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Opened 23 months ago
Closed 23 months ago
#10268 closed defect (duplicate)
Movie recording not stopping
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
when recording a movie, the frame capture doesn't follow the command instruction and keeps capturing continuouly. This happens even if I start a new record and just type "wait 24", (see attached).
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> format session
Log from Thu Nov 30 15:37:18 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> format session
Log from Thu Nov 30 11:28:02 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> format session
Log from Thu Nov 30 11:20:36 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
Log from Thu Jun 1 11:47:06 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
> format session
Log from Sun Dec 18 22:27:04 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
Log from Wed Nov 30 17:50:44 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
> format session
Log from Thu Nov 10 14:42:37 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/overall_color.cxs
Opened run_class001_220.mrc as #2, grid size 448,448,448, pixel 1.03, shown at
level 0.0134, step 1, values float32
Log from Wed Nov 9 14:45:44 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ruigong/Desktop/pentamer_manuscipt/EM_maps/5actin_2cat_1afa_refine25.pdb
Chain information for 5actin_2cat_1afa_refine25.pdb #1
---
Chain | Description
A B C D E | No description available
F H | No description available
G | No description available
> open /Users/ruigong/Desktop/pentamer_manuscipt/EM_maps/run_class001_220.mrc
Opened run_class001_220.mrc as #2, grid size 448,448,448, pixel 1.03, shown at
level 0.00452, step 2, values float32
> volume #2 step 1
> volume #2 level 0.005978
> volume #2 level 0.01392
> select add #1
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select subtract #1
Nothing selected
> select add #1
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> set bgColor white
> lighting soft
> hide #!2 models
> color #1/E liht blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color light blue #1/E
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/E lightblue
> color #1/B deepskyblue blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/B deep sky blue
> color #1/E cornflower blue
> color #1/A light blue
> color #1/C,D light blue
> color #1/B light blue
> color #1/E deep sky blue
> color #1/F coral
> color #1/H orchid
> color #1/F orchid
> color #1/H coral
> color #1/G violet
> color #1/G #FF7F50
> color #1/G turquoise
> select subtract #1
Nothing selected
> color #1/G forestgreen
> color #1/G turquoise
> color #1/G forestgreen
> color #1/H #9966FF
> color #1/H coral
> color #1/G #9966FF
> color #1/G forestgreen
> color #1/H #9966FF
> color #1/H coral
> color #1/E deep sky blue
> color #1/B deep sky blue
> color #1/E cornflower blue
> select #1 D
Expected a keyword
> select #1/D
5795 atoms, 5858 bonds, 372 residues, 1 model selected
> select #1/C
5795 atoms, 5858 bonds, 372 residues, 1 model selected
> ui tool show "Color Actions"
> color sel purple
> color sel medium blue
> color sel indigo
> color sel dark blue
> color sel medium blue
[Repeated 1 time(s)]
> color sel blue
> color sel royal blue
> color sel medium purple
> color sel purple
> color sel dark magenta
> color sel blue violet
> color sel dark violet
> color sel rebecca purple
> color sel slate blue
> color sel medium slate blue
> show #!2 models
> select add #1
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> select add #2
32895 atoms, 33256 bonds, 2364 residues, 3 models selected
> select subtract #2
32895 atoms, 33256 bonds, 2364 residues, 1 model selected
> color zone #2 near #1 distance 5
> hide #!2 models
> show #!2 models
> volume #2 splitbyzone
Expected a keyword
> volume splitbyzone #2
Opened run_class001_220.mrc 0 as #3.1, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 1 as #3.2, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 2 as #3.3, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 3 as #3.4, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 4 as #3.5, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 5 as #3.6, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 6 as #3.7, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
Opened run_class001_220.mrc 7 as #3.8, grid size 448,448,448, pixel 1.03,
shown at level 0.0139, step 1, values float32
> hide #!3 models
> show #!3 models
> hide #!3.1 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.3 models
> show #!3.3 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.5 models
> show #!3.5 models
> hide #!3.6 models
> show #!3.6 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.8 models
> show #!3.8 models
> close #3
> show #!2 models
> hide #1 models
> volume #2 level 0.00768
> volume #2 level 0.006545
> hide #!2 models
> show #!2 models
> show #1 models
> hide #!2 models
> select subtract #1
Nothing selected
> show #!2 models
> hide #1 models
> volume #2 level 0.01108
> volume #2 level 0.01335
> hide #!2 models
> show #1 models
> show #!2 models
> lighting soft
[Repeated 6 time(s)]
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_maps/overall_color.cxs
——— End of log from Wed Nov 9 14:45:44 2022 ———
opened ChimeraX session
> show #1 models
> hide #!2 models
> select #1/G
636 atoms, 644 bonds, 74 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!2 models
> close
> open
> /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/5actin_2cat_1afa_refine25.pdb
Chain information for 5actin_2cat_1afa_refine25.pdb #1
---
Chain | Description
A B C D E | No description available
F H | No description available
G | No description available
> hide atoms
> show cartoons
> select ~#1/F
31253 atoms, 31595 bonds, 2149 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open
> /Users/ruigong/Desktop/afadin_pentamer_project/pentamer_data/meeting_figures/6upv_Lin.pdb
6upv_Lin.pdb title:
Alpha-E-catenin abd-F-actin complex [more info...]
Chain information for 6upv_Lin.pdb #2
---
Chain | Description | UniProt
A B C D E | α-actin-1 | ACTS_CHICK
L M | catenin α-1 | CTNA1_HUMAN
Non-standard residues in 6upv_Lin.pdb #2
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> hide atoms
> show cartoons
> select #2~&chainM
Expected an objects specifier or a keyword
> select #2~&/M
Expected an objects specifier or a keyword
> select #2~/M
Expected an objects specifier or a keyword
> select #2/~&M
Expected an objects specifier or a keyword
> select #2/M
1304 atoms, 1319 bonds, 173 residues, 1 model selected
> select ~sel
17571 atoms, 17920 bonds, 5 pseudobonds, 2253 residues, 3 models selected
> select subtract #1
15929 atoms, 16259 bonds, 5 pseudobonds, 2038 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 6upv_Lin.pdb,
chain M (#2), sequence alignment score = 787.6
RMSD between 142 pruned atom pairs is 0.665 angstroms; (across all 173 pairs:
4.287)
> morph #1,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #!2 models
> morph #2,1 frames 20
Computed 21 frame morph #4
> coordset #4 1,21
> hide #3 models
> open
> /Users/ruigong/Desktop/afadin_pentamer_project/pentamer_data/a_cat_ABD_AF.pdb
Chain information for a_cat_ABD_AF.pdb #5
---
Chain | Description
A | No description available
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!4 models
> hide #5 models
> show #5 models
> close #5
> open
> /Users/ruigong/Desktop/afadin_pentamer_project/pentamer_data/a_cat_ABD_AF.pdb
Chain information for a_cat_ABD_AF.pdb #5
---
Chain | Description
A | No description available
> show #5 cartoons
> show #5 atoms
> select add #5
1808 atoms, 1828 bonds, 236 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
1808 atoms, 1828 bonds, 236 residues, 1 model selected
> show #!4 models
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> hide sel atoms
> select subtract #5
Nothing selected
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!4 models
> morph #5,1 frames 20
Computed 21 frame morph #6
> coordset #6 1,21
> show #1 models
> hide #6 models
> show #6 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
——— End of log from Thu Nov 10 14:42:37 2022 ———
opened ChimeraX session
> lighting shadows false
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #6 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> hide #1 models
> hide #3 models
> show #3 models
> show #!2 models
> show #1 models
> hide #3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show slider
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> coordset slider
Missing or invalid "structures" argument: empty atom specifier
> coordset slider
Missing or invalid "structures" argument: empty atom specifier
> show #3 models
> coordset slider #3
> coordset slider #4
> coordset slider #6
> hide #!2 models
> hide #1 models
> show #!4 models
> hide #3 models
> hide #!4 models
> show #6 models
> show #1 models
> hide #1 models
> show #1 models
> hide #6 models
> open
> /Users/ruigong/Desktop/afadin_pentamer_project/pentamer_data/6dv1_Ikura_ABD.pdb
Chain information for 6dv1_Ikura_ABD.pdb #7
---
Chain | Description
A | No description available
> fitmap #7 to #2
Expected a keyword
Must specify one map, got 0
> hide #1 models
> hide #!7 models
> show #!7 models
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> mmaker #7/A to #2/M
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 6upv_Lin.pdb, chain M (#2) with 6dv1_Ikura_ABD.pdb, chain A (#7),
sequence alignment score = 659.9
RMSD between 78 pruned atom pairs is 1.023 angstroms; (across all 153 pairs:
6.066)
> open
> /Users/ruigong/Desktop/afadin_pentamer_project/pentamer_data/4IGG_ABD.pdb
Chain information for 4IGG_ABD.pdb #8
---
Chain | Description
B | No description available
> mmaker #8/B to #7/A
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 6dv1_Ikura_ABD.pdb, chain A (#7) with 4IGG_ABD.pdb, chain B (#8),
sequence alignment score = 881.7
RMSD between 171 pruned atom pairs is 0.674 angstroms; (across all 188 pairs:
1.857)
> mmaker #8/B to #7/A
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 6dv1_Ikura_ABD.pdb, chain A (#7) with 4IGG_ABD.pdb, chain B (#8),
sequence alignment score = 881.7
RMSD between 171 pruned atom pairs is 0.674 angstroms; (across all 188 pairs:
1.857)
> open
> /Users/ruigong/Desktop/afadin_pentamer_project/pentamer_data/4IGG_ABD_chainA.pdb
Chain information for 4IGG_ABD_chainA.pdb #9
---
Chain | Description
A | No description available
> mmaker #9/A to #8/B
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 4IGG_ABD.pdb, chain B (#8) with 4IGG_ABD_chainA.pdb, chain A (#9),
sequence alignment score = 938.6
RMSD between 145 pruned atom pairs is 0.642 angstroms; (across all 196 pairs:
7.987)
> mmaker #9/A to #8/B
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 4IGG_ABD.pdb, chain B (#8) with 4IGG_ABD_chainA.pdb, chain A (#9),
sequence alignment score = 938.6
RMSD between 145 pruned atom pairs is 0.642 angstroms; (across all 196 pairs:
7.987)
> mmaker #9/A to #8/B
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 4IGG_ABD.pdb, chain B (#8) with 4IGG_ABD_chainA.pdb, chain A (#9),
sequence alignment score = 938.6
RMSD between 145 pruned atom pairs is 0.642 angstroms; (across all 196 pairs:
7.987)
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
> hide #1 models
> hide #!2 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #8 models
> hide #9 models
> show #8 models
> hide #8 models
> show #8 models
> show #9 models
> hide #9 models
> show #1 models
> color #1/F light salmon
> hide #1 models
> hide #!7 models
> hide #8 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #!7 models
> show #9 models
> hide #1 models
> hide #!2 models
> hide #8 models
> hide #9 models
> hide #!7 models
> show #!7 models
> show #8 models
> hide #!7 models
> show #1 models
> show #!2 models
> color #5/F:844-904 #FF66FF
> color #51/F:844-904 #FF66FF
> color #1/F:844-904 #FF66FF
> color #1/F:688-707 #CC66CC
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #1 models
> show #1 models
> hide #8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #1 models
> show #6 models
> hide #6 models
> color #7 #cc0066 transparency 0
> color #7 #cccccc transparency 0
> show #1 models
> cartoon style modeHelix tube radius 2 sides 24
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!2 models
> setattr #1/F:693-706 res ss_type 1
Assigning ss_type attribute to 14 items
> hide #1 models
> show #1 models
> open
> /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/5actin_2cat_1afa_refine29.pdb
Chain information for 5actin_2cat_1afa_refine29.pdb #10
---
Chain | Description
A B C D E | No description available
F H | No description available
G | No description available
> select #10
18458 atoms, 18819 bonds, 2359 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> mmaker #10/F to #1/F
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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with
5actin_2cat_1afa_refine29.pdb, chain F (#10), sequence alignment score =
1071.3
RMSD between 214 pruned atom pairs is 0.246 angstroms; (across all 214 pairs:
0.246)
> select #10~/F
Expected an objects specifier or a keyword
> select #10/~&F
Expected an objects specifier or a keyword
> select #10~&/F
Expected an objects specifier or a keyword
> select #10&~/F
16824 atoms, 17166 bonds, 2145 residues, 1 model selected
> hide sel cartoons
> cartoon style modeHelix tube/default/wrap rad 2 sides 24
Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'
> cartoon style modeHelix tube radius 2 sides 24
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 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
> setattr #1/F:694-705 res ss_id 2
Assigning ss_id attribute to 12 items
> setattr #1/F:694-706 res ss_id 2
Assigning ss_id attribute to 13 items
> setattr #1/F:893-899 res ss_id 1
Assigning ss_id attribute to 7 items
> setattr #1/F:712-732 res ss_id 3
Assigning ss_id attribute to 21 items
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #10 models
> show #10 models
> close #10
> show #1 models
> show #!2 models
> show #6 models
> hide #6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #6 models
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #6 models
> show #6 models
> hide #6 models
> show #1 models
> show #!2 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> color #8 #cccccc transparency 0
> hide #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #8 models
> show #8 models
> show #1 models
> color #1/F light salmon
> transparency #1/F:711-842 70 target c
> transparency #2/M:711-842 70 target c
> transparency #8/A:711-842 70 target c
> hide #1 models
> hide #!2 models
> transparency #8/B:711-842 70 target c
> show #1 models
> show #!2 models
> transparency #8/B:711-842 80 target c
> transparency #2/M:711-842 80 target c
> transparency #1/F:711-842 80 target c
> color #1,8#!2 bynucleotide
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #8 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> setattr #2/M:815-842 res ss_id 4
Assigning ss_id attribute to 28 items
> show #1 models
> show #8 models
> transparency #1/F:711-842 90 target c
> transparency #2/M:711-842 90 target c
[Repeated 1 time(s)]
> transparency #8/B:711-842 90 target c
> transparency #1/F:711-842 80 target c
> transparency #2/M:711-842 80 target c
> transparency #8/B:711-842 80 target c
> view name p2
> view name p1
> view p1
> view p2
> view p1
> view p2
> cartoon style coil thickness 0.25
> cartoon style coil thickness 0.2
> view p2
> view p1
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> view p1
> view p2
> view name p2
> view p1
> view p2
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
> view name p3
> view p1
> view p3
> view p1
> view name p3
> view p1
> view p3
> view name p1
> view p2
> ui tool show "Side View"
> camera ortho
> view p1
> view name p1
> view p2
> view name p2
> view p1
> view p2
> view p1
> view name p1
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> view name p2
> view p1
> view p2
> view p1
> color #4 #99ff99 transparency 0
> view p1
[Repeated 1 time(s)]
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> cartoon style coil thickness 0.25
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> transparency #8/B:664-677 80 target c
> view p1
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
——— End of log from Wed Nov 30 17:50:44 2022 ———
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #!2 models
> hide #1 models
> hide #8 models
> coordset slider
Missing or invalid "structures" argument: empty atom specifier
> coordset slider #3
> show #9 models
> show #!4 models
> hide #3 models
> hide #9 models
> coordset slider #4
> morph #9,2 frames 20
Computed 21 frame morph #10
> coordset #10 1,21
> hide #!4 models
> color #10 #66ff66 transparency 0
[Repeated 1 time(s)]
> color #10 #339933 transparency 0
> color #10 #66ff66 transparency 0
> color #10 #33ff33 transparency 0
> color #10 #00cc00 transparency 0
> color #10 #ffcc00 transparency 0
[Repeated 1 time(s)]
> color #10 #cc9900 transparency 0
> color #10 #ccff66 transparency 0
> color #10 #ccff00 transparency 0
> color #10 #9999ff transparency 0
> color #10 #6666cc transparency 0
> color #10 #9999ff transparency 0
> select #10/A
1225 atoms, 1238 bonds, 163 residues, 1 model selected
> select #10/A:837-906
194 atoms, 198 bonds, 25 residues, 1 model selected
> select #10/A:844-906
136 atoms, 138 bonds, 18 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> color sel tomato
> color sel orange
> color sel dark orange
> color sel salmon
> color sel coral
> color sel chocolate
> color sel brown
> color sel tomato
> color sel coral
[Repeated 6 time(s)]
> select #10/A:666-707
74 atoms, 75 bonds, 9 residues, 1 model selected
> color sel medium purple
> color sel hot pink
> color sel dark orange
> color sel green yellow
> color sel blue violet
> color sel medium purple
> color sel magenta
> color sel teal
> color sel cornflower blue
> color sel deep sky blue
> color sel olive drab
> color sel olive
> color sel salmon
> color sel peru
> color sel light salmon
[Repeated 1 time(s)]
> color sel dark goldenrod
> color sel dark blue
> color sel medium blue
> color sel medium violet red
> color sel medium orchid
> color sel medium violet red
> color sel medium orchid
> color sel hot pink
> color sel magenta
> color sel pale violet red
> color sel medium purple
> color sel purple
> color sel dark magenta
> color sel dark orchid
> color sel medium violet red
> color sel dark olive green
> color sel pale green
> color sel coral
> color #10/A:844-906 #FF66FF
> select clear
> view p1
> view p2
> view p1
[Repeated 1 time(s)]
> movie record supersample 3
> wait 10
> coordset #10 1,21 bounce true loop 2
> wait 10
> movie encode /Users/ruigong/Desktop/pre_post.mp4 quality high
Movie saved to /Users/ruigong/Desktop/pre_post.mp4
> hide #10 models
> show #9 models
> hide #9 models
> show #6 models
> hide #6 models
> show #6 models
> coordset slider #6
> color #6/A:844-906 #FF66FF
> color #6/A:666-707 coral
> color #6/A #9999FF
> color #6/A:666-707 coral
> color #6/A:844-906 #FF66FF
> movie record supersample 3
> wait 10
> coordset #6 1,21 bounce true loop 2
> wait 10
> movie encode /Users/ruigong/Desktop/post_afadin.mp4 quality high
Movie saved to /Users/ruigong/Desktop/post_afadin.mp4
> view p1
> hide #6 models
> show #1 models
> show #!2 models
> show #3 models
> hide #3 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #!2 models
> hide #1 models
> morph #8,2 frames 20
Computed 21 frame morph #11
> coordset #11 1,21
> color #11/A #9999FF
> color #11/B #9999FF
> color #11/B:666-707 coral
> color #11/B:844-906 #FF66FF
> movie record supersample 3
> wait 10
> coordset #11 1,21 bounce true loop 2
> wait 10
> movie encode /Users/ruigong/Desktop/pre_post.mp4 quality high
Movie saved to /Users/ruigong/Desktop/pre_post.mp4
> view p1
> show #1 models
> show #!2 models
> hide #11 models
> show #8 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_compare.cxs
——— End of log from Sun Dec 18 22:27:04 2022 ———
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #1 models
> hide #8 models
> show #8 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 #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #10 models
> hide #10 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> coordset slider #10
> show #10 models
> hide #8 models
> show #11 models
> hide #10 models
> hide #11 models
> show #3 models
> show #!4 models
> hide #3 models
> show #10 models
> coordset slider #11
> coordset slider #3
> coordset slider #4
> hide #10 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #8 models
> hide #8 models
> show #8 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #9 models
> hide #8 models
> hide #9 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #8 models
> morph #2,8 frames 20
Computed 21 frame morph #12
> coordset #12 1,21
> hide #!12 models
> show #!12 models
> morph #8,2 frames 20
Computed 21 frame morph #13
> coordset #13 1,21
> hide #!12 models
> show #8 models
> hide #8 models
> show #8 models
> show #6 models
> show #!2 models
> hide #6 models
> close #3
> close #4
> hide #8 models
> show #8 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> view p1
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!2 models
> show #8 models
> coordset slider #13 computeSs true
> hide #8 models
> show #!2 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> hide #!2 models
> show #13 models
> coordset slider #13 computeSs false
> coordset slider #13 computeSs true
> show #8 models
> hide #8 models
> show #8 models
> hide #13 models
> show #13 models
> coordset slider #13 computeSs false
[Repeated 2 time(s)]
> hide #13 models
> show #13 models
> close #13
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> morph #8,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
> coordset #3 21 computeSs true
> coordset #3 21 computeSs false
> close #3
> morph #8,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> perframe dssp interval 5
> coordset #3 1,21
> perframe dssp interval 1
> coordset #3 1,21
> close #3
> morph #8,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
> perframe dssp interval 20
> coordset #3 1,21
> close #3
> morph #8,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
> coordset #3 21 computeSs false
> show #!2 models
> hide #!2 models
> show #!2 models
> show #8 models
> hide #!2 models
> color #3 #CCFFCC
> color #8 #CCFFCC
> hide #8 models
> show #8 models
> hide #8 models
> setattr #3/F:699-703 res ss_id 2
Assigning ss_id attribute to 0 items
> setattr #3/B:699-703 res ss_id 2
Assigning ss_id attribute to 5 items
> hide #3 models
> show #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
——— End of log from Thu Jun 1 11:47:06 2023 ———
opened ChimeraX session
> show #5 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #5 models
> show #1 models
> show #!2 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!12 models
> show #11 models
> hide #1 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> hide #11 models
> hide #!12 models
> show #!12 models
> coordset slider #11
> coordset slider #12
> show #11 models
> hide #!12 models
> show #6 models
> hide #11 models
> show #10 models
> hide #6 models
> show #3 models
> hide #10 models
> show #1 models
> hide #3 models
> hide #1 models
> show #10 models
> coordset slider #10
> close #10
> show #11 models
> close #11
> show #!12 models
> close #12
> show #!7 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 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
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #6 models
> coordset slider 6
Missing or invalid "structures" argument: invalid structures specifier
> coordset slider #6
> show #3 models
> hide #6 models
> show #1 models
> hide #3 models
> cartoon style modeHelix default
> cartoon style modeHelix tube radius 2 sides 24
> setattr #1/F:693-706 res ss_type 1
Assigning ss_type attribute to 14 items
> setattr #1/F:693-706 res ss_type 2
Assigning ss_type attribute to 14 items
> setattr #1/F:693-706 res ss_type 1
Assigning ss_type attribute to 14 items
> setattr #1/F:693-706 res ss_ID 1
Assigning ss_ID attribute to 14 items
Not creating attribute 'ss_ID'; use 'create true' to override
> setattr #1/F:693-706 res ss_id 1
Assigning ss_id attribute to 14 items
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
——— End of log from Thu Nov 30 11:20:36 2023 ———
opened ChimeraX session
> setattr #1/F:893-899 res ss_id 2
Assigning ss_id attribute to 7 items
> setattr #1/F:712-731 res ss_id 3
Assigning ss_id attribute to 20 items
> show #!2 models
> hide #1 models
> setattr #2/M:773-804 res ss_type 1
Assigning ss_type attribute to 32 items
> setattr #2/M:773-804 res ss_type 1
Assigning ss_type attribute to 32 items
> setattr #2/M:773-804 res ss_id 1
Assigning ss_id attribute to 32 items
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
——— End of log from Thu Nov 30 11:28:02 2023 ———
opened ChimeraX session
> setattr #2/M:773-804 res ss_id 1
Assigning ss_id attribute to 32 items
> setattr #2/M:773-804 res ss_type 1
Assigning ss_type attribute to 32 items
> setattr #2/M:773-804 res ss_id 1
Assigning ss_id attribute to 32 items
> setattr #2/M:816-841 res ss_type 1
Assigning ss_type attribute to 26 items
> setattr #2/M:816-841 res ss_id 2
Assigning ss_id attribute to 26 items
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> setattr #2/M:711-729 res ss_id 3
Assigning ss_id attribute to 19 items
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> show #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #1 models
> hide #!2 models
> show #1 models
> show #!2 models
> hide #3 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #5 models
> hide #3 models
> show #3 models
> show #5 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #5 models
> setattr #1/F:855-858 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #1/F:875-877 res ss_type 0
Assigning ss_type attribute to 3 items
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> hide #!2 models
> hide #1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #5 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> setattr #8/B:813-841 res ss_id 2
Assigning ss_id attribute to 29 items
> show #3 models
> hide #3 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #5 models
> show #!2 models
> hide #8 models
> show #8 models
> hide #!2 models
> show #5 models
> hide #8 models
> setattr #5/A:678-702 res ss_id 1
Assigning ss_id attribute to 25 items
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #5 models
> show #5 models
> hide #8 models
> setattr #5/A:843-845 res ss_type 0
Assigning ss_type attribute to 3 items
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #8 models
> setattr #5/A:711-731 res ss_id 3
Assigning ss_id attribute to 21 items
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #8 models
> hide #8 models
> show #8 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> hide #8 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #5 models
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #!2 models
> hide #1 models
> hide #!2 models
> show #!2 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!2 models
> show #!2 models
> close #3
> close #6
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> morph #8,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
> show #1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #8 models
> hide #8 models
> show #5 models
> morph #5,1 frames 20
Computed 21 frame morph #4
> coordset #4 1,21
> hide #4 models
> show #3 models
> color #3 #CCFFCC
> color #4 #CCFFCC
> show #4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> color #4 pale violet red
> color #4 light salmon
> color #3 light salmon
> hide #4 models
> show #!2 models
> color #3 #CCFFCC
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #!2 models
> hide #!2 models
> hide #!7 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #8 models
> show #8 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> transparency #8/B:664-677 0 target c
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> transparency #8/B:664-694 0 target c
> transparency #8/B:664-994 0 target c
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> align #8 toAtoms #2
Unequal number of atoms to pair, 1633 and 1304
> hide #8 models
> show #1 models
> align #2 toAtoms #1
Unequal number of atoms to pair, 1304 and 1642
> align #2/M:707-844 toAtoms #1/F:707-844
RMSD between 1032 atom pairs is 2.068 angstroms
> align #2/M:863-871 toAtoms #1/F:863-871
RMSD between 70 atom pairs is 1.695 angstroms
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 6upv_Lin.pdb,
chain M (#2), sequence alignment score = 787.6
RMSD between 142 pruned atom pairs is 0.665 angstroms; (across all 173 pairs:
4.287)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 6upv_Lin.pdb,
chain M (#2), sequence alignment score = 787.6
RMSD between 142 pruned atom pairs is 0.665 angstroms; (across all 173 pairs:
4.287)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 6upv_Lin.pdb,
chain M (#2), sequence alignment score = 787.6
RMSD between 142 pruned atom pairs is 0.665 angstroms; (across all 173 pairs:
4.287)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 6upv_Lin.pdb,
chain M (#2), sequence alignment score = 787.6
RMSD between 142 pruned atom pairs is 0.665 angstroms; (across all 173 pairs:
4.287)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 6upv_Lin.pdb,
chain M (#2), sequence alignment score = 787.6
RMSD between 142 pruned atom pairs is 0.665 angstroms; (across all 173 pairs:
4.287)
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!2 models
> mmaker #8 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 4IGG_ABD.pdb,
chain B (#8), sequence alignment score = 833.9
RMSD between 79 pruned atom pairs is 0.889 angstroms; (across all 189 pairs:
10.852)
> mmaker #8 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 4IGG_ABD.pdb,
chain B (#8), sequence alignment score = 833.9
RMSD between 79 pruned atom pairs is 0.889 angstroms; (across all 189 pairs:
10.852)
> mmaker #8 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 4IGG_ABD.pdb,
chain B (#8), sequence alignment score = 833.9
RMSD between 79 pruned atom pairs is 0.889 angstroms; (across all 189 pairs:
10.852)
> mmaker #8 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 4IGG_ABD.pdb,
chain B (#8), sequence alignment score = 833.9
RMSD between 79 pruned atom pairs is 0.889 angstroms; (across all 189 pairs:
10.852)
> mmaker #8 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 4IGG_ABD.pdb,
chain B (#8), sequence alignment score = 833.9
RMSD between 79 pruned atom pairs is 0.889 angstroms; (across all 189 pairs:
10.852)
> mmaker #8 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with 4IGG_ABD.pdb,
chain B (#8), sequence alignment score = 833.9
RMSD between 79 pruned atom pairs is 0.889 angstroms; (across all 189 pairs:
10.852)
> show #!2 models
> show #5 models
> hide #!2 models
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> mmaker #5 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 5actin_2cat_1afa_refine25.pdb, chain F (#1) with a_cat_ABD_AF.pdb,
chain A (#5), sequence alignment score = 938.6
RMSD between 84 pruned atom pairs is 0.912 angstroms; (across all 215 pairs:
20.920)
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #1 models
> hide #5 models
> show #1 models
> hide #1 models
> show #1 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> close #3
> close #4
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> show #!2 models
> hide #8 models
> morph #8,2 frames 20
Computed 21 frame morph #3
> coordset #3 1,21
> morph #5,1 frames 20
Computed 21 frame morph #4
> coordset #4 1,21
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> color #3 #CCFFCC
> color #4 light salmon
> hide #4 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #8 models
> show #8 models
> name H1 #8/B:664-698,872-878
> select H1 #8/B:664-698,872-878
Expected a keyword
> select #8/B:664-698,872-878
329 atoms, 329 bonds, 42 residues, 1 model selected
> select add #8
1633 atoms, 1650 bonds, 215 residues, 1 model selected
> select subtract #8
Nothing selected
> movie record supersample 4 size 1200, 1577
> wait 24
> hide #3
> hide #3 models
> crossfade 24
> hide #8/B cartoons
> show #3 cartoons
> show #3 models
> movie encode /Users/ruigong/Desktop/movie.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie.mp4
> hide #3 models
> show #3 cartoons
> show #3 models
> hide #3 cartoons
> show #3 cartoons
> hide #3 cartoons
> show #8 cartoons
> movie record supersample 4 size 1200, 1577
> wait 24
> crossfade 24
> hide #8 cartoons
> show #3 cartoons
> wait 24
> coordset #3 1,21
> wait 24
> movie encode /Users/ruigong/Desktop/movie_2.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie_2.mp4
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #8 models
> show #8 models
> show #8 cartoons
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> cartoon style modeHelix tube radius 2 sides 24
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> cartoon style coil thickness 0.3
> cartoon style coil thickness 0.2
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
> 2dlabels color black size 32 xpos .53 ypos .12 text H0
> ui mousemode right "move label"
> 2dlabels #6.1 xpos 0.332 ypos 0.864
> 2dlabels color black size 32 xpos .53 ypos .12 text H1
> 2dlabels #6.2 xpos 0.261 ypos 0.504
> 2dlabels color black size 32 xpos .53 ypos .12 text CTE-N
> 2dlabels #6.3 xpos 0.443 ypos 0.096
> 2dlabels #6.1 xpos 0.332 ypos 0.864
> 2dlabels #6.2 xpos 0.263 ypos 0.510
> 2dlabels #6.3 xpos 0.442 ypos 0.091
> 2dlabels #6.3 xpos 0.440 ypos 0.093
> 2dlabels #6.3 xpos 0.447 ypos 0.093
> 2dlabels #6.3 xpos 0.441 ypos 0.092
> show #1 models
> 2dlabels #6.1 xpos 0.347 ypos 0.736
> 2dlabels #6.2 xpos 0.285 ypos 0.476
> hide #1 models
> 2dlabels #6.3 xpos 0.526 ypos 0.084
> show #3 models
> hide #3 models
> show #3 models
> hide #3 cartoons
> hide #6.1-6.3
> hide #6.1,#6.2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #6.1 #6.2
> hide #6.1 #6.2 #6.3
> show #6.1 #6.2 #6.3
> hide #6.1 #6.2 #6.3
> movie record supersample 4 size 1200, 1577
> wait 24
> crossfade 24
> hide #8 cartoons
> show #3 cartoons
> show #6.1 #6.2 #6.3
> wait 24
> movie encode /Users/ruigong/Desktop/movie_2.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie_2.mp4
> show #8
> hide #8 models
> show #8 models
> hide #8
> show #8 cartoons
> 2dlabels #6.1 xpos 0.350 ypos 0.735
> hide #3 cartoons
> movie record supersample 4 size 1200, 1577
> wait 24
> wait
wait requires a frame count argument unless motion is in progress
> stop
> movie encode /Users/ruigong/Desktop/movie_2.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie_2.mp4
> save /Users/ruigong/Desktop/pentamer_manuscipt/EM_structure/ABD_morphing.cxs
——— End of log from Thu Nov 30 15:37:18 2023 ———
opened ChimeraX session
> hide #8 models
> show #8 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #3 cartoons
> hide #3 cartoons
> movie record supersample 4 size 1200, 1577
> wait 24
> movie encode /Users/ruigong/Desktop/movie_2.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie_2.mp4
> movie record supersample 4 size 1200, 1577
> wait 24
> movie encode /Users/ruigong/Desktop/movie_2.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie_2.mp4
> movie record supersample 4 size 1200, 1577
> wait 24
> movie encode /Users/ruigong/Desktop/movie_2.mp4 quality highest
Movie saved to /Users/ruigong/Desktop/movie_2.mp4
> movie record supersample 4 size 1200, 1577
> wait 24
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 8 hours, 2 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
SE2717H/HX:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
Send2Trash: 1.8.2
SEQCROW: 1.8.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
File attachment: movie_2.mp4
Attachments (1)
Change History (3)
by , 23 months ago
| Attachment: | movie_2.mp4 added |
|---|
comment:1 by , 23 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Movie recording not stopping |
Reported by Rui Gong
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