seven.pdb, chain A (#2) with
klk5__spink9_17725.pdb, chain A (#6), sequence alignment score = 274.8
RMSD between 52 pruned atom pairs is 0.000 angstroms; (across all 52 pairs:
0.000)
> matchmaker #6 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 klk5__spink9_all_seven.pdb, chain A (#2) with
klk5__spink9_17725.pdb, chain A (#6), sequence alignment score = 274.8
RMSD between 52 pruned atom pairs is 0.000 angstroms; (across all 52 pairs:
0.000)
> hide #1 models
> hide #6 models
> show #6 models
> hide #5 models
> hide #4 models
> show #4 models
> ui tool show Matchmaker
> matchmaker #6 & sel to #4 & sel
No 'to' model specified
> matchmaker #6 & sel to #4/B & sel pairing bs
No 'to' chains specified
> matchmaker #6 & sel to #4/B & sel pairing bs
No 'to' chains specified
> matchmaker #6 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 klk5__spink9_Native_B.pdb, chain B (#4) with
klk5__spink9_17725.pdb, chain A (#6), sequence alignment score = 252.4
RMSD between 52 pruned atom pairs is 0.298 angstroms; (across all 52 pairs:
0.298)
> show #3 models
> show #2 models
> show #5 models
> select #6/A:48
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel target ab
> ui tool show Matchmaker
> matchmaker #2-4 to #6/A 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 klk5__spink9_17725.pdb, chain A (#6) with
klk5__spink9_all_seven.pdb, chain A (#2), sequence alignment score = 274.8
RMSD between 52 pruned atom pairs is 0.000 angstroms; (across all 52 pairs:
0.000)
Matchmaker klk5__spink9_17725.pdb, chain A (#6) with
klk5__spink9_His48Arg.pdb, chain A (#3), sequence alignment score = 255.9
RMSD between 52 pruned atom pairs is 0.298 angstroms; (across all 52 pairs:
0.298)
Matchmaker klk5__spink9_17725.pdb, chain A (#6) with
klk5__spink9_Native_B.pdb, chain B (#4), sequence alignment score = 252.4
RMSD between 52 pruned atom pairs is 0.298 angstroms; (across all 52 pairs:
0.298)
> show #1 models
> save "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21.cxs"
> delete H
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> close #2
> close #3
> save "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21a.cxs"
——— End of log from Fri Jul 21 12:11:30 2023 ———
opened ChimeraX session
> hide #1 models
> hide #5 models
> hide #6 models
> view clip false
> sel#4:41,43,44,45,46,47,48;show sel;
Unknown command: sel#4:41,43,44,45,46,47,48;show sel;
> select #4:41,43,44,45,46,47,48
61 atoms, 62 bonds, 7 residues, 1 model selected
> show sel
> select #4:41,43,44,45,46,47,48
61 atoms, 62 bonds, 7 residues, 1 model selected
> show sel
> style sel ball
Changed 61 atom styles
> color sel red
> color selby hetatoms;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byatoms;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel by element;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel byatom
> view
> select up
157 atoms, 164 bonds, 18 residues, 1 model selected
> select up
422 atoms, 437 bonds, 52 residues, 1 model selected
> swapaa #4:41,43,44,45,46,47,48 GLU,GLU,LEU,TYR,THR, ARG, GLU
Expected a keyword
> swapaa mousemode #4:41,43,44,45,46,47,48 GLU,GLU,LEU,TYR,THR, ARG, GLU
Missing or invalid "restype" argument: Should be one of 'ALA', 'ARG', 'ASN',
'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE',
'PRO', 'SER', 'THR', 'TRP', 'TYR', or 'VAL'
> swapaa mousemode #4:41 GLU
> swapaa mousemode #4:47 ARG
> save "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21b.cxs"
——— End of log from Fri Jul 21 12:47:56 2023 ———
opened ChimeraX session
> show #1 models
> hide #4 models
> show #6 models
> show #5 models
> hide #5 models
> hide #6 models
> hide #1 models
> show #1 models
> open C:/Users/RKrishnan/Desktop/boardmeeting-CXS-files/morph_nov29.html
Opened morph_nov29.html
> cd "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome"
Current working directory is:
L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for nanome
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5-bilogic"
'L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5-bilogic' has no suffix
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5-biologic.html"
Opened klk5-biologic.html
> open
Missing or invalid "fileNames" argument: Expected a file name
> save "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5.cxs.pdb"
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1051, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 700, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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
Missing or invalid "fileNames" argument: Expected a file name
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5.cxs.pdb"
Summary of feedback from opening
L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
nanome/klk5.cxs.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 165
ALA A 173 1 7
Start residue of secondary structure not found: HELIX 2 2 LEU A 231 PHE A 234
1 4
Start residue of secondary structure not found: HELIX 3 3 LYS A 236 ALA A 244
1 9
Start residue of secondary structure not found: SHEET 1 1 1 GLN A 30 LEU A 37
0
Start residue of secondary structure not found: SHEET 2 2 1 GLN A 39 HIS A 48
0
43 messages similar to the above omitted
Chain information for klk5.cxs.pdb
---
Chain | Description
1.1/A | No description available
1.4/A | No description available
1.2/B | No description available
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1051, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 700, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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 "L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for
> nanome\july-21b.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 335, in interceptRequest
self._callback(info)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 368, in intercept
chimerax_intercept(*args, view=view, session=session)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 470, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 399, in thread_safe
func(*args, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 461, in defer
cxcmd(session, topic)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 479, in cxcmd
run(session, cmd)
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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 "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21b.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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 "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21a.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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 "L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for
> nanome\klk5.cxs.pdb" format pdb
Summary of feedback from opening
L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for
nanome\klk5.cxs.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 165
ALA A 173 1 7
Start residue of secondary structure not found: HELIX 2 2 LEU A 231 PHE A 234
1 4
Start residue of secondary structure not found: HELIX 3 3 LYS A 236 ALA A 244
1 9
Start residue of secondary structure not found: SHEET 1 1 1 GLN A 30 LEU A 37
0
Start residue of secondary structure not found: SHEET 2 2 1 GLN A 39 HIS A 48
0
43 messages similar to the above omitted
Chain information for klk5.cxs.pdb
---
Chain | Description
1.1/A | No description available
1.4/A | No description available
1.2/B | No description available
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> rename #1.1 klk5-6qfe
> hide #1.1 models
> show #1.2 models
> open "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/july-21.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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 "L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for
> nanome\klk5.cxs.pdb" format pdb
Summary of feedback from opening
L:\Graphics\BCRX001\GraphicsBackup\klk5\klk5-biologic\chimerax for
nanome\klk5.cxs.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 165
ALA A 173 1 7
Start residue of secondary structure not found: HELIX 2 2 LEU A 231 PHE A 234
1 4
Start residue of secondary structure not found: HELIX 3 3 LYS A 236 ALA A 244
1 9
Start residue of secondary structure not found: SHEET 1 1 1 GLN A 30 LEU A 37
0
Start residue of secondary structure not found: SHEET 2 2 1 GLN A 39 HIS A 48
0
43 messages similar to the above omitted
Chain information for klk5.cxs.pdb
---
Chain | Description
1.1/A | No description available
1.4/A | No description available
1.2/B | No description available
> rename #1.1 klk5-6qfe
> hide #1.2 models
> hide #1.1 models
> hide #1.4 models
> rename #1.3 bcx13616
[Repeated 1 time(s)]
> hide #1.3 models
> show #1.4 models
> select #1.3:48
Nothing selected
> show #1.1 models
> color #1.1 #aa00ff transparency 0
> select add #1.4/A:48
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> select #1.4:48
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #1.2 models
> select #1.2:48
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> hide #!1.4 models
> rename #1.2 ntive spink9
Expected a keyword
> rename #1.2 nat-pink9
> hide #1.2 models
> show #!1.4 models
> rename #1.4 bcx17725
> select up
163 atoms, 169 bonds, 18 residues, 1 model selected
> select up
428 atoms, 442 bonds, 52 residues, 1 model selected
> rename #1.2 nat-spink9
> show #1.3 models
> hide #1.3 models
> color bymodel
> color bychain
> color #*
> color by#*
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color bypolymer
> color bypolymer byatom
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color byhetatom
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1 byhetero
> show #1.2 models
> hide #1.2 models
> save "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5.cxs"
> close session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1051, in <lambda>
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 700, in file_close_cb
run(session, 'close session')
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\std_commands\close.py", line 60, in close_session
session.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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 "L:/Graphics/BCRX001/GraphicsBackup/klk5/klk5-biologic/chimerax for
> nanome/klk5.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 697, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "C:\Program Files\ChimeraX 1.4\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 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open
return remember_data_format()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 739, in restore
self.reset()
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset
sm.reset_state(container, self)
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\bond_rot\manager.py", line 149, in reset_state
self.clear()
File "C:\Program Files\ChimeraX 1.4\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 1.4\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: 3.3.0 NVIDIA 517.40
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: To Be Filled By O.E.M.
Model: B550M-C
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 17,047,228,416
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5700
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
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-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
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 restore: 'list' object has no attribute 'values' |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
