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Opened 3 years ago
Closed 3 years ago
#7113 closed defect (fixed)
Session save: function 'set_pbgroup_py_instance' not found
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Tried to save a session with a few models, nothing special.(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open E:\\\Work\\\Projects\\\SpOT-ON\\\Models\\\test.cxs
Log from Mon Jun 6 17:58:16 2022
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting soft
> set bgColor white
> distance style color black
[Repeated 1 time(s)]
> distance style decimalPlaces 1
[Repeated 1 time(s)]
> distance style dashes 7
[Repeated 1 time(s)]
> distance style symbol false
[Repeated 1 time(s)]UCSF ChimeraX version: 1.4rc202205140117 (2022-05-14)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/martinpacesa/Documents/Projects/SpOT-ON/Models/SpOT-
> ON_Inactive.pdb /Users/martinpacesa/Documents/Projects/SpOT-ON/Models/SpOT-
> ON_Product.pdb
Chain information for SpOT-ON_Inactive.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
Chain information for SpOT-ON_Product.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> close #1-2
> open /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/6-nt_match.pdb
> /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/8-nt_match.pdb
> /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/10-nt_match.pdb
> /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/12-nt_match.pdb
> /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/14-nt_match.pdb
> /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/16-nt_match.pdb
> /Users/martinpacesa/Downloads/Pacesa_Jinek_R-loop/18-nt_match_checkpoint.pdb
Chain information for 6-nt_match.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for 8-nt_match.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for 10-nt_match.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for 12-nt_match.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for 14-nt_match.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for 16-nt_match.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Chain information for 18-nt_match_checkpoint.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open /Users/martinpacesa/Downloads/Pacesa_Jinek_R-
> loop/18-nt_match_catalytic.pdb
Chain information for 18-nt_match_catalytic.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
c | No description available
> open /Users/martinpacesa/Documents/Projects/SpOT-ON/Models/SpOT-
> ON_Inactive.pdb /Users/martinpacesa/Documents/Projects/SpOT-ON/Models/SpOT-
> ON_Product.pdb
Chain information for SpOT-ON_Inactive.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
Chain information for SpOT-ON_Product.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide atoms
> color #1/B:1-56 dodger blue
> color #1/B:57-94 magenta
> color #1/B:95-174 gainsboro
> color #1/B:175-304 #aaaaff
> color #1/B:305-494 gainsboro
> color #1/B:495-717 tan
> color #1/B:718-766 dodger blue
> color #1/B:767-925 yellow
> color #1/B:926-1099 dodger blue
> color #1/B:1100-1368 salmon
> color #1/C steel blue
> color #1/D medium blue
> color #1/A orange
> show #1/A,C,D atoms
> color #2/B:1-56 dodger blue
> color #2/B:57-94 magenta
> color #2/B:95-174 gainsboro
> color #2/B:175-304 #aaaaff
> color #2/B:305-494 gainsboro
> color #2/B:495-717 tan
> color #2/B:718-766 dodger blue
> color #2/B:767-925 yellow
> color #2/B:926-1099 dodger blue
> color #2/B:1100-1368 salmon
> color #2/C steel blue
> color #2/D medium blue
> color #2/A orange
> show #2/A,C,D atoms
> color #3/B:1-56 dodger blue
> color #3/B:57-94 magenta
> color #3/B:95-174 gainsboro
> color #3/B:175-304 #aaaaff
> color #3/B:305-494 gainsboro
> color #3/B:495-717 tan
> color #3/B:718-766 dodger blue
> color #3/B:767-925 yellow
> color #3/B:926-1099 dodger blue
> color #3/B:1100-1368 salmon
> color #3/C steel blue
> color #3/D medium blue
> color #3/A orange
> show #3/A,C,D atoms
> color #4/B:1-56 dodger blue
> color #4/B:57-94 magenta
> color #4/B:95-174 gainsboro
> color #4/B:175-304 #aaaaff
> color #4/B:305-494 gainsboro
> color #4/B:495-717 tan
> color #4/B:718-766 dodger blue
> color #4/B:767-925 yellow
> color #4/B:926-1099 dodger blue
> color #4/B:1100-1368 salmon
> color #4/C steel blue
> color #4/D medium blue
> color #4/A orange
> show #4/A,C,D atoms
> color #5/B:1-56 dodger blue
> color #5/B:57-94 magenta
> color #5/B:95-174 gainsboro
> color #5/B:175-304 #aaaaff
> color #5/B:305-494 gainsboro
> color #5/B:495-717 tan
> color #5/B:718-766 dodger blue
> color #5/B:767-925 yellow
> color #5/B:926-1099 dodger blue
> color #5/B:1100-1368 salmon
> color #5/C steel blue
> color #5/D medium blue
> color #5/A orange
> show #5/A,C,D atoms
> color #6/B:1-56 dodger blue
> color #6/B:57-94 magenta
> color #6/B:95-174 gainsboro
> color #6/B:175-304 #aaaaff
> color #6/B:305-494 gainsboro
> color #6/B:495-717 tan
> color #6/B:718-766 dodger blue
> color #6/B:767-925 yellow
> color #6/B:926-1099 dodger blue
> color #6/B:1100-1368 salmon
> color #6/C steel blue
> color #6/D medium blue
> color #6/A orange
> show #6/A,C,D atoms
> color #7/B:1-56 dodger blue
> color #7/B:57-94 magenta
> color #7/B:95-174 gainsboro
> color #7/B:175-304 #aaaaff
> color #7/B:305-494 gainsboro
> color #7/B:495-717 tan
> color #7/B:718-766 dodger blue
> color #7/B:767-925 yellow
> color #7/B:926-1099 dodger blue
> color #7/B:1100-1368 salmon
> color #7/C steel blue
> color #7/D medium blue
> color #7/A orange
> show #7/A,C,D atoms
> color #8/B:1-56 dodger blue
> color #8/B:57-94 magenta
> color #8/B:95-174 gainsboro
> color #8/B:175-304 #aaaaff
> color #8/B:305-494 gainsboro
> color #8/B:495-717 tan
> color #8/B:718-766 dodger blue
> color #8/B:767-925 yellow
> color #8/B:926-1099 dodger blue
> color #8/B:1100-1368 salmon
> color #8/C steel blue
> color #8/c steel blue
> color #8/D medium blue
> color #8/A orange
> show #8/A,C,c,D atoms
> style stick
Changed 134859 atom styles
> hide target m
> show #!8 models
> show #!8 cartoons
> show #!1 models
> show #!2 models
> show target m
> nucleotides tube/slab shape box
> ui tool show Matchmaker
> matchmaker #!1-7,9-10 to #8
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 18-nt_match_catalytic.pdb, chain B (#8) with 6-nt_match.pdb, chain
B (#1), sequence alignment score = 6448.4
RMSD between 772 pruned atom pairs is 0.871 angstroms; (across all 1337 pairs:
14.119)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 8-nt_match.pdb, chain
B (#2), sequence alignment score = 6401.2
RMSD between 795 pruned atom pairs is 0.881 angstroms; (across all 1337 pairs:
13.606)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 10-nt_match.pdb, chain
B (#3), sequence alignment score = 6438.4
RMSD between 790 pruned atom pairs is 0.617 angstroms; (across all 1338 pairs:
14.010)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 12-nt_match.pdb, chain
B (#4), sequence alignment score = 5625.2
RMSD between 780 pruned atom pairs is 0.719 angstroms; (across all 1183 pairs:
6.016)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 14-nt_match.pdb, chain
B (#5), sequence alignment score = 6412.1
RMSD between 786 pruned atom pairs is 0.708 angstroms; (across all 1328 pairs:
13.811)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 16-nt_match.pdb, chain
B (#6), sequence alignment score = 6593.8
RMSD between 800 pruned atom pairs is 0.639 angstroms; (across all 1336 pairs:
10.137)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with
18-nt_match_checkpoint.pdb, chain B (#7), sequence alignment score = 6650.2
RMSD between 801 pruned atom pairs is 0.631 angstroms; (across all 1336 pairs:
10.142)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 230.2
RMSD between 4 pruned atom pairs is 0.831 angstroms; (across all 750 pairs:
43.695)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Product.pdb,
chain A (#10), sequence alignment score = 397
RMSD between 37 pruned atom pairs is 1.094 angstroms; (across all 999 pairs:
40.850)
> matchmaker #!1-7,9-10 to #8
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 18-nt_match_catalytic.pdb, chain B (#8) with 6-nt_match.pdb, chain
B (#1), sequence alignment score = 6448.4
RMSD between 772 pruned atom pairs is 0.871 angstroms; (across all 1337 pairs:
14.119)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 8-nt_match.pdb, chain
B (#2), sequence alignment score = 6401.2
RMSD between 795 pruned atom pairs is 0.881 angstroms; (across all 1337 pairs:
13.606)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 10-nt_match.pdb, chain
B (#3), sequence alignment score = 6438.4
RMSD between 790 pruned atom pairs is 0.617 angstroms; (across all 1338 pairs:
14.010)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 12-nt_match.pdb, chain
B (#4), sequence alignment score = 5625.2
RMSD between 780 pruned atom pairs is 0.719 angstroms; (across all 1183 pairs:
6.016)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 14-nt_match.pdb, chain
B (#5), sequence alignment score = 6412.1
RMSD between 786 pruned atom pairs is 0.708 angstroms; (across all 1328 pairs:
13.811)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with 16-nt_match.pdb, chain
B (#6), sequence alignment score = 6593.8
RMSD between 800 pruned atom pairs is 0.639 angstroms; (across all 1336 pairs:
10.137)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with
18-nt_match_checkpoint.pdb, chain B (#7), sequence alignment score = 6650.2
RMSD between 801 pruned atom pairs is 0.631 angstroms; (across all 1336 pairs:
10.142)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 230.2
RMSD between 4 pruned atom pairs is 0.831 angstroms; (across all 750 pairs:
43.695)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Product.pdb,
chain A (#10), sequence alignment score = 397
RMSD between 37 pruned atom pairs is 1.094 angstroms; (across all 999 pairs:
40.850)
> hide #!9 target m
> hide target m
> show #!9 models
> show #!10 models
> hide #!9 models
> show #!9 models
> show #!9-10 cartoons
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!9 models
> hide #!10 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!9-10 to #8 ssFraction 0.7814
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7814
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 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 1776.09
RMSD between 6 pruned atom pairs is 1.407 angstroms; (across all 757 pairs:
46.746)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Product.pdb,
chain A (#10), sequence alignment score = 2456.41
RMSD between 14 pruned atom pairs is 1.157 angstroms; (across all 987 pairs:
47.938)
> matchmaker #!9-10 to #8 ssFraction 0.7814
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7814
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 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 1776.09
RMSD between 6 pruned atom pairs is 1.407 angstroms; (across all 757 pairs:
46.746)
Matchmaker 18-nt_match_catalytic.pdb, chain B (#8) with SpOT-ON_Product.pdb,
chain A (#10), sequence alignment score = 2456.41
RMSD between 14 pruned atom pairs is 1.157 angstroms; (across all 987 pairs:
47.938)
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!7 models
> hide #!8 models
> matchmaker #!9 to #7 ssFraction 0.7814
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.7814
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 18-nt_match_checkpoint.pdb, chain B (#7) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 1850.91
RMSD between 7 pruned atom pairs is 1.167 angstroms; (across all 771 pairs:
42.774)
> matchmaker #!9 to #7 ssFraction 1.0
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 1
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 18-nt_match_checkpoint.pdb, chain B (#7) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 2746
RMSD between 7 pruned atom pairs is 1.204 angstroms; (across all 787 pairs:
42.663)
> matchmaker #!9 to #7 ssFraction 0.2778
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.2778
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 18-nt_match_checkpoint.pdb, chain B (#7) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 210.321
RMSD between 8 pruned atom pairs is 1.413 angstroms; (across all 765 pairs:
40.788)
> matchmaker #!9 to #7 ssFraction 0.2778 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.2778
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 18-nt_match_checkpoint.pdb, chain A (#7) with SpOT-ON_Inactive.pdb,
chain B (#9), sequence alignment score = 117.172
RMSD between 3 pruned atom pairs is 0.887 angstroms; (across all 87 pairs:
23.955)
> matchmaker #!9 to #7 ssFraction 0.9 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.9
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 18-nt_match_checkpoint.pdb, chain A (#7) with SpOT-ON_Inactive.pdb,
chain B (#9), sequence alignment score = 339.9
RMSD between 4 pruned atom pairs is 1.000 angstroms; (across all 96 pairs:
30.626)
> matchmaker #!9 to #7 ssFraction 0.9 matrix BLOSUM-100
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-100
SS fraction | 0.9
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 18-nt_match_checkpoint.pdb, chain B (#7) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 2201.2
RMSD between 7 pruned atom pairs is 1.167 angstroms; (across all 767 pairs:
42.726)
> matchmaker #!9 to #7 ssFraction 0.2278 matrix BLOSUM-100
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-100
SS fraction | 0.2278
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 18-nt_match_checkpoint.pdb, chain B (#7) with SpOT-ON_Inactive.pdb,
chain A (#9), sequence alignment score = 215.019
RMSD between 7 pruned atom pairs is 1.549 angstroms; (across all 613 pairs:
39.614)
> matchmaker #!9 to #7 alg Smith-Waterman ssFraction 0.2278 matrix BLOSUM-100
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-100
SS fraction | 0.2278
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 18-nt_match_checkpoint.pdb (#7) with SpOT-ON_Inactive.pdb (#9),
sequence alignment score = 228.579
RMSD between 5 pruned atom pairs is 1.399 angstroms; (across all 618 pairs:
42.691)
> matchmaker #!9 to #7 alg Smith-Waterman ssFraction 0.2278 matrix BLOSUM-65
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-65
SS fraction | 0.2278
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 18-nt_match_checkpoint.pdb (#7) with SpOT-ON_Inactive.pdb (#9),
sequence alignment score = 169.545
RMSD between 23 pruned atom pairs is 0.556 angstroms; (across all 458 pairs:
36.203)
> matchmaker #!9 to #7 alg Smith-Waterman ssFraction 0.4112 matrix BLOSUM-65
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-65
SS fraction | 0.4112
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 18-nt_match_checkpoint.pdb (#7) with SpOT-ON_Inactive.pdb (#9),
sequence alignment score = 521.83
RMSD between 17 pruned atom pairs is 1.241 angstroms; (across all 714 pairs:
45.489)
> matchmaker #!9 to #7 alg Smith-Waterman ssFraction 0.6166 matrix BLOSUM-65
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-65
SS fraction | 0.6166
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 18-nt_match_checkpoint.pdb (#7) with SpOT-ON_Inactive.pdb (#9),
sequence alignment score = 1210.4
RMSD between 7 pruned atom pairs is 1.442 angstroms; (across all 783 pairs:
42.814)
> matchmaker #!9 to #7 alg Smith-Waterman ssFraction 0.4056 matrix BLOSUM-65
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-65
SS fraction | 0.4056
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 18-nt_match_checkpoint.pdb (#7) with SpOT-ON_Inactive.pdb (#9),
sequence alignment score = 507.315
RMSD between 17 pruned atom pairs is 1.241 angstroms; (across all 714 pairs:
45.489)
> hide #!7 models
> show #!10 models
> show #!8 models
> hide #!9 models
> ui tool show Matchmaker
> matchmaker #!10 to #8 alg Smith-Waterman ssFraction 0.4056 matrix BLOSUM-65
> showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-65
SS fraction | 0.4056
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 18-nt_match_catalytic.pdb (#8) with SpOT-ON_Product.pdb (#10),
sequence alignment score = 738.197
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 18-nt_match_catalytic.pdb
#8/B, SpOT-ON_Product.pdb #10/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 4 pruned atom pairs is 0.971 angstroms; (across all 981 pairs:
47.027)
> ui tool show Matchmaker
> matchmaker #!10 to #8 alg Smith-Waterman ssFraction 0.2786 matrix BLOSUM-65
> showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
Similarity matrix | BLOSUM-65
SS fraction | 0.2786
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 18-nt_match_catalytic.pdb (#8) with SpOT-ON_Product.pdb (#10),
sequence alignment score = 367.612
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 18-nt_match_catalytic.pdb
#8/B, SpOT-ON_Product.pdb #10/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 38 pruned atom pairs is 1.158 angstroms; (across all 803 pairs:
39.468)
> show #8/B:450 atoms
[Repeated 1 time(s)]
> ui mousemode right zoom
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> show #10/A:345 atoms
> select #8/B:8-9,77,837-843,850-860,862-869,871,955-958,966-968,971
> #10/A:30-31,89,776-782,795-805,807-814,816,930-933,942-944,947
605 atoms, 596 bonds, 76 residues, 2 models selected
> ui mousemode right select
> select clear
> save /Users/martinpacesa/Documents/Projects/SpOT-ON/Models/test.cxs
——— End of log from Mon Jun 6 17:58:16 2022 ———
opened ChimeraX session
> select #8/B:14-30 #10/A:36-55
291 atoms, 298 bonds, 37 residues, 2 models selected
> select #8/B:14-30 #10/A:36-55
291 atoms, 298 bonds, 37 residues, 2 models selected
MatchMaker Alignment [ID: 2] region 18-nt_match_catalytic.pdb..SpOT-
ON_Product.pdb [9-28] RMSD: 6.193
> select #8/B:14-30 #10/A:36-55
291 atoms, 298 bonds, 37 residues, 2 models selected
> view #8/B:56
> ui mousemode right select
> select #10/A:70
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/B:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/A:70
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/B:56
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #10/A:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #10/A:68
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:56
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/B:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #10/A:73
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/B:60
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/B:59
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/B:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #8/B:57
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/A:73
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #10/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:71
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #10/A:70
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #10/A:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> view #8/B:94
> select clear
[Repeated 1 time(s)]
> ui tool show "Side View"
> select clear
[Repeated 1 time(s)]
> select #8/B:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:93
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #10/A:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:415
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/A:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:104
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #10/A:105
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:105
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:95
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:94
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:103
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #10/A:104
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 19 residues, 1 shapes
> select clear
> select #8/B:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #8/B:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:414
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #10/A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!9 models
> hide #!8 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!7 models
Drag select of 11 residues
> show #!10 models
> hide #!7 models
> hide #!9 models
> show #!8 models
> select #10/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> open 8CSZ
Summary of feedback from opening 8CSZ fetched from pdb
---
notes | Fetching compressed mmCIF 8csz from
http://files.rcsb.org/download/8csz.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
8csz title:
IscB and wRNA bound to Target DNA [more info...]
Chain information for 8csz #11
---
Chain | Description
B | DNA target strand
C | RNA (222-mer)
D | IscB
E | DNA non-target strand
Non-standard residues in 8csz #11
---
MG — magnesium ion
ZN — zinc ion
Drag select of 11 residues, 3 shapes
> select clear
> ui tool show Matchmaker
> matchmaker #!11 to #10
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 SpOT-ON_Product.pdb, chain A (#10) with 8csz, chain D (#11),
sequence alignment score = 62.6
RMSD between 37 pruned atom pairs is 1.068 angstroms; (across all 390 pairs:
37.716)
> matchmaker #!11 to #10
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 SpOT-ON_Product.pdb, chain A (#10) with 8csz, chain D (#11),
sequence alignment score = 62.6
RMSD between 37 pruned atom pairs is 1.068 angstroms; (across all 390 pairs:
37.716)
> hide #!8 models
> hide #!10 models
> color #!11 bychain
> nucleotides #!11 tube/slab shape box
[Repeated 1 time(s)]
> show #!10 models
> hide #!11 models
> color #!10 bychain
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> color #!10-11 bychain
> show #!9 models
> color #!9-11 bychain
> hide #!11 models
> ui tool show Matchmaker
> matchmaker #!9 to #10
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 SpOT-ON_Product.pdb, chain A (#10) with SpOT-ON_Inactive.pdb, chain
A (#9), sequence alignment score = 4032.2
RMSD between 891 pruned atom pairs is 0.587 angstroms; (across all 893 pairs:
1.046)
> matchmaker #!9 to #10
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 SpOT-ON_Product.pdb, chain A (#10) with SpOT-ON_Inactive.pdb, chain
A (#9), sequence alignment score = 4032.2
RMSD between 891 pruned atom pairs is 0.587 angstroms; (across all 893 pairs:
1.046)
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select #10/A:965
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> hide #!8 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!8 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select #11/C:109
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/C:110
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/C:111
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/C:108
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #11/C:172
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!10 models
> hide #!10 models
> select clear
> show #!10 models
> hide #!11 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!7 models
> show #!11 models
> hide #!7 models
> select clear
> select #11/D:39
7 atoms, 7 bonds, 1 residue, 1 model selected
> save E:/Work/Projects/SpOT-ON/Models/overlays.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map
f = c_function('set_pbgroup_py_instance',
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function
f = getattr(self._c_lib, func_name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__
func = self.__getitem__(name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'set_pbgroup_py_instance' not found
AttributeError: function 'set_pbgroup_py_instance' not found
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
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\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map
f = c_function('set_pbgroup_py_instance',
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function
f = getattr(self._c_lib, func_name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__
func = self.__getitem__(name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'set_pbgroup_py_instance' not found
AttributeError: function 'set_pbgroup_py_instance' not found
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
See log for complete Python traceback.
> select add #11
8948 atoms, 9620 bonds, 238 pseudobonds, 733 residues, 4 models selected
> select subtract #11
Nothing selected
> hide #11.3 models
> show #!10 models
> hide #!11 models
> save E:/Work/Projects/SpOT-ON/Models/test.cxs
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map
f = c_function('set_pbgroup_py_instance',
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function
f = getattr(self._c_lib, func_name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__
func = self.__getitem__(name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'set_pbgroup_py_instance' not found
AttributeError: function 'set_pbgroup_py_instance' not found
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
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\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
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\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 249, in discovery
if hasattr(sm, 'include_state') and not sm.include_state(value):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 543, in include_state
return bool(self.group_map)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 536, in group_map
f = c_function('set_pbgroup_py_instance',
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molc.py", line 31, in c_function
f = getattr(self._c_lib, func_name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 387, in
__getattr__
func = self.__getitem__(name)
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
AttributeError: function 'set_pbgroup_py_instance' not found
AttributeError: function 'set_pbgroup_py_instance' not found
File "C:\Program Files\ChimeraX\bin\lib\ctypes\\__init__.py", line 392, in
__getitem__
func = self._FuncPtr((name_or_ordinal, self))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 516.40
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B09
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 137,325,518,848
MaxProcessMemory: 137,438,953,344
CPU: 24 AMD Ryzen Threadripper 1920X 12-Core Processor
OSLanguage: en-GB
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Session save: function 'set_pbgroup_py_instance' not found |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Hi Martin,
--Eric
fix: https://github.com/RBVI/ChimeraX/commit/1de302f5516472c56ba7345524d7c68fc1b29048