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Opened 20 months ago
Closed 18 months ago
#14733 closed defect (can't reproduce)
Session restore: blast protein: KeyError: '_protein_chain'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> G:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
Opened pk2_bth-1.cif map 9.8 as #5, grid size 43,34,37, pixel 3.27, shown at
level 0.0143, step 1, values float32
Opened dimmer.cif map 10.5 as #7, grid size 50,39,35, pixel 3.5, shown at
level 0.00657, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\tool.py", line 244, in restore_snapshot
return BlastProteinTool.from_snapshot(session, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\tool.py", line 222, in from_snapshot
, chain = data['_protein_chain']
KeyError: '_protein_chain'
Log from Wed Feb 21 12:27:38 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dimer_dammin/pk1_bth-1.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dimer_dammin/pk1_bth-1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
790 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pk1_bth-1.cif #1
---
Chain | Description
A | No description available
> style ball
Changed 795 atom styles
> show target ab
> style sphere
Changed 795 atom styles
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume showOutlineBox true
No volumes specified
> style sphere
Changed 795 atom styles
> color bychain
> set bgColor black
> set bgColor white
[Repeated 1 time(s)]
> lighting simple
> set bgColor black
> lighting soft
> lighting full
> ui tool show "Selection Inspector"
> hide #1.1 models
> show #1.1 models
> select /A
795 atoms, 79 pseudobonds, 80 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select subtract #1
Nothing selected
> molmap #1 3.5
Opened pk1_bth-1.cif map 3.5 as #2, grid size 115,82,69, pixel 1.17, shown at
level 0.0173, step 1, values float32
> molmap #1 10.5
Opened pk1_bth-1.cif map 10.5 as #2, grid size 50,39,35, pixel 3.5, shown at
level 0.00657, step 1, values float32
> hide target a
> volume #2 style mesh
> volume #2 style surface
> transparency 50
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dammif/pk2_bth-1.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dammif/pk2_bth-1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
946 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pk2_bth-1.cif #3
---
Chain | Description
A | No description available
> select add #3
951 atoms, 95 pseudobonds, 96 residues, 2 models selected
> cartoon hide (#!3 & sel)
> show (#!3 & sel) target ab
> molmap #2 9.8
No atoms specified
> select subtract #3
Nothing selected
> molmap #3 9.8
Opened pk2_bth-1.cif map 9.8 as #4, grid size 43,34,37, pixel 3.27, shown at
level 0.0143, step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> transparency #4 40
> show #!2 models
> hide #1.1 models
> volume style mesh
> transparency 0
> volume style surface
> transparency 50
> volume style mesh
> volume style image
> volume style surface
> volume style image
> volume style mesh
> close session
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch02375.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch02375.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 447 in chain A
Atom HG1 is not in the residue template for VAL /A:2
Atom HH1 is not in the residue template for ARG /A:4
Atom HE2 is not in the residue template for GLN /A:6
Atom HD1 is not in the residue template for LEU /A:9
Atom HG1 is not in the residue template for VAL /A:14
Atom HD1 is not in the residue template for LEU /A:16
Atom HH1 is not in the residue template for ARG /A:22
Atom HG2 is not in the residue template for THR /A:23
Atom HD1 is not in the residue template for LEU /A:27
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
note | Fetching CCD CXM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/CXM/CXM.cif
Chain information for ranch02375.cif #1
---
Chain | Description
A | No description available
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch04127.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch04127.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 447 in chain A
Atom HG1 is not in the residue template for VAL /A:2
Atom HH1 is not in the residue template for ARG /A:4
Atom HE2 is not in the residue template for GLN /A:6
Atom HD1 is not in the residue template for LEU /A:9
Atom HG1 is not in the residue template for VAL /A:14
Atom HD1 is not in the residue template for LEU /A:16
Atom HH1 is not in the residue template for ARG /A:22
Atom HG2 is not in the residue template for THR /A:23
Atom HD1 is not in the residue template for LEU /A:27
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for ranch04127.cif #2
---
Chain | Description
A | No description available
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch09631.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch09631.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 447 in chain A
Atom HG1 is not in the residue template for VAL /A:2
Atom HH1 is not in the residue template for ARG /A:4
Atom HE2 is not in the residue template for GLN /A:6
Atom HD1 is not in the residue template for LEU /A:9
Atom HG1 is not in the residue template for VAL /A:14
Atom HD1 is not in the residue template for LEU /A:16
Atom HH1 is not in the residue template for ARG /A:22
Atom HG2 is not in the residue template for THR /A:23
Atom HD1 is not in the residue template for LEU /A:27
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for ranch09631.cif #3
---
Chain | Description
A | No description available
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> ui tool show "Blast Protein"
> ui tool show "Model Loops"
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 260 pruned atom pairs is 0.001 angstroms; (across all 451 pairs:
25.935)
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 2369.8
RMSD between 99 pruned atom pairs is 0.197 angstroms; (across all 451 pairs:
22.302)
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> ui tool show Matchmaker
> 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 ranch09631.cif, chain A (#3) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 263 pruned atom pairs is 0.073 angstroms; (across all 451 pairs:
19.682)
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 2369.8
RMSD between 99 pruned atom pairs is 0.197 angstroms; (across all 451 pairs:
22.302)
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 260 pruned atom pairs is 0.001 angstroms; (across all 451 pairs:
25.935)
> hide #!1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> 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 ranch09631.cif, chain A (#3) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 263 pruned atom pairs is 0.073 angstroms; (across all 451 pairs:
19.682)
> show #!1 models
> ui tool show Matchmaker
> select sequence
> 1cylesqnyihrdlaarnilvgentlckvgdfglarlikedvylshdhnipykwtapeals361rghystksdvwsfgillhemfsrgqvpypgmsnheaflrvdagyrmpcplecppsvhklm421ltcwcrdpeqrpcfkalrerlssftsyenpt
Nothing selected
> select sequence CWCRDPEQRPCFKALRERLSSFTSYENPT
Nothing selected
> select add #1
4881 atoms, 4952 bonds, 19 pseudobonds, 451 residues, 2 models selected
> select sequence CWCRDPEQRPCFKALRERLSSFTSYENPT
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A
Alignment identifier is 1
> select #1/A:411 #2/A:411 #3/A:411
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:411-452 #2/A:411-452 #3/A:411-452
954 atoms, 963 bonds, 15 pseudobonds, 126 residues, 6 models selected
1 [ID: 1] region 3 chains [410-451] RMSD: 27.068
> ui tool show Matchmaker
> matchmaker #!2-3 & sel to #1 & sel
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 ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 228.6
RMSD between 37 pruned atom pairs is 0.001 angstroms; (across all 42 pairs:
3.142)
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 228.6
RMSD between 37 pruned atom pairs is 0.001 angstroms; (across all 42 pairs:
4.245)
> select #1/A:121 #2/A:121 #3/A:121
42 atoms, 39 bonds, 3 residues, 3 models selected
> select #1/A:121 #2/A:121 #3/A:121
42 atoms, 39 bonds, 3 residues, 3 models selected
1 [ID: 1] region 3 chains [121] RMSD: 46.687
> select clear
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dammif/pk2_bth-1.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dammif/pk2_bth-1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
946 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pk2_bth-1.cif #4
---
Chain | Description
A | No description available
> molmap #4 9.8
Opened pk2_bth-1.cif map 9.8 as #5, grid size 43,34,37, pixel 3.27, shown at
level 0.0143, step 1, values float32
> volume style mesh
> vop gaussian #5 sdev 9.8
Opened pk2_bth-1.cif map 9.8 gaussian as #6, grid size 43,34,37, pixel 3.27,
shown at step 1, values float32
> vop gaussian #6 sdev 9.8
Opened pk2_bth-1.cif map 9.8 gaussian as #7, grid size 43,34,37, pixel 3.27,
shown at step 1, values float32
> undo
[Repeated 1 time(s)]
> volume #!7 style surface
> hide #!7 target m
> select add #5
42 atoms, 39 bonds, 3 residues, 5 models selected
> select subtract #5
42 atoms, 39 bonds, 3 residues, 3 models selected
> show #!5 models
> close #6
> close #7
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 1 maps.
[Repeated 1 time(s)]
> select add #2
4909 atoms, 4978 bonds, 19 pseudobonds, 453 residues, 4 models selected
> hide #!2 models
> hide #!3 models
> select subtract #2
28 atoms, 26 bonds, 2 residues, 2 models selected
> select add #3
4895 atoms, 4965 bonds, 19 pseudobonds, 452 residues, 3 models selected
> select subtract #3
14 atoms, 13 bonds, 1 residue, 1 model selected
> fitmap #1 inMap #5
Fit molecule ranch02375.cif (#1) to map pk2_bth-1.cif map 9.8 (#5) using 4881
atoms
average map value = 0.04272, steps = 240
shifted from previous position = 10
rotated from previous position = 86.6 degrees
atoms outside contour = 637, contour level = 0.014263
Position of ranch02375.cif (#1) relative to pk2_bth-1.cif map 9.8 (#5)
coordinates:
Matrix rotation and translation
0.49728549 0.56773046 0.65604060 -7.95148992
-0.83229288 0.09869128 0.54548015 -9.41153272
0.24494021 -0.81727728 0.52159576 -4.77920827
Axis -0.68255914 0.20590629 -0.70122437
Axis point -9.83258393 -2.92519064 0.00000000
Rotation angle (degrees) 86.62985224
Shift along axis 6.84076564
> hide #!4 models
> show #!3 models
> show #!2 models
> select #1/A:394-395 #2/A:394-395 #3/A:394-395
54 atoms, 54 bonds, 6 residues, 3 models selected
> select #1/A:394-452 #2/A:394-452 #3/A:394-452
1365 atoms, 1389 bonds, 15 pseudobonds, 177 residues, 6 models selected
1 [ID: 1] region 3 chains [393-451] RMSD: 43.473
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
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 ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 323
RMSD between 55 pruned atom pairs is 0.001 angstroms; (across all 59 pairs:
2.651)
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 323
RMSD between 53 pruned atom pairs is 0.001 angstroms; (across all 59 pairs:
3.581)
> save
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
> select clear
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dimer_dammin/dimmer.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dimer_dammin/dimmer.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
790 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for dimmer.cif #6
---
Chain | Description
A | No description available
> molmap #6 10.5
Opened dimmer.cif map 10.5 as #7, grid size 50,39,35, pixel 3.5, shown at
level 0.00657, step 1, values float32
> hide #!6 models
> volume style mesh
> save
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
> volume step 2
> volume showOutlineBox true
> volume step 1
> volume showOutlineBox false
> volume style surface
> transparency 50
> transparency #1-3,5,7 20
> transparency #1-3,5,7 80
> hide #!7 models
> save
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
——— End of log from Wed Feb 21 12:27:38 2024 ———
opened ChimeraX session
> open
> G:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
Opened pk2_bth-1.cif map 9.8 as #5, grid size 43,34,37, pixel 3.27, shown at
level 0.0143, step 1, values float32
Opened dimmer.cif map 10.5 as #7, grid size 50,39,35, pixel 3.5, shown at
level 0.00657, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\tool.py", line 244, in restore_snapshot
return BlastProteinTool.from_snapshot(session, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\ui\tool.py", line 222, in from_snapshot
, chain = data['_protein_chain']
KeyError: '_protein_chain'
Log from Wed Feb 21 12:27:38 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dimer_dammin/pk1_bth-1.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dimer_dammin/pk1_bth-1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
790 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pk1_bth-1.cif #1
---
Chain | Description
A | No description available
> style ball
Changed 795 atom styles
> show target ab
> style sphere
Changed 795 atom styles
> volume style mesh
No volumes specified
> volume style surface
No volumes specified
> volume showOutlineBox true
No volumes specified
> style sphere
Changed 795 atom styles
> color bychain
> set bgColor black
> set bgColor white
[Repeated 1 time(s)]
> lighting simple
> set bgColor black
> lighting soft
> lighting full
> ui tool show "Selection Inspector"
> hide #1.1 models
> show #1.1 models
> select /A
795 atoms, 79 pseudobonds, 80 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select subtract #1
Nothing selected
> molmap #1 3.5
Opened pk1_bth-1.cif map 3.5 as #2, grid size 115,82,69, pixel 1.17, shown at
level 0.0173, step 1, values float32
> molmap #1 10.5
Opened pk1_bth-1.cif map 10.5 as #2, grid size 50,39,35, pixel 3.5, shown at
level 0.00657, step 1, values float32
> hide target a
> volume #2 style mesh
> volume #2 style surface
> transparency 50
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dammif/pk2_bth-1.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dammif/pk2_bth-1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
946 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pk2_bth-1.cif #3
---
Chain | Description
A | No description available
> select add #3
951 atoms, 95 pseudobonds, 96 residues, 2 models selected
> cartoon hide (#!3 & sel)
> show (#!3 & sel) target ab
> molmap #2 9.8
No atoms specified
> select subtract #3
Nothing selected
> molmap #3 9.8
Opened pk2_bth-1.cif map 9.8 as #4, grid size 43,34,37, pixel 3.27, shown at
level 0.0143, step 1, values float32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> transparency #4 40
> show #!2 models
> hide #1.1 models
> volume style mesh
> transparency 0
> volume style surface
> transparency 50
> volume style mesh
> volume style image
> volume style surface
> volume style image
> volume style mesh
> close session
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch02375.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch02375.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 447 in chain A
Atom HG1 is not in the residue template for VAL /A:2
Atom HH1 is not in the residue template for ARG /A:4
Atom HE2 is not in the residue template for GLN /A:6
Atom HD1 is not in the residue template for LEU /A:9
Atom HG1 is not in the residue template for VAL /A:14
Atom HD1 is not in the residue template for LEU /A:16
Atom HH1 is not in the residue template for ARG /A:22
Atom HG2 is not in the residue template for THR /A:23
Atom HD1 is not in the residue template for LEU /A:27
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
note | Fetching CCD CXM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/CXM/CXM.cif
Chain information for ranch02375.cif #1
---
Chain | Description
A | No description available
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch04127.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch04127.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 447 in chain A
Atom HG1 is not in the residue template for VAL /A:2
Atom HH1 is not in the residue template for ARG /A:4
Atom HE2 is not in the residue template for GLN /A:6
Atom HD1 is not in the residue template for LEU /A:9
Atom HG1 is not in the residue template for VAL /A:14
Atom HD1 is not in the residue template for LEU /A:16
Atom HH1 is not in the residue template for ARG /A:22
Atom HG2 is not in the residue template for THR /A:23
Atom HD1 is not in the residue template for LEU /A:27
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for ranch04127.cif #2
---
Chain | Description
A | No description available
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch09631.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/EOM/gajoe/GA002/curve_1/pdbs/ranch09631.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Skipping residue with duplicate label_seq_id 447 in chain A
Atom HG1 is not in the residue template for VAL /A:2
Atom HH1 is not in the residue template for ARG /A:4
Atom HE2 is not in the residue template for GLN /A:6
Atom HD1 is not in the residue template for LEU /A:9
Atom HG1 is not in the residue template for VAL /A:14
Atom HD1 is not in the residue template for LEU /A:16
Atom HH1 is not in the residue template for ARG /A:22
Atom HG2 is not in the residue template for THR /A:23
Atom HD1 is not in the residue template for LEU /A:27
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for ranch09631.cif #3
---
Chain | Description
A | No description available
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> ui tool show "Blast Protein"
> ui tool show "Model Loops"
> ui tool show Matchmaker
> matchmaker #!2-3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 260 pruned atom pairs is 0.001 angstroms; (across all 451 pairs:
25.935)
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 2369.8
RMSD between 99 pruned atom pairs is 0.197 angstroms; (across all 451 pairs:
22.302)
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> ui tool show Matchmaker
> 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 ranch09631.cif, chain A (#3) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 263 pruned atom pairs is 0.073 angstroms; (across all 451 pairs:
19.682)
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 2369.8
RMSD between 99 pruned atom pairs is 0.197 angstroms; (across all 451 pairs:
22.302)
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 260 pruned atom pairs is 0.001 angstroms; (across all 451 pairs:
25.935)
> hide #!1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> 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 ranch09631.cif, chain A (#3) with ranch04127.cif, chain A (#2),
sequence alignment score = 2369.8
RMSD between 263 pruned atom pairs is 0.073 angstroms; (across all 451 pairs:
19.682)
> show #!1 models
> ui tool show Matchmaker
> select sequence
> 1cylesqnyihrdlaarnilvgentlckvgdfglarlikedvylshdhnipykwtapeals361rghystksdvwsfgillhemfsrgqvpypgmsnheaflrvdagyrmpcplecppsvhklm421ltcwcrdpeqrpcfkalrerlssftsyenpt
Nothing selected
> select sequence CWCRDPEQRPCFKALRERLSSFTSYENPT
Nothing selected
> select add #1
4881 atoms, 4952 bonds, 19 pseudobonds, 451 residues, 2 models selected
> select sequence CWCRDPEQRPCFKALRERLSSFTSYENPT
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/A
Alignment identifier is 1
> select #1/A:411 #2/A:411 #3/A:411
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #1/A:411-452 #2/A:411-452 #3/A:411-452
954 atoms, 963 bonds, 15 pseudobonds, 126 residues, 6 models selected
1 [ID: 1] region 3 chains [410-451] RMSD: 27.068
> ui tool show Matchmaker
> matchmaker #!2-3 & sel to #1 & sel
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 ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 228.6
RMSD between 37 pruned atom pairs is 0.001 angstroms; (across all 42 pairs:
3.142)
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 228.6
RMSD between 37 pruned atom pairs is 0.001 angstroms; (across all 42 pairs:
4.245)
> select #1/A:121 #2/A:121 #3/A:121
42 atoms, 39 bonds, 3 residues, 3 models selected
> select #1/A:121 #2/A:121 #3/A:121
42 atoms, 39 bonds, 3 residues, 3 models selected
1 [ID: 1] region 3 chains [121] RMSD: 46.687
> select clear
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dammif/pk2_bth-1.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dammif/pk2_bth-1.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
946 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for pk2_bth-1.cif #4
---
Chain | Description
A | No description available
> molmap #4 9.8
Opened pk2_bth-1.cif map 9.8 as #5, grid size 43,34,37, pixel 3.27, shown at
level 0.0143, step 1, values float32
> volume style mesh
> vop gaussian #5 sdev 9.8
Opened pk2_bth-1.cif map 9.8 gaussian as #6, grid size 43,34,37, pixel 3.27,
shown at step 1, values float32
> vop gaussian #6 sdev 9.8
Opened pk2_bth-1.cif map 9.8 gaussian as #7, grid size 43,34,37, pixel 3.27,
shown at step 1, values float32
> undo
[Repeated 1 time(s)]
> volume #!7 style surface
> hide #!7 target m
> select add #5
42 atoms, 39 bonds, 3 residues, 5 models selected
> select subtract #5
42 atoms, 39 bonds, 3 residues, 3 models selected
> show #!5 models
> close #6
> close #7
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 1 maps.
[Repeated 1 time(s)]
> select add #2
4909 atoms, 4978 bonds, 19 pseudobonds, 453 residues, 4 models selected
> hide #!2 models
> hide #!3 models
> select subtract #2
28 atoms, 26 bonds, 2 residues, 2 models selected
> select add #3
4895 atoms, 4965 bonds, 19 pseudobonds, 452 residues, 3 models selected
> select subtract #3
14 atoms, 13 bonds, 1 residue, 1 model selected
> fitmap #1 inMap #5
Fit molecule ranch02375.cif (#1) to map pk2_bth-1.cif map 9.8 (#5) using 4881
atoms
average map value = 0.04272, steps = 240
shifted from previous position = 10
rotated from previous position = 86.6 degrees
atoms outside contour = 637, contour level = 0.014263
Position of ranch02375.cif (#1) relative to pk2_bth-1.cif map 9.8 (#5)
coordinates:
Matrix rotation and translation
0.49728549 0.56773046 0.65604060 -7.95148992
-0.83229288 0.09869128 0.54548015 -9.41153272
0.24494021 -0.81727728 0.52159576 -4.77920827
Axis -0.68255914 0.20590629 -0.70122437
Axis point -9.83258393 -2.92519064 0.00000000
Rotation angle (degrees) 86.62985224
Shift along axis 6.84076564
> hide #!4 models
> show #!3 models
> show #!2 models
> select #1/A:394-395 #2/A:394-395 #3/A:394-395
54 atoms, 54 bonds, 6 residues, 3 models selected
> select #1/A:394-452 #2/A:394-452 #3/A:394-452
1365 atoms, 1389 bonds, 15 pseudobonds, 177 residues, 6 models selected
1 [ID: 1] region 3 chains [393-451] RMSD: 43.473
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
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 ranch02375.cif, chain A (#1) with ranch04127.cif, chain A (#2),
sequence alignment score = 323
RMSD between 55 pruned atom pairs is 0.001 angstroms; (across all 59 pairs:
2.651)
Matchmaker ranch02375.cif, chain A (#1) with ranch09631.cif, chain A (#3),
sequence alignment score = 323
RMSD between 53 pruned atom pairs is 0.001 angstroms; (across all 59 pairs:
3.581)
> save
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
> select clear
> open
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/dimer_dammin/dimmer.cif
Summary of feedback from opening
D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
algo-010/atsas/dimer_dammin/dimmer.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
Atom CA has no neighbors to form bonds with according to residue template for
ASP /A:1
790 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for dimmer.cif #6
---
Chain | Description
A | No description available
> molmap #6 10.5
Opened dimmer.cif map 10.5 as #7, grid size 50,39,35, pixel 3.5, shown at
level 0.00657, step 1, values float32
> hide #!6 models
> volume style mesh
> save
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
> volume step 2
> volume showOutlineBox true
> volume step 1
> volume showOutlineBox false
> volume style surface
> transparency 50
> transparency #1-3,5,7 20
> transparency #1-3,5,7 80
> hide #!7 models
> save
> D:/EXPERIMENTS/Brk/saxs/SAXS-20221211/20221211/Ugajin/uBRK/sub3/analysis-
> algo-010/atsas/EOM_dammif.cxs
——— End of log from Wed Feb 21 12:27:38 2024 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 536.19
OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: ja_JP.cp932
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 8940
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 16,825,712,640
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: ja-JP
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 20 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session restore: blast protein: KeyError: '_protein_chain' |
comment:2 by , 18 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Most likely. Can't reproduce without the session.
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Guessing restoring a new session in an old ChimeraX