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Opened 2 years ago
Closed 2 years ago
#10225 closed defect (limitation)
Restore new session in old ChimeraX
| 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-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\Users\shard\Downloads\ChimeraX\N-ALFA_SPPL2a_ALFA-nanobody PDB
> based.cxs" format session
Log from Wed Oct 4 17:39:54 2023UCSF ChimeraX version: 1.7.dev202310030223
(2023-10-03)
© 2016-2023 Regents of the University of California. All rights reserved.
> open F:\Shardul\N-ALFA_SPPL2a_ALFA-nanobody.cxs format session
Log from Wed Oct 4 16:17:20 2023 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.dev202310030223 (2023-10-03)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> MPSRLEEELRRRLTEPQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTSTPLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFISYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMRKKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIACRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIVPGLLIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMKKFWKGNSYQMMDHLDCATNEENPVISGEQIVQQ,MSGEVQLQESGGGLVQPGGSLRLSCTASGVTISALNAMAMGWYRQAPGERRVMVAAVSERGNAMYRESVQGRFTVTRDFTNKMVSLQMDNLKPEDTAVYYCHVLEDRVDSFHDYWGQGTQVTVSSLEHHHHHH
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> alphafold predict
> MPSRLEEELRRRLTEPQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTSTPLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFISYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMRKKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIACRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIVPGLLIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMKKFWKGNSYQMMDHLDCATNEENPVISGEQIVQQ,MSGEVQLQESGGGLVQPGGSLRLSCTASGVTISALNAMAMGWYRQAPGERRVMVAAVSERGNAMYRESVQGRFTVTRDFTNKMVSLQMDNLKPEDTAVYYCHVLEDRVDSFHDYWGQGTQVTVSSLEHHHHHH
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\akta-pure-rt/Downloads/ChimeraX/AlphaFold/prediction_2
> open C:\Users\akta-pure-
> rt/Downloads/ChimeraX/AlphaFold/prediction_2\best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> save F:/Shardul/N-ALFA_SPPL2a_ALFA-nanobody.cxs
——— End of log from Wed Oct 4 16:17:20 2023 ———
opened ChimeraX session
> close
> ui tool show AlphaFold
> alphafold predict
> MPSRLEEELRRRLTEPQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTSTPLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFISYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMRKKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIACRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIVPGLLIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMKKFWKGNSYQMMDHLDCATNEENPVISGEQIVQQ,MSGEVQLQESGGGLVQPGGSLRLSCTASGVTISALNAMAMGWYRQAPGERRVMVAAVSERGNAMYRESVQGRFTVTRDFTNKMVSLQMDNLKPEDTAVYYCHVLEDRVDSFHDYWGQGTQVTVSSLEHHHHHH
> templates true
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> alphafold predict
> MPSRLEEELRRRLTEPQEAILHASGNGTTKDYCMLYNPYWTALPSTLENATSISLMNLTSTPLCNLSDIPPVGIKSKAVVVPWGSCHFLEKARIAQKGGAEAMLVVNNSVLFPPSGNRSEFPDVKILIAFISYKDFRDMNQTLGDNITVKMYSPSWPNFDYTMVVIFVIAVFTVALGGYWSGLVELENLKAVTTEDREMRKKKEEYLTFSPLTVVIFVVICCVMMVLLYFFYKWLVYVMIAIFCIASAMSLYNCLAALIHKIPYGQCTIACRGKNMEVRLIFLSGLCIAVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDVFFVFITPFITKNGESIMVELAAGPFGNNEKLPVVIRVPKLIYFSVMSVCLMPVSILGFGDIIVPGLLIAYCRRFDVQTGSSYIYYVSSTVAYAIGMILTFVVLVLMKKGQPALLYLVPCTLITASVVAWRRKEMKKFWKGNSYQMMDHLDCATNEENPVISGEQIVQQ,MSGEVQLQESGGGLVQPGGSLRLSCTASGVTISALNAMAMGWYRQAPGERRVMVAAVSERGNAMYRESVQGRFTVTRDFTNKMVSLQMDNLKPEDTAVYYCHVLEDRVDSFHDYWGQGTQVTVSSLEHHHHHH
> templates true
Running AlphaFold prediction
AlphaFold prediction finished
Results in C:\Users\akta-pure-rt/Downloads/ChimeraX/AlphaFold/prediction_3
> open C:\Users\akta-pure-
> rt/Downloads/ChimeraX/AlphaFold/prediction_3\best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
> save "F:/Shardul/N-ALFA_SPPL2a_ALFA-nanobody PDB based.cxs"
——— End of log from Wed Oct 4 17:39:54 2023 ———
opened ChimeraX session
> close
> open C:/Users/shard/Downloads/ChimeraX/N-ALFA_SPPL2a_Nb_3EAAAK.cxs
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\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\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/shard/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
> set bgColor black
> set bgColor white
> open C:/Users/shard/Downloads/ChimeraX/AlphaFold/prediction_7/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
B | No description available
> 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 best_model.pdb, chain A (#2) with best_model.pdb, chain A (#1),
sequence alignment score = 150.8
RMSD between 30 pruned atom pairs is 0.670 angstroms; (across all 32 pairs:
2.200)
> hide #1 models
> hide #2 models
> show #1 models
> ui mousemode right select
Drag select of 22 residues
> select add #1/A:23
180 atoms, 4 bonds, 23 residues, 1 model selected
> select add #1/A:24
189 atoms, 12 bonds, 24 residues, 1 model selected
> select add #1/A:25
198 atoms, 20 bonds, 25 residues, 1 model selected
> select add #1/A:26
203 atoms, 24 bonds, 26 residues, 1 model selected
> select add #1/A:27
208 atoms, 28 bonds, 27 residues, 1 model selected
> select add #1/A:28
213 atoms, 32 bonds, 28 residues, 1 model selected
> show #2 models
> hide #2 models
> show #2 models
> select clear
> undo
> select add #2/A:1
221 atoms, 39 bonds, 29 residues, 2 models selected
> select up
234 atoms, 53 bonds, 31 residues, 2 models selected
> select up
4648 atoms, 4763 bonds, 592 residues, 2 models selected
> select down
234 atoms, 53 bonds, 31 residues, 2 models selected
> select subtract #2/A:1
226 atoms, 45 bonds, 30 residues, 2 models selected
> select up
234 atoms, 53 bonds, 31 residues, 2 models selected
> select up
4648 atoms, 4763 bonds, 592 residues, 2 models selected
> select down
234 atoms, 53 bonds, 31 residues, 2 models selected
> select up
4648 atoms, 4763 bonds, 592 residues, 2 models selected
> select down
234 atoms, 53 bonds, 31 residues, 2 models selected
> select down
226 atoms, 45 bonds, 30 residues, 2 models selected
> select down
226 atoms, 45 bonds, 30 residues, 2 models selected
> select up
234 atoms, 53 bonds, 31 residues, 2 models selected
> select up
4648 atoms, 4763 bonds, 592 residues, 2 models selected
> select up
5682 atoms, 5819 bonds, 725 residues, 2 models selected
> select down
4648 atoms, 4763 bonds, 592 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select down
234 atoms, 53 bonds, 31 residues, 2 models selected
> show sel atoms
> hide #2 models
> show #2 models
> hide #1 models
Drag select of 13 atoms, 14 residues, 11 bonds
Drag select of 15 residues
Drag select of 1 residues
> select clear
[Repeated 1 time(s)]Drag select of 12 atoms, 23 residues, 11 bonds
> select clear
Drag select of 11 atoms, 31 residues, 10 bonds
> select add #2/A:5
241 atoms, 17 bonds, 32 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> show #1 models
> select clear
> lighting simple
> lighting soft
> graphics silhouettes true
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> view orient
> ui tool show "Side View"
> select #2/B
1034 atoms, 1056 bonds, 133 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ff0000ff
> color sel #ff5500ff
> color sel #ff557fff
> color sel #55aaffff
> color sel #ff557fff
> select #2/A
241 atoms, 243 bonds, 32 residues, 1 model selected
> color sel #55ffffff
> color sel #00ffffff
> color sel #aaffffff
> color sel #5500ffff
> color sel #ffff00ff
> color sel #ffff7fff
> select clear
> select #1/A
4407 atoms, 4520 bonds, 560 residues, 1 model selected
> color sel #5555ffff
> select clear
> color #5500ffff
> undo
> select #1/A
4407 atoms, 4520 bonds, 560 residues, 1 model selected
> select clear
> hide #2 models
Drag select of 123 atoms, 26 residues, 100 bonds
> select add #1/A:27
208 atoms, 104 bonds, 27 residues, 1 model selected
> select add #1/A:28
213 atoms, 108 bonds, 28 residues, 1 model selected
> select add #1/A:29
222 atoms, 116 bonds, 29 residues, 1 model selected
> select add #1/A:30
227 atoms, 120 bonds, 30 residues, 1 model selected
> select add #1/A:31
234 atoms, 127 bonds, 31 residues, 1 model selected
> select add #1/A:32
241 atoms, 134 bonds, 32 residues, 1 model selected
> color sel red
> select clear
Drag select of 12 residues
> select clear
> undo
[Repeated 3 time(s)]
> hide sel atoms
> select clear
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting simple
> graphics silhouettes true
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> save C:/Users/shard/Downloads/ChimeraX/N-ALFA_3EAAK_SPPL2a.png width 959
> height 596 supersample 3
[Repeated 1 time(s)]
> show #2 models
> hide #2 models
Drag select of 28 residues
> select #1/A:11
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 15 residues
> select clear
Drag select of 3 residues
> select clear
Drag select of 15 residues
> select clear
Drag select of 28 residues
> select add #1/A:29
222 atoms, 8 bonds, 29 residues, 1 model selected
> select add #1/A:30
227 atoms, 12 bonds, 30 residues, 1 model selected
> select add #1/A:31
234 atoms, 19 bonds, 31 residues, 1 model selected
> select add #1/A:32
241 atoms, 26 bonds, 32 residues, 1 model selected
> show sel atoms
> select clear
> show #2 models
> undo
[Repeated 4 time(s)]
> select clear
> show #2 models
Drag select of 462 residues, 148 atoms, 119 bonds
> hide sel atoms
> select clear
> save "C:/Users/shard/Downloads/ChimeraX/N-ALFA_3EAAK_SPPL2a overlay with
> nanobody overlay.png" width 959 height 596 supersample 3
> hide #2 models
> show #2 models
> hide #1 models
Drag select of 32 residues
> show sel atoms
> select clear
> hide #2 models
> show #1 models
Drag select of 14 residues
> select clear
Drag select of 19 residues
Drag select of 5 residues
Drag select of 30 residues
> select clear
Drag select of 29 residues
> select add #1/A:30
227 atoms, 4 bonds, 30 residues, 1 model selected
> select add #1/A:31
234 atoms, 11 bonds, 31 residues, 1 model selected
> select add #1/A:32
241 atoms, 18 bonds, 32 residues, 1 model selected
> show sel atoms
> select clear
> show #2 models
> undo
[Repeated 3 time(s)]
> select clear
> show #2 models
Drag select of 416 residues, 148 atoms, 119 bonds
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> save "C:/Users/shard/Downloads/ChimeraX/N-ALFA_3EAAK_SPPL2a overlay with
> nanobody overlay side view.png" width 959 height 596 supersample 3
Drag select of 79 residues
> select clear
Drag select of 382 residues
> select clear
Drag select of 379 residues
> hide sel cartoons
Drag select of 88 residues
> hide sel cartoons
Drag select of 41 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 8 residues
Drag select of 12 residues
> hide sel cartoons
> save "C:/Users/shard/Downloads/ChimeraX/3EAAK_ALFA_nanobody and ALFA
> overlay.png" width 959 height 596 supersample 3
> save "C:/Users/shard/Downloads/ChimeraX/3EAAK_ALFA_nanobody and ALFA overlay
> front view.png" width 959 height 596 supersample 3
Drag select of 64 residues
> show sel atoms
> select clear
Drag select of 27 atoms, 22 residues, 19 bonds
Drag select of 101 atoms, 36 residues, 75 bonds
> select subtract #1/A:15
227 atoms, 75 bonds, 35 residues, 2 models selected
> select subtract #2/A:15
218 atoms, 75 bonds, 34 residues, 2 models selected
> hide sel atoms
> select clear
> undo
> show sel atoms
> hide sel atoms
> select clear
> undo
> color sel black
> select clear
> undo
[Repeated 2 time(s)]
> color sel dim gray
Drag select of 5 residues
> select clear
[Repeated 1 time(s)]
> select #1/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/B:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 1 atoms, 2 bonds
> select clear
> hide sel cartoons
> undo
> hide sel atoms
[Repeated 1 time(s)]
> select #2/B:109@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 4 atoms, 3 residues, 3 bonds
> hide sel atoms
> select clear
> select #2/B:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #2/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
[Repeated 2 time(s)]
> open C:/Users/shard/Downloads/ChimeraX/6i2g.pdb
6i2g.pdb title:
ALFA-tag binding nanobody (nbalfa) bound to ALFA-tag peptide. [more info...]
Chain information for 6i2g.pdb #3
---
Chain | Description
A | ALFA nanobody
B | N7P-ser-arg-leu-glu-glu-glu-leu-arg-arg-arg-leu-THR-glu- LPD
Non-standard residues in 6i2g.pdb #3
---
LPD — L-prolinamide
N7P — 1-acetyl-L-proline (N-acetylproline)
SO4 — sulfate ion
> hide #2 models
> matchmaker #1 to #3
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 6i2g.pdb, chain B (#3) with best_model.pdb, chain A (#1), sequence
alignment score = 55.7
RMSD between 13 pruned atom pairs is 0.367 angstroms; (across all 14 pairs:
1.837)
Drag select of 46 atoms, 45 residues, 35 bonds
> show sel atoms
> select clear
Drag select of 17 atoms, 7 residues, 15 bonds
Drag select of 37 atoms, 13 residues, 31 bonds
> hide sel atoms
> select #1/A:19
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:17
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:18
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide #3 models
> select clear
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> show #2 models
> matchmaker #2 to #3
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 6i2g.pdb, chain A (#3) with best_model.pdb, chain B (#2), sequence
alignment score = 641.6
RMSD between 121 pruned atom pairs is 0.475 angstroms; (across all 121 pairs:
0.475)
> hide #2 models
Drag select of 219 atoms, 163 residues, 181 bonds
> hide sel atoms
> select clear
Drag select of 46 residues
[Repeated 1 time(s)]
> show sel atoms
> select clear
> select #1/A:16
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
205 atoms, 205 bonds, 27 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #3 models
Drag select of 60 atoms, 18 residues, 45 bonds
> select subtract #1/A:15
109 atoms, 45 bonds, 17 residues, 1 model selected
> hide sel atoms
> select clear
> show #3 models
> select clear
> hide #3 models
Drag select of 85 atoms, 15 residues, 72 bonds
> style sel stick
Changed 132 atom styles
> style sel stick
Changed 132 atom styles
> select clear
> undo
> style sel ball
Changed 132 atom styles
> undo
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> color sel byhetero
> select clear
> show #2 models
> hide #2 models
> show #3 models
> select clear
> ui mousemode right label
> label #1/A:13
> label delete residues
[Repeated 2 time(s)]
> label #1/A:13
> label #3/B:12
> ui mousemode right "move label"
> ui mousemode right label
> label #3/A:112
> label #1/A:9
> undo
[Repeated 1 time(s)]
> label delete residues
> undo
> show #3 models
> label #1/A:13
> label #3/B:12
> ui mousemode right "move label"
> ui mousemode right label
> label #1/A:9
> label #3/B:8
> ui mousemode right "move label"
> ui mousemode right label
> label #1/A:6
> label delete residues
[Repeated 1 time(s)]
> label #3/B:5
[Repeated 1 time(s)]
> label delete residues
[Repeated 3 time(s)]
> hide #3 models
> label delete residues
[Repeated 1 time(s)]
> show #3 models
> label #3/A:98
> label delete residues
[Repeated 2 time(s)]
> label #3/A:91
> label delete residues
> label #3/A:91
> label delete residues
> label #3/A:94
> label #3/A:91
> label #3/A:92
> label #3/A:93
> label delete residues
> label #1/A:13
> label #3/B:12
> label #1/A:9
> label #3/B:8
> label #3/B:4
> label #1/A:5
> label #3/B:5
> label delete residues
> label #1/A:6
> label #3/B:5
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> ui mousemode right select
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 14 atoms, 7 residues, 11 bonds
> select clear
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 18 atoms, 10 residues, 17 bonds
> select #1/A:6@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #1/A:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #3/B:5@OE2
1 atom, 4 bonds, 1 residue, 1 model selected
> select add #3/B:5@OE1
2 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> select add #3/B:5@CD
1 atom, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> select #1/A:5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> volume style image
No volumes specified
> volume style image
No volumes specified
> volume style image
No volumes specified
> ui mousemode right "move label"
> ui mousemode right label
> label #3/B:12
> label #1/A:13
> label #1/A:9
> label #3/B:8
> label #1/A:5
> label delete residues
> label #3/B:4
> label #1/A:5
> label #3/B:8
> label #1/A:9
> label #3/B:12
> label #1/A:13
> ui mousemode right "move label"
> save "C:/Users/shard/Downloads/ChimeraX/ALFA-tag hydrophobic interaction
> view.png" width 959 height 596 supersample 3
> save "C:/Users/shard/Downloads/ChimeraX/ALFA-tag hydrophobic interaction
> view 2.png" width 959 height 596 supersample 3
[Repeated 1 time(s)]
> ui mousemode right label
> label delete residues
> select #1/A
4407 atoms, 4520 bonds, 560 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
1275 atoms, 1299 bonds, 165 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #3
1194 atoms, 1091 bonds, 256 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
1194 atoms, 1091 bonds, 256 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/A
1045 atoms, 956 bonds, 227 residues, 1 model selected
> hide #3 models
> show #3 models
> hide sel cartoons
> label delete residues
[Repeated 2 time(s)]
> ui mousemode right select
Drag select of 44 atoms, 15 residues, 36 bonds
Drag select of 154 atoms, 30 residues, 133 bonds
> select clear
Drag select of 162 atoms, 31 residues, 137 bonds
> select subtract #1/A:17
264 atoms, 137 bonds, 30 residues, 2 models selected
> select subtract #1/A:16
259 atoms, 137 bonds, 29 residues, 2 models selected
> show sel atoms
> select clear
> select add #3
1194 atoms, 1091 bonds, 256 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
1194 atoms, 1091 bonds, 256 residues, 1 model selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> select #3/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Drag select of 147 atoms, 46 residues, 128 bonds
> select clear
Drag select of 66 atoms, 33 residues, 54 bonds
> hide sel atoms
> select clear
> select #1/A:12
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> show sel atoms
> select clear
> select #1/A:13@CG
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 2 residues
> hide sel atoms
> select clear
> select #3/A:42
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right label
> label #1/A:12
> label #3/B:11
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> label #1/A:12
> label #3/B:11
> label #3/A:42
> label delete residues
> label #3/A:42
> label #3/A:112
> label delete residues
> label #1/A:12
> label #3/B:11
> label delete residues
> label #3/A:112
> label #3/B:11
> label #1/A:12
> label #3/A:42
> ui mousemode right "move label"
> save "C:/Users/shard/Downloads/ChimeraX/ALFA-tag hydrophilic interaction
> .png" width 959 height 596 supersample 3
> save C:/Users/shard/Downloads/ChimeraX/N-ALFA-EAAK_Nb.cxs
> open "C:/Users/shard/Downloads/ChimeraX/N-ALFA_SPPL2a_ALFA-nanobody PDB
> based.cxs"
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\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\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\shard\Downloads\ChimeraX\N-ALFA-EAAK_Nb.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\shard\Downloads\ChimeraX\N-ALFA-EAAK_Nb.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\shard\Downloads\ChimeraX\N-ALFA-EAAK_Nb.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: 3.3.0 NVIDIA 528.79
OpenGL renderer: NVIDIA GeForce RTX 3050 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_IN.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Dell G15 5515
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 16,483,872,768
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5600H 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 → Restore new session in old ChimeraX |
comment:2 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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