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Opened 17 months ago
Closed 17 months ago
#15290 closed defect (can't reproduce)
MatchMaker: KeyError in item chooser
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-35-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.gro
Chain information for LA BOUND TO RBD in water #1
---
Chain | Description
? | No description available
> set bgColor white
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.xtc
Replaced existing frames of LA BOUND TO RBD in water #1 with 459 new frames
> open /home/ahr/Desktop/rbd_la_pull/other/vector_calculations/open.pdb
open.pdb title:
Sars-COV2 S protein At open state [more info...]
Chain information for open.pdb #2
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
> open /home/ahr/Downloads/7cak.pdb
7cak.pdb title:
Sars-cov-2 S trimer with three RBD In the open state and complexed with three
H014 fab [more info...]
Chain information for 7cak.pdb #3
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
D F H | light chain of H014 fab |
E G I | heavy chain of H014 fab |
Non-standard residues in 7cak.pdb #3
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide atoms
> show cartoons
> 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 LA BOUND TO RBD in water, chain (blank) (#1) with 7cak.pdb, chain A
(#3), sequence alignment score = 1100.9
RMSD between 4 pruned atom pairs is 1.168 angstroms; (across all 456 pairs:
49.716)
> select #3
30263 atoms, 31049 bonds, 21 pseudobonds, 3831 residues, 2 models selected
> select #3:314-541
5399 atoms, 5552 bonds, 3 pseudobonds, 678 residues, 2 models selected
> select ~sel
37318 atoms, 38267 bonds, 18 pseudobonds, 4503 residues, 4 models selected
> delete atoms (#1-2#!3 & sel)
> delete bonds (#1-2#!3 & sel)
> select #3
5399 atoms, 5552 bonds, 3 pseudobonds, 678 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> open /home/ahr/Downloads/7dx3.pdb
7dx3.pdb title:
S protein of sars-cov-2 bound with Pd of ACE2 In the conformation 1 (1 up RBD
and No Pd bound) [more info...]
Chain information for 7dx3.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2
B C | spike glycoprotein | SPIKE_SARS2
Non-standard residues in 7dx3.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select #1:314-541
4590 atoms, 4718 bonds, 3 pseudobonds, 579 residues, 2 models selected
> select ~sel
19162 atoms, 19640 bonds, 24 pseudobonds, 2406 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.gro
Chain information for LA BOUND TO RBD in water #2
---
Chain | Description
? | No description available
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.xtc
Replaced existing frames of LA BOUND TO RBD in water #2 with 459 new frames
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7dx3.pdb, chain A
(#1), sequence alignment score = 832.9
RMSD between 134 pruned atom pairs is 0.807 angstroms; (across all 193 pairs:
12.220)
> view
> matchmaker #1/A to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7dx3.pdb, chain A
(#1), sequence alignment score = 832.9
RMSD between 134 pruned atom pairs is 0.807 angstroms; (across all 193 pairs:
12.220)
> matchmaker #1/B to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7dx3.pdb, chain B
(#1), sequence alignment score = 832.9
RMSD between 162 pruned atom pairs is 0.939 angstroms; (across all 193 pairs:
7.584)
> matchmaker #1/C to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7dx3.pdb, chain C
(#1), sequence alignment score = 822.1
RMSD between 164 pruned atom pairs is 0.931 angstroms; (across all 193 pairs:
7.492)
> select #2/?:511
24 atoms, 21 bonds, 3 residues, 1 model selected
> color sel yellow
> select #1/A:511
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> open /home/ahr/Downloads/7cac.pdb
7cac.pdb title:
Sars-cov-2 S trimer with one RBD In the open state and complexed with one H014
fab. [more info...]
Chain information for 7cac.pdb #3
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
D | light chain of H014 fab |
E | heavy chain of H014 fab |
Non-standard residues in 7cac.pdb #3
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide sel atoms
> hide sel cartoons
> style sel stick
Changed 7 atom styles
> style sel stick
Changed 7 atom styles
> hide sel atoms
> show sel cartoons
> hide sel atoms
> select #3
28116 atoms, 28847 bonds, 22 pseudobonds, 3559 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #3/C to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7cac.pdb, chain C
(#3), sequence alignment score = 1047.1
RMSD between 128 pruned atom pairs is 1.254 angstroms; (across all 542 pairs:
43.460)
> select clear
> matchmaker #3/B to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7cac.pdb, chain B
(#3), sequence alignment score = 1057
RMSD between 7 pruned atom pairs is 1.415 angstroms; (across all 403 pairs:
32.034)
> select #3:314-541
5397 atoms, 5549 bonds, 3 pseudobonds, 678 residues, 2 models selected
> select ~sel
34393 atoms, 35257 bonds, 22 pseudobonds, 4135 residues, 5 models selected
> hide sel atoms
> select #3:314-541
5397 atoms, 5549 bonds, 3 pseudobonds, 678 residues, 2 models selected
> select ~sel
34393 atoms, 35257 bonds, 22 pseudobonds, 4135 residues, 5 models selected
> select clear
> matchmaker #3/C to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7cac.pdb, chain C
(#3), sequence alignment score = 1054.2
RMSD between 7 pruned atom pairs is 1.401 angstroms; (across all 401 pairs:
34.772)
> matchmaker #3/C to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7dx3.pdb, chain A (#1) with 7cac.pdb, chain C (#3), sequence
alignment score = 3565.7
RMSD between 132 pruned atom pairs is 0.985 angstroms; (across all 191 pairs:
8.932)
> select #3
28116 atoms, 28847 bonds, 22 pseudobonds, 3559 residues, 2 models selected
> select ~sel
11674 atoms, 11959 bonds, 3 pseudobonds, 1254 residues, 3 models selected
> ~select #2
4590 atoms, 4718 bonds, 3 pseudobonds, 579 residues, 2 models selected
> ~select #1
Nothing selected
> delete atoms
> delete bonds
> open /home/ahr/Downloads/7cac.pdb
7cac.pdb title:
Sars-cov-2 S trimer with one RBD In the open state and complexed with one H014
fab. [more info...]
Chain information for 7cac.pdb #1
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
D | light chain of H014 fab |
E | heavy chain of H014 fab |
Non-standard residues in 7cac.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide atoms
> show cartoons
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.gro
Chain information for LA BOUND TO RBD in water #2
---
Chain | Description
? | No description available
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'LA BOUND TO RBD in water #2/?'
KeyError: 'LA BOUND TO RBD in water #2/?'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 347, in _match_value_change
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'LA BOUND TO RBD in water #2/?'
KeyError: 'LA BOUND TO RBD in water #2/?'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'LA BOUND TO RBD in water #2/?'
KeyError: 'LA BOUND TO RBD in water #2/?'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'LA BOUND TO RBD in water #2/?'
KeyError: 'LA BOUND TO RBD in water #2/?'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 347, in _match_value_change
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'LA BOUND TO RBD in water #2/?'
KeyError: 'LA BOUND TO RBD in water #2/?'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
> matchmaker #1/A to #2/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#2) with 7cac.pdb, chain A
(#1), sequence alignment score = 1084.6
RMSD between 129 pruned atom pairs is 1.129 angstroms; (across all 398 pairs:
43.478)
> view
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.xtc
Replaced existing frames of LA BOUND TO RBD in water #2 with 459 new frames
Drag select of 1947 residues, 11 pseudobonds
> hide sel cartoons
Drag select of 60 residues
> hide sel atoms
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 93 residues, 3 pseudobonds
> select up
1099 atoms, 1128 bonds, 3 pseudobonds, 134 residues, 2 models selected
> select up
8158 atoms, 8364 bonds, 3 pseudobonds, 1036 residues, 2 models selected
> select down
1099 atoms, 1128 bonds, 3 pseudobonds, 134 residues, 2 models selected
> select down
751 atoms, 3 pseudobonds, 93 residues, 2 models selected
> hide sel cartoons
Drag select of 164 residues, 1 pseudobonds
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> select #1:314-541
5397 atoms, 5549 bonds, 3 pseudobonds, 678 residues, 2 models selected
> select ~sel
29803 atoms, 30539 bonds, 19 pseudobonds, 3556 residues, 3 models selected
> ~select #2
22719 atoms, 23298 bonds, 19 pseudobonds, 2881 residues, 2 models selected
> hide sel cartoons
> select #1/E
1608 atoms, 1652 bonds, 1 pseudobond, 214 residues, 2 models selected
> show sel cartoons
> select #1/D
1605 atoms, 1644 bonds, 207 residues, 1 model selected
> show sel cartoons
> set bgColor white
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> select #1/B:511
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> select #2/?:511
24 atoms, 21 bonds, 3 residues, 1 model selected
> color sel yellow
> select #1/E
1608 atoms, 1652 bonds, 1 pseudobond, 214 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/D
1605 atoms, 1644 bonds, 207 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1
24903 atoms, 25551 bonds, 21 pseudobonds, 3138 residues, 2 models selected
> save /home/ahr/Desktop/rbd_la_pull/pmf/NoLA/open.pdb models #1 selectedOnly
> true relModel #2
> select clear
> open /home/ahr/Desktop/rbd_la_pull/pmf/NoLA/open.pdb
open.pdb title:
Sars-cov-2 S trimer with one RBD In the open state and complexed with one H014
fab. [more info...]
Chain information for open.pdb #3
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
Non-standard residues in open.pdb #3
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> hide #!1 models
> select #3
24903 atoms, 25551 bonds, 21 pseudobonds, 3138 residues, 2 models selected
> save /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/open.pdb
> models #3 selectedOnly true relModel #2
> select #3:314-541
5397 atoms, 5549 bonds, 3 pseudobonds, 678 residues, 2 models selected
> select ~sel
51493 atoms, 52794 bonds, 39 pseudobonds, 6273 residues, 5 models selected
> delete atoms (#2#!3 & sel)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 379, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 495, in <lambda>
filter_func=lambda c, ref=chain: c.structure != ref.structure)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> delete bonds (#2#!3 & sel)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: '7cac.pdb #1/A'
KeyError: '7cac.pdb #1/A'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 347, in _match_value_change
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: '7cac.pdb #1/A'
KeyError: '7cac.pdb #1/A'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: '7cac.pdb #1/A'
KeyError: '7cac.pdb #1/A'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
> show #!1 models
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /C:317
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3:317-541
5331 atoms, 5483 bonds, 3 pseudobonds, 669 residues, 2 models selected
> select ~sel
66 atoms, 66 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/open.pdb
> relModel #3
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.gro
Chain information for LA BOUND TO RBD in water #1
---
Chain | Description
? | No description available
> open
> /home/ahr/Desktop/rbd_la_pull/other/rbd_la_pull/rbd_pull/B/pull_nowat.xtc
Replaced existing frames of LA BOUND TO RBD in water #1 with 459 new frames
> select #3:317-541
5331 atoms, 5483 bonds, 3 pseudobonds, 669 residues, 2 models selected
> select clear
> open /home/ahr/Desktop/rbd_la_pull/other/vectors/open.pdb
open.pdb title:
Sars-COV2 S protein At open state [more info...]
Chain information for open.pdb #2
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
> ui tool show Matchmaker
> matchmaker #3/A to #1/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#1) with open.pdb, chain A
(#3), sequence alignment score = 1026.1
RMSD between 163 pruned atom pairs is 1.164 angstroms; (across all 223 pairs:
2.061)
> matchmaker #3/B to #1/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#1) with open.pdb, chain B
(#3), sequence alignment score = 1031.5
RMSD between 168 pruned atom pairs is 1.127 angstroms; (across all 223 pairs:
5.091)
> matchmaker #3/C to #1/? pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker LA BOUND TO RBD in water, chain (blank) (#1) with open.pdb, chain C
(#3), sequence alignment score = 1026.1
RMSD between 163 pruned atom pairs is 1.164 angstroms; (across all 223 pairs:
2.061)
> select #2
5370 atoms, 5529 bonds, 675 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3
5331 atoms, 5483 bonds, 3 pseudobonds, 669 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> open /home/ahr/Desktop/rbd_la_pull/other/vectors/open.pdb
open.pdb title:
Sars-COV2 S protein At open state [more info...]
Chain information for open.pdb #2
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/B'
KeyError: 'open.pdb #2/B'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 347, in _match_value_change
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/B'
KeyError: 'open.pdb #2/B'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 186, in run_matchmaker
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/B'
KeyError: 'open.pdb #2/B'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 186, in run_matchmaker
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/B'
KeyError: 'open.pdb #2/B'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 65, in refresh
self._items_change()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 161, in _items_change
item_names = self._item_names()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 40, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 307, in _filter_bring_models
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/A'
KeyError: 'open.pdb #2/A'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 347, in _match_value_change
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/A'
KeyError: 'open.pdb #2/A'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 186, in run_matchmaker
match_value = match_widget.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 518, in value
match_chain = match_menu.value
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 323, in value
return self.get_value()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
KeyError: 'open.pdb #2/A'
KeyError: 'open.pdb #2/A'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 337, in get_value
return self.item_map[text]
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: RENOIR (renoir, LLVM 15.0.7, DRM 3.54, 6.5.0-35-generic)
OpenGL vendor: AMD
Manufacturer: HP
Model: HP Laptop 15-ef2xxx
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 7.1Gi 3.9Gi 1.3Gi 63Mi 1.9Gi 2.8Gi
Swap: 2.0Gi 961Mi 1.1Gi
Graphics:
03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Lucienne [1002:164c] (rev c2)
DeviceName: Onboard IGD
Subsystem: Hewlett-Packard Company Lucienne [103c:887a]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 17 months ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → MatchMaker: KeyError in item chooser |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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1.3