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Opened 23 months ago
Closed 23 months ago
#10265 closed defect (not a bug)
Movie record records too many frames
| 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 record records too many frames |
comment:2 by , 23 months ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
Are you putting your movie recording commands in a script (.cxc) file? Movie recording is not intended for you to just type commands on the command-line because you will not be able to control how many frames are rendered. So the commands are put in a file, for example movie2.cxc:
movie record
turn y 1 24
wait 24
movie encode movie2.mp4 quality highest
Then open this file to record the movie and avoid getting extra frames that occur if you hand typed the commands into the ChimeraX command-line.
open movie2.cxc
I also suggest not using supersample 4 unless you want the rendering to take especially long time. The maximum recommended is supersample 2. Also I would not recommend specifying the movie size in the movie record command, because if you ChimeraX window is a different aspect ratio it will create padding that is not like what you see on screen. So it is better to just use the windowsize command to set the window to the desired size. If you need larger size than your screen then you would use the movie record size option but make sure you set the actual onscreen window size to have the same aspect ratio to avoid strange padding.
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