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Opened 3 years ago
Closed 3 years ago
#7486 closed defect (can't reproduce)
Crash computing ribbons
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Documentation | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00011e00 (most recent call first):
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Current thread 0x0001360c (most recent call first):
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 436 in _ribbon_geometry
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 162 in _make_ribbon_graphics
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 589 in compute_ribbons
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 600 in _create_ribbon_graphics
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 337 in update_graphics_if_needed
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\atomic\structure.py", line 1650 in _update_graphics_if_needed
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 134 in invoke
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 217 in _activate
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 186 in activate
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\triggerset.py", line 354 in activate_trigger
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\view.py", line 271 in check_for_drawing_change
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 65 in draw_new_frame
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\updateloop.py", line 139 in _redraw_timer_callback
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x800706ba
Thread 0x000106c4 (most recent call first):
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x800706ba
Thread 0x000106c4 (most recent call first):
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x800706ba
Thread 0x000106c4 (most recent call first):
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "D:\ProgramFiles(x86)\chimerax\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Opened tail_15A_resample.mrc as #3, grid size 480,480,480, pixel 1.05, shown
at level 2.14, step 2, values float32
opened ChimeraX session
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> ui tool show "Side View"
> 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
> close session
> open E:/cryo-EM-data/gp1314/coot_model/final_map_pdb/gp14-hexamer-fullcap-
> RAO.pdb E:/cryo-EM-data/gp1314/coot_model/final_map_pdb/gp15-hexamer-
> fullcap-RAO.pdb
Chain information for gp14-hexamer-fullcap-RAO.pdb #1
---
Chain | Description
A B C D E F | No description available
Chain information for gp15-hexamer-fullcap-RAO.pdb #2
---
Chain | Description
A B C D E F | No description available
> hide atoms
> show cartoons
> select #1
11958 atoms, 12252 bonds, 1464 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
11958 atoms, 12252 bonds, 1464 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for gp14-hexamer-fullcap-RAO.pdb_A SES surface #1.1: minimum,
-19.72, mean -3.08, maximum 15.01
Coulombic values for gp14-hexamer-fullcap-RAO.pdb_B SES surface #1.2: minimum,
-21.45, mean -3.11, maximum 15.14
Coulombic values for gp14-hexamer-fullcap-RAO.pdb_C SES surface #1.3: minimum,
-18.92, mean -3.11, maximum 14.99
Coulombic values for gp14-hexamer-fullcap-RAO.pdb_D SES surface #1.4: minimum,
-18.53, mean -3.10, maximum 15.12
Coulombic values for gp14-hexamer-fullcap-RAO.pdb_E SES surface #1.5: minimum,
-23.35, mean -3.12, maximum 15.17
Coulombic values for gp14-hexamer-fullcap-RAO.pdb_F SES surface #1.6: minimum,
-24.84, mean -3.07, maximum 15.18
To also show corresponding color key, enter the above coulombic command and
add key true
> select #2
13308 atoms, 13668 bonds, 1632 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for gp15-hexamer-fullcap-RAO.pdb_A SES surface #2.1: minimum,
-23.04, mean -1.98, maximum 17.70
Coulombic values for gp15-hexamer-fullcap-RAO.pdb_B SES surface #2.2: minimum,
-25.09, mean -1.96, maximum 17.53
Coulombic values for gp15-hexamer-fullcap-RAO.pdb_C SES surface #2.3: minimum,
-23.88, mean -1.96, maximum 17.21
Coulombic values for gp15-hexamer-fullcap-RAO.pdb_D SES surface #2.4: minimum,
-22.16, mean -2.00, maximum 18.20
Coulombic values for gp15-hexamer-fullcap-RAO.pdb_E SES surface #2.5: minimum,
-32.09, mean -1.97, maximum 18.04
Coulombic values for gp15-hexamer-fullcap-RAO.pdb_F SES surface #2.6: minimum,
-26.94, mean -1.97, maximum 17.10
To also show corresponding color key, enter the above coulombic command and
add key true
> ~select #2
6 models selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
cxcmd_as_cmd">select clear
> hide #!2,6 atoms
> show #!2,6 cartoons
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #5 models
> hide #5 models
> show #7 models
> hide #7 models
> hide #!1 models
> select #7
5154 atoms, 5250 bonds, 660 residues, 1 model selected
> show #!6 cartoons
> show #7 models
> show sel cartoons
> show #!1 models
> hide #!6 models
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
GTA-stopper-6mer.pdb #7/3B ALA 112 OXT
GTA-stopper-6mer.pdb #7/3C ALA 112 OXT
GTA-stopper-6mer.pdb #7/3E ALA 112 OXT
GTA-stopper-6mer.pdb #7/3F ALA 112 OXT
GTA-stopper-6mer.pdb #7/3D ALA 112 OXT
GTA-stopper-6mer.pdb #7/3A ALA 112 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for GTA-stopper-6mer.pdb_3A SES surface #7.1: minimum,
-12.44, mean 0.29, maximum 11.98
Coulombic values for GTA-stopper-6mer.pdb_3B SES surface #7.2: minimum,
-12.37, mean 0.30, maximum 10.65
Coulombic values for GTA-stopper-6mer.pdb_3C SES surface #7.3: minimum,
-12.24, mean 0.29, maximum 9.73
Coulombic values for GTA-stopper-6mer.pdb_3D SES surface #7.4: minimum,
-12.22, mean 0.31, maximum 10.41
Coulombic values for GTA-stopper-6mer.pdb_3E SES surface #7.5: minimum,
-12.56, mean 0.30, maximum 10.38
Coulombic values for GTA-stopper-6mer.pdb_3F SES surface #7.6: minimum,
-12.58, mean 0.28, maximum 9.65
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!2 models
> hide #!2 models
> show #!2 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
> undo
> coulombic sel
Coulombic values for GTA-stopper-6mer.pdb_3A SES surface #7.1: minimum,
-12.44, mean 0.29, maximum 11.98
Coulombic values for GTA-stopper-6mer.pdb_3B SES surface #7.2: minimum,
-12.37, mean 0.30, maximum 10.65
Coulombic values for GTA-stopper-6mer.pdb_3C SES surface #7.3: minimum,
-12.24, mean 0.29, maximum 9.73
Coulombic values for GTA-stopper-6mer.pdb_3D SES surface #7.4: minimum,
-12.22, mean 0.31, maximum 10.41
Coulombic values for GTA-stopper-6mer.pdb_3E SES surface #7.5: minimum,
-12.56, mean 0.30, maximum 10.38
Coulombic values for GTA-stopper-6mer.pdb_3F SES surface #7.6: minimum,
-12.58, mean 0.28, maximum 9.65
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> show #!2 models
> select #2
3174 atoms, 3078 bonds, 6 pseudobonds, 528 residues, 2 models selected
> select clear
> hide #!7 models
> show #!6 models
> hide #!1-2,6 surfaces
> hide #!2 models
> select #1/F:44
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
130 atoms, 129 bonds, 17 residues, 1 model selected
> select up
1316 atoms, 1348 bonds, 167 residues, 1 model selected
> select add #6/E:40
1323 atoms, 1355 bonds, 168 residues, 2 models selected
> select up
1588 atoms, 1628 bonds, 200 residues, 3 models selected
> select up
2207 atoms, 2259 bonds, 276 residues, 3 models selected
> select ~sel
27495 atoms, 27858 bonds, 11 pseudobonds, 3516 residues, 8 models selected
> hide sel & #!1,6 cartoons
> show #3 models
> hide #3 models
> show #3 models
> select #3/A:70
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
105 atoms, 110 bonds, 12 residues, 1 model selected
> select up
1031 atoms, 998 bonds, 177 residues, 1 model selected
> show #!7 models
> show #!2 models
> hide #!2 models
> select #7/3B:51@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
31 atoms, 31 bonds, 4 residues, 2 models selected
> select up
859 atoms, 875 bonds, 110 residues, 2 models selected
> select up
5154 atoms, 5250 bonds, 660 residues, 2 models selected
> coulombic sel
Coulombic values for GTA-stopper-6mer.pdb_3A SES surface #7.1: minimum,
-12.44, mean 0.29, maximum 11.98
Coulombic values for GTA-stopper-6mer.pdb_3B SES surface #7.2: minimum,
-12.37, mean 0.30, maximum 10.65
Coulombic values for GTA-stopper-6mer.pdb_3C SES surface #7.3: minimum,
-12.24, mean 0.29, maximum 9.73
Coulombic values for GTA-stopper-6mer.pdb_3D SES surface #7.4: minimum,
-12.22, mean 0.31, maximum 10.41
Coulombic values for GTA-stopper-6mer.pdb_3E SES surface #7.5: minimum,
-12.56, mean 0.30, maximum 10.38
Coulombic values for GTA-stopper-6mer.pdb_3F SES surface #7.6: minimum,
-12.58, mean 0.28, maximum 9.65
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\CryoEM\\\KCRI\\\PAPER\\\9_movies\\\CSN\\\CSN_movie_0819.cxs
registering illegal selector name "helix bundle "
registering illegal selector name "helix bundle"
registering illegal selector name "helix_bundle"
registering illegal selector name "4HB"
Log from Mon Aug 22 17:28:01 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\CryoEM\\\KCRI\\\PAPER\\\9_movies\\\CSN\\\CSN_movie_0819.cxs
registering illegal selector name "helix bundle "
registering illegal selector name "helix bundle"
registering illegal selector name "helix_bundle"
registering illegal selector name "4HB"
Log from Mon Aug 22 13:56:21 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs format session
Log from Sun Aug 21 08:34:05 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\CryoEM\\\KCRI\\\PAPER\\\9_movies\\\CSN\\\CSN_movie_0819.cxs
Log from Sun Aug 21 08:18:24 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs format session
Log from Sat Aug 20 21:43:34 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\CryoEM\\\KCRI\\\PAPER\\\9_movies\\\CSN\\\CSN_movie_0819.cxs
Log from Sat Aug 20 21:39:26 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs format session
Log from Sat Aug 20 20:55:22 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\CryoEM\\\KCRI\\\PAPER\\\9_movies\\\CSN\\\CSN_movie_0819.cxs
Log from Sat Aug 20 20:50:23 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open CSN_movie_0819.cxs
Log from Sat Aug 20 19:05:25 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\\\cryo-EM\\\KCRI\\\PAPER\\\9_movies\\\CSN\\\CSN_movie_0819.cxs
Log from Sat Aug 20 15:34:08 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\cryo-EM\KCRI\PAPER\9_movies\CSN\CSN_movie_0819.cxs format session
Log from Fri Aug 19 20:52:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer.pdb
Chain information for KCR-8mer.pdb #1
---
Chain | Description
A B G J N P S U | No description available
C F H I M O T V | No description available
D E K L Q R W X | No description available
> open E:/cryo-
> EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR_dimer_j369_0806.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR_dimer_j369_0806.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (77 )
Cannot find LINK/SSBOND residue CYS (56 )
Cannot find LINK/SSBOND residue CYS (68 )
Cannot find LINK/SSBOND residue HIS (82 )
Cannot find LINK/SSBOND residue HIS (82 )
17 messages similar to the above omitted
Chain information for KCR_dimer_j369_0806.pdb #2
---
Chain | Description
S | No description available
T V | No description available
U | No description available
W X | No description available
> open E:/cryo-
> EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8~KCR_dimer_j526_0626_final.pdb
Chain information for N8~KCR_dimer_j526_0626_final.pdb #3
---
Chain | Description
S | No description available
T V | No description available
U | No description available
W X | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-dimer.pdb
Chain information for N8-dimer.pdb #4
---
Chain | Description
N O | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/CSN-4d10.pdb
Chain information for CSN-4d10.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/HA-CSN-
> KCR~N8_whole_0725.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/HA-CSN-KCR~N8_whole_0725.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (80 )
Cannot find LINK/SSBOND residue CYS (56 )
Cannot find LINK/SSBOND residue CYS (75 )
Cannot find LINK/SSBOND residue CYS (68 )
Cannot find LINK/SSBOND residue HIS (82 )
17 messages similar to the above omitted
Chain information for HA-CSN-KCR~N8_whole_0725.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
N | No description available
S | No description available
T V | No description available
U | No description available
W X | No description available
> open E:/cryo-
> EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/CSN-N8~KCR_combinemap_0725.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/CSN-N8~KCR_combinemap_0725.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (45 )
Cannot find LINK/SSBOND residue CYS (42 )
Cannot find LINK/SSBOND residue HIS (77 )
Cannot find LINK/SSBOND residue HIS (80 )
Cannot find LINK/SSBOND residue CYS (68 )
8 messages similar to the above omitted
Chain information for CSN-N8~KCR_combinemap_0725.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W X | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-
> CSN_whole_job489_0725.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-CSN_whole_job489_0725.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (42 )
Cannot find LINK/SSBOND residue CYS (83 )
Cannot find LINK/SSBOND residue CYS (42 )
Cannot find LINK/SSBOND residue HIS (77 )
Cannot find LINK/SSBOND residue HIS (82 )
13 messages similar to the above omitted
Chain information for KCR-CSN_whole_job489_0725.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W X | No description available
> hide atoms
> show cartoons
> save E:/cryo-EM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Fri Aug 19 20:52:18 2022 ———
opened ChimeraX session
> ui tool show "Side View"
> turn x 90
> hide #4#!2-3,5-8 target m
> turn x 90
> turn y 90
[Repeated 3 time(s)]
> windowsize 640 480
> turn y 90
[Repeated 7 time(s)]
> roll 1 y 360
Expected an axis vector or a keyword
> roll y 1 360
> roll y 1 90
> roll y 1 45
> roll y 1 90
[Repeated 1 time(s)]
> view name p1
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink
> color /O gold
> color #1/H,K,J,G,I,L chocolate target c
> color #1/M,N,O,P,Q,R lime green target c
> color #1/A,B,C,D,E,F olive target c
> combine #1/A/B/C/D/E/F modelId #9
> hide #!1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> close #9
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-3.pdb
> E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-2.pdb E:/cryo-
> EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-4.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
462 messages similar to the above omitted
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
471 messages similar to the above omitted
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 87 87 ALA J
14 GLU J 26 1 13
Start residue of secondary structure not found: HELIX 88 88 LYS J 46 CYS J 52
1 7
Start residue of secondary structure not found: HELIX 89 89 PHE J 56 MET J 61
1 6
Start residue of secondary structure not found: HELIX 90 90 ALA J 79 THR J 91
1 13
Start residue of secondary structure not found: HELIX 91 91 VAL J 101 LEU J
111 1 11
463 messages similar to the above omitted
Chain information for KCR-8mer-3.pdb #9
---
Chain | Description
M O | No description available
N P | No description available
Q R | No description available
Chain information for KCR-8mer-2.pdb #10
---
Chain | Description
H I M | No description available
J | No description available
K L | No description available
Chain information for KCR-8mer-4.pdb #11
---
Chain | Description
A B | No description available
C F | No description available
D E | No description available
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink
> color /O gold
> color #1,9,10,11/H,K,J,G,I,L chocolate
> color #1,9,10,11/M,N,O,P,Q,R lime green
> color #1,9,10,11/A,B,C,D,E,F olive
> hide #!9-11 atoms
> show #!9-11 cartoons
> fly p1
> select #9
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> ui mousemode right "translate selected atoms"
> undo
> select clear
> hide #!9 models
> hide #!10 models
> show #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> close #9-11
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-2.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
462 messages similar to the above omitted
Chain information for KCR-8mer-2.pdb #9
---
Chain | Description
G J | No description available
H I | No description available
K L | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-3.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
462 messages similar to the above omitted
Chain information for KCR-8mer-3.pdb #10
---
Chain | Description
M O | No description available
N P | No description available
Q R | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-4.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 87 87 ALA J
14 GLU J 26 1 13
Start residue of secondary structure not found: HELIX 88 88 LYS J 46 CYS J 52
1 7
Start residue of secondary structure not found: HELIX 89 89 PHE J 56 MET J 61
1 6
Start residue of secondary structure not found: HELIX 90 90 ALA J 79 THR J 91
1 13
Start residue of secondary structure not found: HELIX 91 91 VAL J 101 LEU J
111 1 11
463 messages similar to the above omitted
Chain information for KCR-8mer-4.pdb #11
---
Chain | Description
A B | No description available
C F | No description available
D E | No description available
> color #1,9,10,11/H,K,J,G,I,L chocolate
> color #1,9,10,11/M,N,O,P,Q,R lime green
> color #1,9,10,11/A,B,C,D,E,F olive
> hide #!9-11 atoms
> show #!9-11 cartoons
> fly p1
> select #9
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #10
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #9
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> ~select #9
Nothing selected
> select #10
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> show #!1 models
> ~select #10
Nothing selected
> select #11
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #9
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #10
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #11
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #10
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #9
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> fly p1
> hide #!9 models
> hide #!10 models
> hide #!11 models
> ~select #9
Nothing selected
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> turn y 90
> view name p1
> show #!9 models
> show #!10 models
> show #!11 models
> select #10
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #11
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> fly p1
[Repeated 2 time(s)]
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-2.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
462 messages similar to the above omitted
Chain information for KCR-8mer-2.pdb #12
---
Chain | Description
G J | No description available
H I | No description available
K L | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-3.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
462 messages similar to the above omitted
Chain information for KCR-8mer-3.pdb #13
---
Chain | Description
M O | No description available
N P | No description available
Q R | No description available
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-4.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 87 87 ALA J
14 GLU J 26 1 13
Start residue of secondary structure not found: HELIX 88 88 LYS J 46 CYS J 52
1 7
Start residue of secondary structure not found: HELIX 89 89 PHE J 56 MET J 61
1 6
Start residue of secondary structure not found: HELIX 90 90 ALA J 79 THR J 91
1 13
Start residue of secondary structure not found: HELIX 91 91 VAL J 101 LEU J
111 1 11
463 messages similar to the above omitted
Chain information for KCR-8mer-4.pdb #14
---
Chain | Description
A B | No description available
C F | No description available
D E | No description available
> color #1,9-14/H,K,J,G,I,L chocolate
> color #1,9-14,11/M,N,O,P,Q,R lime green
> color #1,9-14,11/A,B,C,D,E,F olive
> ~select #11
Nothing selected
> morph #9,11 frames 30
Computed 31 frame morph #15
> coordset #15 1,31
> show #!9 models
> close #15
> morph #12,9 frames 30
Computed 31 frame morph #15
> coordset #15 1,31
> morph #13,10 frames 30
Computed 31 frame morph #16
> coordset #16 1,31
> morph #14,11 frames 30
Computed 31 frame morph #17
> coordset #17 1,31
> hide #!1,15-17 atoms
> show #!1,15-17 cartoons
> coordset #15,16,17
> hide #!1 models
> show #!2 models
> coordset #15,16,17
> style #!2,15-17 ball
Changed 89317 atom styles
> set bgColor white
> set bgColor black
> show #!12 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!9 models
> show #!10 models
> show #!11 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> show #!9 models
> show #!10 models
> show #!11 models
> select #9
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> ~select #9
Nothing selected
> select #10
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> select #11
22340 atoms, 22778 bonds, 6 pseudobonds, 2748 residues, 2 models selected
> fly p1
> show #!16 models
> show #!17 models
> show #!15 models
> close #15-17
> morph #12,9 frames 30
Computed 31 frame morph #15
> coordset #15 1,31
> morph #13,10 frames 30
Computed 31 frame morph #16
> coordset #16 1,31
> morph #14,11 frames 30
Computed 31 frame morph #17
> coordset #17 1,31
> hide #!2,15-17 atoms
> show #!2,15-17 cartoons
> coordset #15,16,17
> save E:/cryo-EM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
> undo
> fly p1
> turn z 90
> hide #!15 models
> hide #!16 models
> hide #!17 models
> fly p1
> turn z 90
> turn y 180
[Repeated 9 time(s)]
> view name p2
> fly p1
> ~ribbon # *
> ribbon #2,15-17
> coordset #15-17
> view p2 60
> wait 60
> show #!15 models
> show #!16 models
> show #!17 models
> ~ribbon # *
> ribbon #2,15-17
> coordset #15-17
> view p2 60
> wait 60
> fly p1
> ~ribbon # *
> ribbon #2,15-17
> coordset #15-17
> view p2 60
> wait 60
> show #4 models
> ribbone# *
Unknown command: ribbone# *
> ribbon # *
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #4 models
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/HA-CSN-
> KCR~N8_whole_0725.pdb
Summary of feedback from opening E:/cryo-
EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/HA-CSN-KCR~N8_whole_0725.pdb
---
warnings | Cannot find LINK/SSBOND residue HIS (80 )
Cannot find LINK/SSBOND residue CYS (56 )
Cannot find LINK/SSBOND residue CYS (75 )
Cannot find LINK/SSBOND residue CYS (68 )
Cannot find LINK/SSBOND residue HIS (82 )
17 messages similar to the above omitted
Chain information for HA-CSN-KCR~N8_whole_0725.pdb #18
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
N | No description available
S | No description available
T V | No description available
U | No description available
W X | No description available
> close #18
> close #4
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-dimer-before-
> removal.pdb
Chain information for N8-dimer-before-removal.pdb #4
---
Chain | Description
N O | No description available
> select #4/N:40
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
591 atoms, 596 bonds, 76 residues, 1 model selected
> preset cartoons/nucleotides licorice/ovals
Changed 463995 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show sel atoms
> style sel sphere
Changed 591 atom styles
> show sel surfaces
> hide sel atoms
> hide sel cartoons
> transparency (#!4 & sel) 50
> select clear
> select #4/N:71@O
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
40 atoms, 39 bonds, 6 residues, 2 models selected
> select up
591 atoms, 596 bonds, 76 residues, 2 models selected
> color (#!4 & sel) white
> transparency (#!4 & sel) 50
> select clear
> select #4/N:39@O
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
25 atoms, 25 bonds, 3 residues, 2 models selected
> select up
591 atoms, 596 bonds, 76 residues, 2 models selected
> transparency (#!4 & sel) 80
> select clear
> select #4/N:8@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
35 atoms, 34 bonds, 5 residues, 2 models selected
> select up
591 atoms, 596 bonds, 76 residues, 2 models selected
> transparency (#!4 & sel) 50
> graphics silhouettes true
> graphics silhouettes false
> select clear
> select #4/N:40@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
25 atoms, 25 bonds, 3 residues, 2 models selected
> select up
591 atoms, 596 bonds, 76 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> save E:/cryo-EM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Sat Aug 20 15:34:08 2022 ———
opened ChimeraX session
> surface #4/N resolution 10
1 Gaussian surfaces, threshold level 0.054
> hide sel cartoons
> select clear
> surface #4/N/O resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> select #4/N:40@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
25 atoms, 25 bonds, 3 residues, 2 models selected
> select up
591 atoms, 596 bonds, 76 residues, 2 models selected
> transparency (#!4 & sel) 70
> select clear
> transparency #4.2 70
> hide #!2,4 cartoons
> undo
> hide #!2,4 cartoons
> undo
> select #4
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide sel cartoons
> select clear
> color #4.2 white
> transparency #4.2 70
> select clear
> hide #4.1 models
> show #4.1 models
> hide #4.2 models
> show #4.2 models
> select #4/N:70@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
40 atoms, 40 bonds, 5 residues, 2 models selected
> select up
591 atoms, 596 bonds, 76 residues, 2 models selected
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-dimer-before-
> removal.pdb
Chain information for N8-dimer-before-removal.pdb #18
---
Chain | Description
N O | No description available
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\Plum Thirteen\Desktop\movie1.mp4"
Movie saved to \C:Users\\...\Desktop\movie1.mp4
> surface #18/N/O resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> hide #!4 models
> hide #4.1 models
> hide #4.2 models
> ~select #4.1
596 bonds, 3 models selected
> select #4.2
591 atoms, 76 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18.1
591 atoms, 76 residues, 1 model selected
> select #18.2
591 atoms, 76 residues, 1 model selected
> select #18.1
591 atoms, 76 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> color #18.1-2 white
> transparency #18.1-2 70
> select clear
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide sel cartoons
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> show sel cartoons
> delete atoms sel
> delete bonds sel
> open E:/cryo-EM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-dimer-before-
> removal.pdb
Chain information for N8-dimer-before-removal.pdb #18
---
Chain | Description
N O | No description available
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide sel cartoons
> surface #18/N/O resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> color #18.1-2 white
> transparency #18.1-2 70
> select clear
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #18.1 models
> show #18.1 models
> hide #18
> hide #18.1
> hide #18
> show #18.1 models
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide #!18 models
> show #!18 models
> ui mousemode right "translate selected atoms"
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18.1
591 atoms, 76 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18.1
591 atoms, 76 residues, 1 model selected
> select #18.2
591 atoms, 76 residues, 1 model selected
> hide #18.1 models
> hide #18.2 models
> show #18.2 models
> show #18.1 models
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #18
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> fly p2
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #4.1 models
> show #4.2 models
> rename #4 name N8-dimer-br-bound
> rename #18 name N8-dimer-br-far
> combine #4 name N8-dimer-near
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide #19 models
> show #19 models
> fly p1
> ~select #19
Nothing selected
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> ui mousemode right "translate selected atoms"
[Repeated 3 time(s)]
> ~select #19
Nothing selected
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> select up
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> hide #19 models
> show #19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show sel cartoons
> show #!18 models
> hide #!18 models
> hide #!4 models
> show #!4 models
> hide sel cartoons
> surface #19/N/O resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> color #19.1-2 white
> transparency #19.1-2 70
> ui mousemode right "translate selected atoms"
[Repeated 1 time(s)]
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> fly p1
> show #!1 models
> hide #!4 models
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> ui mousemode right "translate selected atoms"
[Repeated 1 time(s)]
> ~select #19.2
Nothing selected
> select #19.1
591 atoms, 76 residues, 1 model selected
> select #19.1
591 atoms, 76 residues, 1 model selected
> select #19.1
591 atoms, 76 residues, 1 model selected
> select #19.2
591 atoms, 76 residues, 1 model selected
> select #19.2
591 atoms, 76 residues, 1 model selected
> select #19.2
591 atoms, 76 residues, 1 model selected
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #19
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #19/O
591 atoms, 596 bonds, 76 residues, 1 model selected
> select #19/N
591 atoms, 596 bonds, 76 residues, 1 model selected
> show #!18 models
> ui mousemode right "translate selected atoms"
> select #18/O
591 atoms, 596 bonds, 76 residues, 1 model selected
> select #18/N
591 atoms, 596 bonds, 76 residues, 1 model selected
> fly p1
> select #18/N
591 atoms, 596 bonds, 76 residues, 1 model selected
> select #18/O
591 atoms, 596 bonds, 76 residues, 1 model selected
> fly p1
> morph #18,19 frames 30
Computed 31 frame morph #20
> coordset #20 1,31
> surface #20 resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> hide #!1-2,20 cartoons
> undo
> transparency #20.1-2 70
> color #20.1-2 white
> transparency #20.1-2 70
> coordset #20
> morph #19,4 frames 60
Computed 61 frame morph #21
> coordset #21 1,61
> rename #19 N8-dimer-br-near
> select #21
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> surface #21 resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> hide #!1 models
> color #21.1-2 white
> transparency #21.1-2 70
> select clear
> coordset #21
> save E:/cryo-EM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Sat Aug 20 19:05:25 2022 ———
opened ChimeraX session
> hide # *
> show #1
> fly p1
> wait 40
> turn y 2 180
> wait
> coordset #20
> wait 10
> hide # *
> show #2,15-17,21
> coordset #15-17,21
> view p2 60
> wait 100
> hide # *
> hide #!21 models
> hide #!20 models
> hide #!2 models
> show #4 cartoons
> show #4 ribbons
> show #!4 models
> show #4 cartoons
> hide #4 ribbons
> hide #!4 models
> hide #4.1 models
> hide #4.2 models
> show #4 ribbons
> show #4 surfaces
> show #!4 models
> hide #4
> ~ribbon
> ~ribbon # *
> show #4.1,4.2
> hide #4.1,4.2
> hide #4.1,4.2 surfaces
> show #4.1 surfaces
> hide #4.1 surfaces
> hide #4 surfaces
> show #4 surfaces
> hide #4 surfaces
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> hide #4.2 models
> show #4.2 models
> show #4.1 surfaces
> hide #4 surfaces
> ~surface #4
> hide #!4 models
> show #!4 models
> surface close #4
> surface #4 resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> color #4.1-2 white
> transparency #4.1-2 70
> hide #4.2 models
> show #4.2 models
> hide #4.1 models
> show #4.1 models
> surface #4 resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> color #4.1,4.2 white
> transparency #4.1,4.2 70
> surface close #4
> surface #4 resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> color #4.1,4.2 white
> transparency #4.1,4.2 70
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color #4.1-2 white
> transparency #4.1-2 70
> hide #!4 models
> show #!4 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!*
> hide # !*
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!*
> select clear
> hide #!*
> hide #!* models
> ribbon #1
> show #4#!1-3,5-21 target m
> ~ribbon # *
> hide #!4,!20,!21 models; ribbon #1;
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~ribbon # *
> hide #!4,20,21 models
> ribbon #1
> ~ribbon # *
> hide #!4,20,21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> coordset #20
> wait 10
> ~ribbon # *
> ribbon #2,15-17
> show #!20 models
> coordset #15-17,20
> view p2 60
> wait 100
> show #!4 models
> show #!21 models
> hide #!4,#!20,#!21 models;
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!4,20,21 models
> ~ribbon # *
> ribbon #1
> fly p1
> hide #!4,18-21 models
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> coordset #20
> wait 10
> ~ribbon # *
> ribbon #2,15-17
> show #!20 models
> coordset #15-17,20
> view p2 60
> wait 100
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 10
> ~ribbon # *
> ribbon #2,15-17
> show #!21 models
> coordset #15-17,21
> view p2 60
> wait 100
> ui favorite true "Model Panel"
> ui favorite false "Model Panel"
> view #20 clip false
> slider
Unknown command: slider
> morph slider
Missing or invalid "structures" argument: invalid structures specifier
> coordset #20 slider
Expected a keyword
> coordset slider
Missing or invalid "structures" argument: empty atom specifier
> coordset slider #20
> ui tool show "Model Loops"
> ui tool show Toolbar
> close #20
> morph #18,19 frames 10 #20
Expected a keyword
> morph #18,19 frames 10
Computed 11 frame morph #20
> coordset #20 1,11
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> view
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> ~ribbon # *
> ribbon #2,15-17
> show #!21 models
> coordset #15-17,21
> view p2 60
> wait 100
> hide #20 models
> show #20 models
> fly p1
> coordset #20
> hide #20 models
> show #20 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> coordset #20
> coordset #21
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> close #20
> show #!18 models
> show #!19 models
> fly p1
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> morph #18,19 frames 10
Computed 11 frame morph #20
> coordset #20 1,11
> hide #20 models
> show #20 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> hide #!21 models
> show #!21 models
> close #20
> morph #18,19 frames 20
Computed 21 frame morph #20
> coordset #20 1,21
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> show #!19 models
> ribbon # 18,19
> morph #18,19 frames 10
Computed 11 frame morph #22
> coordset #22 1,11
> show #!18 models
> hide #!18 models
> hide #20 models
> show #20 models
> close #20
> close #22
> morph #18,19 frames 10
Computed 11 frame morph #20
> coordset #20 1,11
> select #20
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> surface #20 resolution 10
2 Gaussian surfaces, threshold level 0.053 - 0.054
> select #20
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #20
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> color #20.1-2 white
> transparency #20.1-2 70
> ~ribbon #20
> coordset #20
> fly p1
> coordset #20
> show #!18 models
> show #!19 models
> show #!4 models
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17
> show #!21 models
> coordset #15-17,21
> view p2 60
> wait 100
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17
> show #!21 models
> coordset #15-17,21
> view p2 30
> wait 100
> fly p1
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
——— End of log from Sat Aug 20 20:50:23 2022 ———
opened ChimeraX session
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-1.pdb
Summary of feedback from opening
D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 87 87 ALA J
14 GLU J 26 1 13
Start residue of secondary structure not found: HELIX 88 88 LYS J 46 CYS J 52
1 7
Start residue of secondary structure not found: HELIX 89 89 PHE J 56 MET J 61
1 6
Start residue of secondary structure not found: HELIX 90 90 ALA J 79 THR J 91
1 13
Start residue of secondary structure not found: HELIX 91 91 VAL J 101 LEU J
111 1 11
463 messages similar to the above omitted
Chain information for KCR-8mer-1.pdb #22
---
Chain | Description
A B | No description available
C F | No description available
D E | No description available
> close #22
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-1.pdb
Summary of feedback from opening
D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-8mer-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 14
GLU A 26 1 13
Start residue of secondary structure not found: HELIX 2 2 LYS A 46 CYS A 52 1
7
Start residue of secondary structure not found: HELIX 3 3 PHE A 56 MET A 61 1
6
Start residue of secondary structure not found: HELIX 4 4 ALA A 79 THR A 91 1
13
Start residue of secondary structure not found: HELIX 5 5 VAL A 101 LEU A 111
1 11
462 messages similar to the above omitted
Chain information for KCR-8mer-1.pdb #22
---
Chain | Description
S U | No description available
T V | No description available
W X | No description available
> hide #!1-3,5-17,21-22 atoms
> coordset #22,2 frame 10
Expected a keyword
> morph #22,2 frames 10
Computed 11 frame morph #23
> coordset #23 1,11
> fly p1
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> ribbon #23
> save D:/CryoEM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Sat Aug 20 20:55:22 2022 ———
opened ChimeraX session
> show #!22 models
> show #!21 models
> show #!20 models
> show #!19 models
> show #!18 models
> windowsize 640 480
[Repeated 1 time(s)]
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 100
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink
> color /O gold
> color #1,9-14/H,K,J,G,I,L chocolate
> color #1,9-14,11/M,N,O,P,Q,R lime green
> color #1,9-14,11/A,B,C,D,E,F olive
> show #!4 models
> ~ribbon # *
[Repeated 1 time(s)]
> hide #!21 models
> hide #!4 models
> show #!4 models
> select #4
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #4
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #4
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> select #4.1
591 atoms, 76 residues, 1 model selected
> select #4.2
591 atoms, 76 residues, 1 model selected
> select #4
1182 atoms, 1192 bonds, 152 residues, 1 model selected
> color #4.1-2 white
> transparency #4.1-2 70
> color #4 red target c
> color #4 red
> undo
> show #!18 models
> show #!19 models
> hide #!19 models
> select clear
> color #18.1-2 white
> transparency #18.1-2 70
> select clear
> show #!19 models
> color #19.1-2 white
> transparency #19.1-2 70
> select clear
> show #!20 models
> show #!21 models
> hide #!18 models
> hide #!19 models
> hide #!4 models
> color #20.1-2#21.1-2 white
> transparency #20.1-2#21.1-2 70
> select clear
> show #!19 models
> show #!18 models
> show #!2 models
> hide #!3 models
> show #!3 models
> show #!4 models
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-14/H,K,J,G,I,L chocolate
> color #1,9-14,11/M,N,O,P,Q,R lime green
> color #1,9-14,11/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> ~ribbon #15-17
> wait 100
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ribbon #9
> fly p1
> ribbon #10
> ribbon #11
> ribbon #12
> ribbon #13
> ribbon #14
> show #!18 models
> show #!19 models
> show #!20 models
> show #!4 models
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ribbon #3
> morph #2,3 frames 60
Computed 61 frame morph #24
> coordset #24 1,61
> ~ribbon # *
> ribbon #24
> coordset #24
> wait 60
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
——— End of log from Sat Aug 20 21:39:26 2022 ———
opened ChimeraX session
> fly p1
> fly p2
> color #3/V/T: 381-463 dark slate blue
> show #!3 models
> hide #!24 models
> show #!24 models
> color #3/V: 381-463 dark slate blue
> ribbon #3
> ~ribbon # *
> ribbon #3
> redo
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #3/V,T: 381-463 dark slate blue
> ribbon #24
> color #3,24/V,T: 381-463 dark slate blue
> hide #!3 models
> show #!3 models
> ~ribbon # *
> ribbon #3
> color #3,24/V,T: 381-463 dark slate blue
> color #3,24/V,T: 464-572 dark goldenrod
> color #3,24/V,T: 573-679 cadet blue
> color #3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #3
> ribbon #24
> coordset #24
> wait 60
> save D:/CryoEM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Sat Aug 20 21:43:34 2022 ———
opened ChimeraX session
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> ~ribbon # *
> ribbon #3
> color #3,24/V,T: 381-463 dark slate blue
> color #3,24/V,T: 464-572 dark goldenrod
> color #3,24/V,T: 573-679 cadet blue
> color #3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #3
> ribbon #24
> coordset #24
> wait 60
> close #24
> morph #2,3 frames 60 warp true
Expected a keyword
> morph #2,3 frames 60 wrap true
Computed 121 frame morph #24
> coordset #24 1,121
> ~ribbon # *
> ribbon #2
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24
> wait 120
> coordset #24
> wait 120
> close #24
> morph #2,3 frames 60
Computed 61 frame morph #24
> coordset #24 1,61
> ~ribbon # *
> ribbon #2
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24 bounce true
> wait 120
> coordset #24
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ~ribbon # *
> ribbon #2
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24 bounce true
> wait 120
> coordset #24
> wait 60
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> view name p3
> roll y 1 360
> color
> color # * white
> ribbon #6
> view name p4
> fly p3
> view p4 60
> combine #3 name N8~KCR-dimer-out
> select #25
22404 atoms, 22842 bonds, 6 pseudobonds, 2750 residues, 2 models selected
> ribbon #25
> ui mousemode right "translate selected atoms"
> fly p4
> morph #25,3 frames 60
Computed 61 frame morph #26
> coordset #26 1,61
> fly p3
> ~ribbon # *
[Repeated 1 time(s)]
> hide #!4,18-21 models
> ribbon #5
> fly p3
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> view name p5
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
[Repeated 1 time(s)]
> color /B light sky blue
> color /D medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> select /B/D /V:381-768
80238 atoms, 81712 bonds, 20 pseudobonds, 9903 residues, 30 models selected
> ~ribbon ~sel
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!25 models
> ~ribbon # *
> ribbon #3,5
> select clear
> select /B/D /V:381-768
80238 atoms, 81712 bonds, 20 pseudobonds, 9903 residues, 30 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> ribbon #3,5
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
——— End of log from Sun Aug 21 08:18:24 2022 ———
opened ChimeraX session
> close #6
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-CSN-removing.pdb
Chain information for KCR-CSN-removing.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
S | No description available
T V | No description available
U | No description available
W X | No description available
> rename #2 KCR-dimer-apo
> rename #3 N8~KCR-dimer-br
> rename #3 N8~KCR-dimer-before
> hide #!1-3,5-17,22-26 atoms
> show #!1-3,5-17,22-26 cartoons
> ~ribbon # *
> ribbon #3,5
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-1-before-
> removal.pdb
Summary of feedback from opening
D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-1-before-removal.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO V 686
SER V 713 1 28
Start residue of secondary structure not found: HELIX 2 2 VAL V 721 GLN V 728
1 8
Start residue of secondary structure not found: HELIX 3 3 PRO V 738 ILE V 745
1 8
Start residue of secondary structure not found: HELIX 4 4 GLY V 747 GLU V 750
1 4
Chain information for N8-1-before-removal.pdb #27
---
Chain | Description
N | No description available
> color /N deep pink target c
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-1-removing.pdb
Summary of feedback from opening
D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/N8-1-removing.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 84
SER A 90 1 7
Start residue of secondary structure not found: HELIX 2 2 LEU A 94 HIS A 106 1
13
Start residue of secondary structure not found: HELIX 3 3 ARG A 111 VAL A 122
1 12
Start residue of secondary structure not found: HELIX 4 4 ASP A 129 GLN A 146
1 18
Start residue of secondary structure not found: HELIX 5 5 THR A 164 ASN A 191
1 28
308 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (94 )
Cannot find LINK/SSBOND residue HIS (82 )
Cannot find LINK/SSBOND residue CYS (83 )
Cannot find LINK/SSBOND residue CYS (68 )
Cannot find LINK/SSBOND residue HIS (80 )
17 messages similar to the above omitted
Chain information for N8-1-removing.pdb #28
---
Chain | Description
N | No description available
> color /N deep pink target c
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-removing.pdb
> D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/CSN-removing.pdb
Summary of feedback from opening
D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/KCR-removing.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 84
SER A 90 1 7
Start residue of secondary structure not found: HELIX 2 2 LEU A 94 HIS A 106 1
13
Start residue of secondary structure not found: HELIX 3 3 ARG A 111 VAL A 122
1 12
Start residue of secondary structure not found: HELIX 4 4 ASP A 129 GLN A 146
1 18
Start residue of secondary structure not found: HELIX 5 5 THR A 164 ASN A 191
1 28
148 messages similar to the above omitted
Summary of feedback from opening
D:/CryoEM/KCRI/PAPER/9_movies/CSN/movie_models_CSN/CSN-removing.pdb
---
warnings | Start residue of secondary structure not found: HELIX 123 123 ALA S
14 GLU S 26 1 13
Start residue of secondary structure not found: HELIX 124 124 LYS S 46 CYS S
52 1 7
Start residue of secondary structure not found: HELIX 125 125 PHE S 56 MET S
59 1 4
Start residue of secondary structure not found: HELIX 126 126 ALA S 79 THR S
91 1 13
Start residue of secondary structure not found: HELIX 127 127 VAL S 101 LEU S
111 1 11
155 messages similar to the above omitted
Cannot find LINK/SSBOND residue HIS (80 )
Cannot find LINK/SSBOND residue CYS (56 )
Cannot find LINK/SSBOND residue CYS (75 )
Cannot find LINK/SSBOND residue CYS (75 )
Cannot find LINK/SSBOND residue CYS (68 )
17 messages similar to the above omitted
Chain information for KCR-removing.pdb #29
---
Chain | Description
S | No description available
T V | No description available
U | No description available
W X | No description available
Chain information for CSN-removing.pdb #30
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> hide #27-28#!1-3,5-17,22-26,29-30 atoms
> show #27-28#!1-3,5-17,22-26,29-30 cartoons
> ~ribbon # *
> ribbon #3,5
> morph #3,29 frames 30
Computed 31 frame morph #31
> coordset #31 1,31
> close #31
> morph #3,29 frames 60
Computed 61 frame morph #31
> coordset #31 1,61
> morph #5,28 frames 60
models have different number of chains, 8 (Morph - CSN-4d10.pdb #/A,Morph -
CSN-4d10.pdb #/B,Morph - CSN-4d10.pdb #/C,Morph - CSN-4d10.pdb #/D,Morph -
CSN-4d10.pdb #/E,Morph - CSN-4d10.pdb #/F,Morph - CSN-4d10.pdb #/G,Morph -
CSN-4d10.pdb #/H) and 1 (N8-1-removing.pdb #28/N)
> morph #5,30 frames 60
Computed 61 frame morph #32
> coordset #32 1,61
> morph #27,28 frames 60
Computed 61 frame morph #33
> coordset #33 1,61
> ~ribbon # *
> ribbon #31-33
> save D:/CryoEM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Sun Aug 21 08:34:05 2022 ———
opened ChimeraX session
> fly p5
> ~ribbon # *
> ribbon #3,5
> show #!3 models
> show #!5 models
> view name p5
> ~ribbon # *
> ribbon #31-33
> color /B light sky blue
> color /D medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> select /B/D /V:381-768
99374 atoms, 101164 bonds, 23 pseudobonds, 12266 residues, 37 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31,33 bounce true
> wait 120
> coordset #31,33 wait 60;
Expected a keyword
> ~ribbon # *
> ribbon #31-33
> view p5 60
> color /B light sky blue
> color /D medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> select /B/D/N /V:381-768
122358 atoms, 124616 bonds, 31 pseudobonds, 15122 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31,33
> wait 60
> color /N red
> color /N deep pink target c
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> ~ribbon # *
> ribbon #31-33
> view p5 60
> color /B light sky blue
> color /D medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> select /B/D/N /V:381-768
122358 atoms, 124616 bonds, 31 pseudobonds, 15122 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31,33
> wait 60
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> open /home/zgchen/data/KCRI/movie/CSN/N8_script.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ~ribbon # *
> ribbon #2
> wait 30
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24 bounce true
> wait 120
> coordset #24
> wait 60
executed N8_script.cxc
> close #23
> morph #22,2 frames 30
Computed 31 frame morph #23
> coordset #23 1,31
> open /home/zgchen/data/KCRI/movie/CSN/N8_script.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ~ribbon # *
> ribbon #2
> wait 30
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24 bounce true
> wait 120
> coordset #24
> wait 60
executed N8_script.cxc
> show #!2 models
> select surface
Expected an objects specifier or a keyword
> show #!4 models
> transparency #4.1-2 70
> hide #!4 models
> transparency #21.1-2 70
> select clear
> show #!20 models
> hide #!21 models
> show #!21 models
> transparency #20.1-2 70
> select clear
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> open /home/zgchen/data/KCRI/movie/CSN/N8_script.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #2,15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ~ribbon # *
> ribbon #2
> wait 30
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24 bounce true
> wait 120
> coordset #24
> wait 60
executed N8_script.cxc
> coordset #23
> open /home/zgchen/data/KCRI/movie/CSN/N8_script.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #1
> fly p1
> wait 40
> turn y 2 180
> wait
> show #!20 models
> coordset #20
> wait 60
> hide #!20 models
> ~ribbon # *
> ribbon #15-17,23
> show #!21 models
> coordset #15-17,21,23
> view p2 30
> wait 30
> ~ribbon #15-17
> wait 60
> ~ribbon # *
> ribbon #2
> wait 30
> color #2,3,24/V,T: 381-463 dark slate blue
> color #2,3,24/V,T: 464-572 dark goldenrod
> color #2,3,24/V,T: 573-679 cadet blue
> color #2,3,24/V,T: 680-768 dodger blue
> wait 60
> ~ribbon #2
> ribbon #24
> coordset #24 bounce true
> wait 120
> coordset #24
> wait 60
executed N8_script.cxc
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> fly p5
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #31-33
> view p5 60
> color /B light sky blue
> color /D medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> select /B/D/N /V:381-768
122358 atoms, 124616 bonds, 31 pseudobonds, 15122 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #31-33
> view p5 60
> wait 60
> color /B:415-443 light sky blue
> color /D:363-406 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /N deep pink target c
> select /N /B:415-443 /D:363-406 /V:381-768
65738 atoms, 66914 bonds, 21 pseudobonds, 8138 residues, 46 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #31-33
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /N deep pink target c
> select /N /B:1-414 /D:1-362 /V:381-768
113428 atoms, 115482 bonds, 27 pseudobonds, 14008 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> show #27 models
> show #28 models
> show #!29 models
> show #!30 models
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /N deep pink target c
> select /N /B:1-414 /D:1-362 /V:381-768
113428 atoms, 115482 bonds, 27 pseudobonds, 14008 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /N deep pink target c
> select /N /B:1-414 /D:1-362 /V:381-768
113428 atoms, 115482 bonds, 27 pseudobonds, 14008 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N /B:1-414 /D:1-362 /V:381-768
113428 atoms, 115482 bonds, 27 pseudobonds, 14008 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /W plum
> color /N deep pink target c
> select /N/W /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 82 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N /B:1-414 /D:1-362 /V:381-768
113428 atoms, 115482 bonds, 27 pseudobonds, 14008 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> ribbon #31-33
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> FLY P5
Unknown command: FLY P5
> fly p5
> turn y 70
> turn y -70
> turn y -60
> turn y -50
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> view name p6
> fly p5
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> fly p2
> ~ribbon # *
> ribbon #23
> ribbon #23,2
> coordset #23 computeSs
Missing "computeSs" keyword's argument
> coordset #23 computeSs ture
Invalid "computeSs" argument: Expected true or false (or 1 or 0)
> coordset #23 computeSs true
> movie record
> movie encode /home/zgchen/Desktop/movie.mp4 framerate 25.0
Movie saved to /home/zgchen/Desktop/movie.mp4
> movie record
> movie encode /home/zgchen/Desktop/movie.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!23 models
> show #!23 models
> coordset #23 computeSs true
> hide #!2 models
> coordset #23 computeSs true
> 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
> fly p6
> fly p5
> fly p6
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> fly p4
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ribbon #3,5 ~sel
> cartoon #3,5 ~sel
Expected a keyword
> select ~sel
568228 atoms, 579203 bonds, 205 pseudobonds, 70164 residues, 61 models
selected
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon sel
> ribbon #3,5
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon sel
> ribbon #3,5
> ~select
Nothing selected
> ~ribbon # *
> ribbon #31-33
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> ribbon #3,5
> select #3,5 /N/X /B:1-414 /D:1-362 /V:381-768
9666 atoms, 9832 bonds, 2 pseudobonds, 1192 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> hide #!3 models
> show #!3 models
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5
> select #3,5 /N/X /B:1-414 /D:1-362 /V:381-768
9666 atoms, 9832 bonds, 2 pseudobonds, 1192 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> view name p7
> view p7 60
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N/X /E:1-252 /F:1-214 /V:381-768
99881 atoms, 101875 bonds, 63 pseudobonds, 12367 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5
> select #3,5 /N/X /B:1-414 /D:1-362 /V:381-768
9666 atoms, 9832 bonds, 2 pseudobonds, 1192 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> color /E:1-252 orange
> color /F:1-214 pink
> view p7 60
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N/X /E:1-252 /F:1-214 /V:381-768
99881 atoms, 101875 bonds, 63 pseudobonds, 12367 residues, 51 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5
> select #3,5 /N/X /B:1-414 /D:1-362 /V:381-768
9666 atoms, 9832 bonds, 2 pseudobonds, 1192 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #31-33
> select /X /E:1-252 /F:1-214 /V:381-768
76897 atoms, 78423 bonds, 55 pseudobonds, 9511 residues, 37 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5
> select #3,5 /N/X /B:1-414 /D:1-362 /V:381-768
9666 atoms, 9832 bonds, 2 pseudobonds, 1192 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #31-33
> select /X /E:1-252 /F:1-214 /V:381-768
76897 atoms, 78423 bonds, 55 pseudobonds, 9511 residues, 37 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> select #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
12921 atoms, 13165 bonds, 2 pseudobonds, 1600 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> select #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
10257 atoms, 10428 bonds, 2 pseudobonds, 1268 residues, 5 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #31-33
> select /X /E:1-252 /F:1-214 /V:381-768
76897 atoms, 78423 bonds, 55 pseudobonds, 9511 residues, 37 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> select #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
12921 atoms, 13165 bonds, 2 pseudobonds, 1600 residues, 4 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> ribbon #31
> coordset #31 slidebar on
Expected a keyword
> coordset slider #31
> coordset slider #32
> coordset slider #30
> ribbon #30
> ~ribbon #30
> ribbon #5
> ~ribbon # *
> ribbon #31-33
> select /N/X /B:1-414 /D:1-362 /V:381-768
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> select #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
10257 atoms, 10428 bonds, 2 pseudobonds, 1268 residues, 5 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #30 /V:381-768 /X
> ribbon #31-33 /E:1-252 /F:1-214
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> select #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
10257 atoms, 10428 bonds, 2 pseudobonds, 1268 residues, 5 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #31-33 /E:1-252 /F:1-214
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> fly p5
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #31-33 /E:1-252 /F:1-214
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> fly p4
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #31-33 /E:1-252 /F:1-214
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #31-33 /E:1-252 /F:1-214
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #30
> hide #!30 models
> show #!30 models
> ribbon #5
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #31-33 /E:1-252 /F:1-214
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #32
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> wait 60
> view p4 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 60
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> view name p7
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> view name p8
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> ~ribbon # *
> ribbon #3 /U/S:264-605
> ribbon #5 /A:1-463
> name CSN1 /A:1-463
> select CSN1
32211 atoms, 32854 bonds, 15 pseudobonds, 4012 residues, 20 models selected
> ~ribbon # *
> ribbon #5
> ~ribbon # *
> ribbon #30
> name CSN2 /B:1-414
> name CSN4 /D:1-362
> name CSN3 /C:1-364
> name CSN5 /E:1-252
> name CSN6 /F:1-214
> name CSN7 /G:1-162
> name CSN8 /H:1-193
> name "helix bundle "
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
registering illegal selector name "helix bundle "
> name "lsit\\\"
"lsit\" is not defined
> name list
CSN1 /A:1-463
CSN2 /B:1-414
CSN3 /C:1-364
CSN4 /D:1-362
CSN5 /E:1-252
CSN6 /F:1-214
CSN7 /G:1-162
CSN8 /H:1-193
> name helix bundle
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
"helix" is reserved and cannot be redefined
> name "helix bundle"
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
registering illegal selector name "helix bundle"
> name helix_bundle
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
registering illegal selector name "helix_bundle"
> name helixbundle
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> name 4HB /V: 381-463
registering illegal selector name "4HB"
> ~ribbon # *
> ribbon # 3
> select 4HB
Expected an objects specifier or a keyword
> name fourHB /V: 381-463
> select /V: 464-572
10140 atoms, 10387 bonds, 1287 residues, 13 models selected
> select /V: 573-679
9724 atoms, 9854 bonds, 1209 residues, 13 models selected
> name ab /V: 464-572
> name WHA /V: 573-679
> name WHB /V: 680-768
> name Rbx1-1 /X
> name N8-1 /N
> ~ribbon # *
> ribbon N8-1 Rbx1-1 CSN2 CSN4
> cartoon N8-1 Rbx1-1 CSN2 CSN4
Expected a keyword
> ~ribbon # *
> ribbon N8-1,Rbx1-1,CSN2,CSN4
> cartoon N8-1,Rbx1-1,CSN2,CSN4
Expected an atoms specifier or a keyword
> ~ribbon # *
> ribbon N8-1 , Rbx1-1, CSN2, CSN4
> cartoon N8-1 , Rbx1-1, CSN2, CSN4
Expected a keyword
> ~ribbon # *
> ribbon #3 n8
> cartoon #3 n8
Expected a keyword
> ~ribbon # *
> ribbon #3 N8-1
> cartoon #3 N8-1
Expected a keyword
> ~ribbon # *
> ribbon #3,5,27
> select N8-1 Rbx1-1 CSN2 CSN4; ~ribbon ~sel
Expected a keyword
> ~ribbon # *
> ribbon #3,5,27
> select N8-1,Rbx1-1,CSN2,CSN4; ~ribbon ~sel
Expected an objects specifier or a keyword
> ~ribbon # *
> ribbon #3,5,27
> select N8-1//Rbx1-1//CSN2//CSN4; ~ribbon ~sel
Expected an objects specifier or a keyword
> ~ribbon # *
> ribbon #3,5,27
> select N8-1
22984 atoms, 23452 bonds, 8 pseudobonds, 2856 residues, 16 models selected
> select Rbx1-1
9611 atoms, 9867 bonds, 42 pseudobonds, 1187 residues, 18 models selected
> select CSN2
31784 atoms, 32388 bonds, 6 pseudobonds, 3896 residues, 16 models selected
> select CSN4
20336 atoms, 20694 bonds, 2528 residues, 10 models selected
> ~ribbon ~sel
> ~ribbon # *
> ribbon #3,5,27
> select N8-1
22984 atoms, 23452 bonds, 8 pseudobonds, 2856 residues, 16 models selected
> select add Rbx1-1
32595 atoms, 33319 bonds, 50 pseudobonds, 4043 residues, 33 models selected
> select CSN2
31784 atoms, 32388 bonds, 6 pseudobonds, 3896 residues, 16 models selected
> select CSN4
20336 atoms, 20694 bonds, 2528 residues, 10 models selected
> ~ribbon ~sel
> ~ribbon # *
> ribbon #3,5,27
> select N8-1
22984 atoms, 23452 bonds, 8 pseudobonds, 2856 residues, 16 models selected
> select add Rbx1-1
32595 atoms, 33319 bonds, 50 pseudobonds, 4043 residues, 33 models selected
> select add CSN2
64379 atoms, 65707 bonds, 56 pseudobonds, 7939 residues, 44 models selected
> select add CSN4
84715 atoms, 86401 bonds, 56 pseudobonds, 10467 residues, 44 models selected
> ~ribbon ~sel
> name CTD /V:381-768
> name list
CSN1 /A:1-463
CSN2 /B:1-414
CSN3 /C:1-364
CSN4 /D:1-362
CSN5 /E:1-252
CSN6 /F:1-214
CSN7 /G:1-162
CSN8 /H:1-193
CTD /V:381-768
N8-1 /N
Rbx1-1 /X
WHA /V: 573-679
WHB /V: 680-768
ab /V: 464-572
fourHB /V: 381-463
helixbundle
/A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
> name zone1 /N/X /B:1-414 /D:1-362 /V:381-768
> name zone2 /E:1-252 /F:1-214 /V:381-768 /X
> name zone3 /U:264-605 /S:264-605 /A:1-463
> ~ribbon # *
> ribbon #3,5,27
> select zone1
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~ribbon # *
> ribbon #3,5,27
> select zone1
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> wait 60
> ~ribbon # *
> ribbon #31-33
> select zone1
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon ~sel
> ~select
Nothing selected
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> select zone1
123039 atoms, 125349 bonds, 69 pseudobonds, 15195 residues, 56 models selected
> ~ribbon sel
> ~select
Nothing selected
> wait 60
> view p4 60
> wait 120
> ~ribbon # *
> ribbon #29
> ribbon #6
> setattr /B:1-414 atoms domain CSN2
Assigning domain attribute to 31784 items
Not creating attribute 'domain'; use 'create true' to override
> setattr /B:1-414 atoms domain CSN2 create true
Assigning domain attribute to 31784 items
> select #5@@domain CSN2
Expected a keyword
> select #5@@domain=CSN2
3078 atoms, 3132 bonds, 1 pseudobond, 374 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select #6@@domain=CSN2
3204 atoms, 3260 bonds, 391 residues, 1 model selected
> setattr /D:1-362 atoms domain CSN4 create true
Assigning domain attribute to 20336 items
> setattr /C:1-364 atoms domain CSN3 create true
Assigning domain attribute to 28348 items
> setattr /E:1-252 atoms domain CSN5 create true
Assigning domain attribute to 13994 items
> setattr /F:1-214 atoms domain CSN6 create true
Assigning domain attribute to 14968 items
> setattr /G:1-162 atoms domain CSN7 create true
Assigning domain attribute to 12313 items
> setattr /H:1-193 atoms domain CSN8 create true
Assigning domain attribute to 13212 items
> setattr /V:381-768 atoms domain CTD create true
Assigning domain attribute to 38324 items
> setattr /N atoms domain N8-1 create true
Assigning domain attribute to 22984 items
> setattr /X atoms domain Rbx1-1 create true
Assigning domain attribute to 9611 items
> setattr /V: 573-679 atoms domain WHA create true
Assigning domain attribute to 9724 items
> setattr /V: 680-768 atoms domain WHB create true
Assigning domain attribute to 9581 items
> setattr /V: 464-572 atoms domain ab create true
Assigning domain attribute to 10140 items
> setattr /V: 381-463 atoms domain fourHB create true
Assigning domain attribute to 8879 items
> setattr
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
> atoms domain helixbundle create true
Assigning domain attribute to 27669 items
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> select #6@@domain=CSN3
2873 atoms, 2927 bonds, 363 residues, 1 model selected
> select #6@@domain=CSN4
2898 atoms, 2943 bonds, 362 residues, 1 model selected
> select #6@@domain=CSN5
1844 atoms, 1892 bonds, 230 residues, 1 model selected
> select #6@@domain=CSN6
1463 atoms, 1493 bonds, 186 residues, 1 model selected
> select #6@@domain=CSN7
1217 atoms, 1233 bonds, 156 residues, 1 model selected
> select #6@@domain=CSN7
1217 atoms, 1233 bonds, 156 residues, 1 model selected
> select #6@@domain=CSN8
1276 atoms, 1308 bonds, 1 pseudobond, 161 residues, 2 models selected
> select #6@@domain=ctd
Nothing selected
> select #6@@domain=CTD
Nothing selected
> select #6@@domain=CTD
Nothing selected
> setattr /V:381-768 atoms region CTD create true
Assigning region attribute to 38324 items
> select #6@@region=CTD
2950 atoms, 2998 bonds, 1 pseudobond, 364 residues, 2 models selected
> select #6@@domain=WHA
748 atoms, 758 bonds, 93 residues, 1 model selected
> select #6@@domain=WHB
739 atoms, 748 bonds, 89 residues, 1 model selected
> select #6@@domain=fourHB
683 atoms, 691 bonds, 83 residues, 1 model selected
> select #6@@domain=AB
780 atoms, 799 bonds, 99 residues, 1 model selected
> INFO
Unknown command: INFO
> info
76 models
#1, KCR-8mer.pdb, shown
89360 atoms, 91112 bonds, 10992 residues, 24 chains
(A,E,C,B,D,F,J,K,H,G,L,I,U,X,V,S,W,T,P,R,M,N,Q,O)
24 missing structure
#1.1, missing structure, shown, 24 pseudobonds
#2, KCR-dimer-apo, shown
22297 atoms, 22735 bonds, 2748 residues, 6 chains (S,W,T,U,V,X)
22 metal coordination bonds, 6 missing structure
#2.1, metal coordination bonds, shown, 22 pseudobonds
#2.2, missing structure, shown, 6 pseudobonds
#3, N8~KCR-dimer-before, shown
22404 atoms, 22842 bonds, 2750 residues, 6 chains (W,X,T,S,U,V)
6 missing structure
#3.1, missing structure, shown, 6 pseudobonds
#4, N8-dimer-br-bound, hidden
1182 atoms, 1192 bonds, 152 residues, 2 chains (N,O)
#4.1, N8-dimer-br-bound_N Gaussian surface, shown, 11408 triangles
#4.2, N8-dimer-br-bound_O Gaussian surface, shown, 11360 triangles
#5, CSN-4d10.pdb, shown
20711 atoms, 21085 bonds, 2590 residues, 8 chains (A,B,C,D,E,F,G,H)
4 metal coordination bonds, 5 missing structure
#5.1, metal coordination bonds, shown, 4 pseudobonds
#5.2, missing structure, shown, 5 pseudobonds
#6, KCR-CSN-removing.pdb, shown
43336 atoms, 44154 bonds, 5380 residues, 14 chains
(A,B,C,D,E,F,G,H,S,W,T,V,U,X)
22 metal coordination bonds, 9 missing structure
#6.1, metal coordination bonds, shown, 22 pseudobonds
#6.2, missing structure, shown, 9 pseudobonds
#7, CSN-N8~KCR_combinemap_0725.pdb, shown
43316 atoms, 44133 bonds, 5377 residues, 14 chains
(A,B,C,D,F,G,H,S,W,T,V,U,X,E)
13 metal coordination bonds, 9 missing structure
#7.1, metal coordination bonds, shown, 13 pseudobonds
#7.2, missing structure, shown, 9 pseudobonds
#8, KCR-CSN_whole_job489_0725.pdb, shown
43323 atoms, 44140 bonds, 5378 residues, 14 chains
(A,B,C,D,F,G,H,S,W,T,X,U,V,E)
18 metal coordination bonds, 9 missing structure
#8.1, metal coordination bonds, shown, 18 pseudobonds
#8.2, missing structure, shown, 9 pseudobonds
#9, KCR-8mer-2.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (J,K,H,G,L,I)
6 missing structure
#9.1, missing structure, shown, 6 pseudobonds
#10, KCR-8mer-3.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (P,R,M,N,Q,O)
6 missing structure
#10.1, missing structure, shown, 6 pseudobonds
#11, KCR-8mer-4.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (A,E,C,B,D,F)
6 missing structure
#11.1, missing structure, shown, 6 pseudobonds
#12, KCR-8mer-2.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (J,K,H,G,L,I)
6 missing structure
#12.1, missing structure, shown, 6 pseudobonds
#13, KCR-8mer-3.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (P,R,M,N,Q,O)
6 missing structure
#13.1, missing structure, shown, 6 pseudobonds
#14, KCR-8mer-4.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (A,E,C,B,D,F)
6 missing structure
#14.1, missing structure, shown, 6 pseudobonds
#15, Morph - KCR-8mer-2.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (J,K,H,G,L,I), 31 coordsets
6 missing structure
#15.1, missing structure, shown, 6 pseudobonds
#16, Morph - KCR-8mer-3.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (P,R,M,N,Q,O), 31 coordsets
6 missing structure
#16.1, missing structure, shown, 6 pseudobonds
#17, Morph - KCR-8mer-4.pdb, shown
22340 atoms, 22778 bonds, 2748 residues, 6 chains (A,E,C,B,D,F), 31 coordsets
6 missing structure
#17.1, missing structure, shown, 6 pseudobonds
#18, N8-dimer-br-far, hidden
1182 atoms, 1192 bonds, 152 residues, 2 chains (N,O)
#18.1, N8-dimer-before-removal.pdb_N Gaussian surface, shown, 11408 triangles
#18.2, N8-dimer-before-removal.pdb_O Gaussian surface, shown, 11360 triangles
#19, N8-dimer-br-near, hidden
1182 atoms, 1192 bonds, 152 residues, 2 chains (N,O)
#19.1, N8-dimer-near_N Gaussian surface, shown, 11408 triangles
#19.2, N8-dimer-near_O Gaussian surface, shown, 11360 triangles
#20, Morph - N8-dimer-br-far, hidden
1182 atoms, 1192 bonds, 152 residues, 2 chains (N,O), 11 coordsets
#20.1, Morph - N8-dimer-br-far_N Gaussian surface, shown, 11408 triangles
#20.2, Morph - N8-dimer-br-far_O Gaussian surface, shown, 11360 triangles
#21, Morph - N8-dimer-near, hidden
1182 atoms, 1192 bonds, 152 residues, 2 chains (N,O), 61 coordsets
#21.1, Morph - N8-dimer-near_N Gaussian surface, shown, 11408 triangles
#21.2, Morph - N8-dimer-near_O Gaussian surface, shown, 11360 triangles
#22, KCR-8mer-1.pdb, hidden
22340 atoms, 22778 bonds, 2748 residues, 6 chains (U,X,V,S,W,T)
6 missing structure
#22.1, missing structure, shown, 6 pseudobonds
#23, Morph - KCR-8mer-1.pdb, shown
22273 atoms, 22717 bonds, 2739 residues, 6 chains (U,X,V,S,W,T), 31 coordsets
6 missing structure
#23.1, missing structure, shown, 6 pseudobonds
#24, Morph - KCR_dimer_j369_0806.pdb, shown
22291 atoms, 22735 bonds, 2742 residues, 6 chains (S,W,T,U,V,X), 61 coordsets
0 metal coordination bonds, 6 missing structure
#24.1, metal coordination bonds, shown, 0 pseudobonds
#24.2, missing structure, shown, 6 pseudobonds
#25, N8~KCR-dimer-out, shown
22404 atoms, 22842 bonds, 2750 residues, 6 chains (W,X,T,S,U,V)
6 missing structure
#25.1, missing structure, shown, 6 pseudobonds
#26, Morph - N8~KCR-dimer-out, shown
22404 atoms, 22842 bonds, 2750 residues, 6 chains (W,X,T,S,U,V), 61 coordsets
6 missing structure
#26.1, missing structure, shown, 6 pseudobonds
#27, N8-1-before-removal.pdb, shown
591 atoms, 596 bonds, 76 residues, 1 chains (N)
#28, N8-1-removing.pdb, shown
591 atoms, 596 bonds, 76 residues, 1 chains (N)
#29, KCR-removing.pdb, shown
22278 atoms, 22715 bonds, 2745 residues, 6 chains (S,W,T,V,U,X)
22 metal coordination bonds, 6 missing structure
#29.1, metal coordination bonds, shown, 22 pseudobonds
#29.2, missing structure, shown, 6 pseudobonds
#30, CSN-removing.pdb, shown
21058 atoms, 21439 bonds, 2635 residues, 8 chains (A,B,C,D,E,F,G,H)
3 missing structure
#30.1, missing structure, shown, 3 pseudobonds
#31, Morph - N8~KCR-dimer-before, shown
22272 atoms, 22715 bonds, 2739 residues, 6 chains (W,X,T,S,U,V), 61 coordsets
6 missing structure
#31.1, missing structure, shown, 6 pseudobonds
#32, Morph - CSN-4d10.pdb, shown
20457 atoms, 20818 bonds, 2576 residues, 8 chains (A,B,C,D,E,F,G,H), 61
coordsets
0 metal coordination bonds, 6 missing structure
#32.1, metal coordination bonds, shown, 0 pseudobonds
#32.2, missing structure, shown, 6 pseudobonds
#33, Morph - N8-1-before-removal.pdb, shown
591 atoms, 596 bonds, 76 residues, 1 chains (N), 61 coordsets
> setattr list
Missing or invalid "attrName" argument: Expected a text string
> setattr /N/X /B:1-414 /D:1-362 /V:381-768 atoms zone zone1 create true
Assigning zone attribute to 123039 items
> ~ribbon # *
> ribbon #3,5,27@@zone=zone1
> wait 60
> ~ribbon # *
> ribbon #31-33@@zone=zone1
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28@@zone!=zone1
> wait 60
> view p4 60
> wait 120
> ribbon #3,5,28@@zone!==zone1
> ribbon #3,5,28@@zone<zone1
> ribbon #3,5,28@@zone>zone1
> ~ribbon # *
> ribbon #3,5,27@@domain=CSN2|domain=CSN4|region=CTD
> wait 60
> ~ribbon # *
> ribbon #31-33@@domain=CSN2|domain=CSN4|region=CTD
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28@@domain=CSN2|domain=CSN4|region=CTD
> wait 60
> view p4 60
> wait 120
> ~ribbon # *
> ribbon #6
> select @@domain=CSN2|domain=CSN4|region=CTD;
Nothing selected
> select @@domain=CSN2 | domain=CSN4 | region=CTD;
Expected a keyword
> select @@CSN2
Nothing selected
> select CSN2
31784 atoms, 32388 bonds, 6 pseudobonds, 3896 residues, 16 models selected
> select CSN2 | CSN4
52120 atoms, 53082 bonds, 6 pseudobonds, 6424 residues, 16 models selected
> select CSN2 | CSN4 | CTD
90444 atoms, 92030 bonds, 19 pseudobonds, 11152 residues, 37 models selected
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> select #6 CSN2
Expected a keyword
> select #6:CSN2
Nothing selected
> select #6@@CSN2
Nothing selected
> select #6 CSN2
Expected a keyword
> select #6 :CSN2
Nothing selected
> select #6@CSN2
Nothing selected
> select CSN2
31784 atoms, 32388 bonds, 6 pseudobonds, 3896 residues, 16 models selected
> select #6@@domain=CSN2
3204 atoms, 3260 bonds, 391 residues, 1 model selected
> select #6@CSN2
Nothing selected
> select #6 @CSN2
Nothing selected
> select #6 @CSN4
Nothing selected
> select #6 @CTD
Nothing selected
> select @CTD
Nothing selected
> select ::CTD
Nothing selected
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> ~ribbon # *
> ribbon #31-33
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> wait 60
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view name p4
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> open /home/zgchen/data/KCRI/movie/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> setattr /D:1-362 atoms domain CSN4 create true
Assigning domain attribute to 20336 items
> setattr /C:1-364 atoms domain CSN3 create true
Assigning domain attribute to 28348 items
> setattr /E:1-252 atoms domain CSN5 create true
Assigning domain attribute to 13994 items
> setattr /F:1-214 atoms domain CSN6 create true
Assigning domain attribute to 14968 items
> setattr /G:1-162 atoms domain CSN7 create true
Assigning domain attribute to 12313 items
> setattr /H:1-193 atoms domain CSN8 create true
Assigning domain attribute to 13212 items
> setattr /V:381-768 atoms region CTD create true
Assigning region attribute to 38324 items
> setattr /N atoms domain N8-1 create true
Assigning domain attribute to 22984 items
> setattr /X atoms domain Rbx1-1 create true
Assigning domain attribute to 9611 items
> setattr /V: 573-679 atoms domain WHA create true
Assigning domain attribute to 9724 items
> setattr /V: 680-768 atoms domain WHB create true
Assigning domain attribute to 9581 items
> setattr /V: 464-572 atoms domain ab create true
Assigning domain attribute to 10140 items
> setattr /V: 381-463 atoms domain fourHB create true
Assigning domain attribute to 8879 items
> setattr
> /A:464-505/B:415-443/C:365-403/D:363-406/E:253-333/F:215-316/G:163-215/H:194-209
> atoms domain helixbundle create true
Assigning domain attribute to 27669 items
> setattr /N/X /B:1-414 /D:1-362 /V:381-768 atoms zone zone1 create true
Assigning zone attribute to 123039 items
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color CSN2 light sky blue
> color CSN4 medium orchid
> color fourHB dark slate blue
> color ab dark goldenrod
> color WHA cadet blue
> color WHB dodger blue
> color Rbx1-1 plum
> color N8 deep pink target c;
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> open /home/zgchen/data/KCRI/movie/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33 bounce true
> wait 120
> coordset #31-33
> wait 60
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> wait 60
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 60
executed removing.cxc
> open /home/zgchen/data/KCRI/movie/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> wait 60
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 60
executed removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X plum
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> roll y 2 180
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X plum
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33 bounce true
> wait 120
> view p6 60
> wait 60
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> 2dlabels text CSN1 color tomato
> fly p1
> fly p3
> ui mousemode right label
> label delete residues
[Repeated 2 time(s)]
> ui mousemode right "move label"
> 2dlabels #34.1 xpos 0.095 ypos 0.398
> 2dlabels text CSN2 color light sky blue
> 2dlabels #34.2 xpos 0.587 ypos 0.181
> 2dlabels #34.1 xpos 0.127 ypos 0.381
> 2dlabels text CSN3 color medium slate blue
> 2dlabels #34.3 xpos 0.052 ypos 0.671
> 2dlabels text CSN4 color medium orchid
> 2dlabels #34.4 xpos 0.705 ypos 0.394
> 2dlabels text CSN5 color orange
> 2dlabels #34.5 xpos 0.194 ypos 0.481
> 2dlabels #34.5 xpos 0.547 ypos 0.435
> 2dlabels text CSN6 color pink
> 2dlabels #34.6 xpos 0.639 ypos 0.698
> 2dlabels #34.5 xpos 0.537 ypos 0.460
> 2dlabels text CSN7 color cornflower blue
> 2dlabels #34.7 xpos 0.597 ypos 0.850
> 2dlabels text CSN8 color dark sea green
> 2dlabels #34.8 xpos 0.284 ypos 0.852
> 2dlabels #34.7 xpos 0.614 ypos 0.852
> 2dlabels #34.6 xpos 0.623 ypos 0.710
> 2dlabels #34.1,34.2 visibility false
> 2dlabels #34.1 #34.2 visibility false
> 2dlabels #34.1 #34.2 visibility true
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> 2dlabels #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 visibility true
> wait 120
> roll y 2 180
> wait
> wait 60
> 2dlabels text COP9 color white
> 2dlabels #34.9 xpos 0.772 ypos 0.773
> 2dlabels #34.9 xpos 0.808 ypos 0.638
> 2dlabels #34.9 xpos 0.812 ypos 0.652
> 2dlabels visibility false
> 2dlabels #34.9 visibility true
> roll y 1 360
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> 2dlabels #34.9 xpos 0.831 ypos 0.787
> 2dlabels text CRL3 dimer color white
Expected a keyword
> 2dlabels text CRL3-dimer color white
> 2dlabels #34.10 xpos 0.659 ypos 0.083
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> 2dlabels #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 visibility true
> wait 120
> 2dlabels visibility false
> 2dlabels #34.9 visibility true
> roll y 1 360
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> 2dlabels #34.10 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X gold
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels text CSN2 color light sky blue
> 2dlabels #34.11 xpos 0.066 ypos 0.248
> 2dlabels text CSN4 color medium orchid
> 2dlabels #34.12 xpos 0.820 ypos 0.606
> 2dlabels text 4HB color dark slate blue
> 2dlabels #34.13 xpos 0.108 ypos 0.425
> set bgColor white
> set bgColor gray
> set bgColor black
> 2dlabels text a/b color dark goldenrod
> 2dlabels #34.14 xpos 0.523 ypos 0.392
> 2dlabels #34.14 xpos 0.372 ypos 0.188
> 2dlabels text WHA color cadet blue
> 2dlabels #34.15 xpos 0.619 ypos 0.200
> 2dlabels text Rbx1 color gold
> 2dlabels #34.16 xpos 0.528 ypos 0.492
> 2dlabels text N8 color deep pink
> 2dlabels #34.17 xpos 0.242 ypos 0.704
> 2dlabels #34.17 xpos 0.217 ypos 0.802
> 2dlabels #34.16 xpos 0.537 ypos 0.469
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 visibility true
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> 2dlabels #34.14 xpos 0.392 ypos 0.427
> 2dlabels #34.14 xpos 0.542 ypos 0.054
> 2dlabels #34.14 xpos 0.406 ypos 0.394
> fly p5
> 2dlabels #34.14 xpos 0.370 ypos 0.219
> 2dlabels #34.15 xpos 0.539 ypos 0.048
> 2dlabels #34.13 xpos 0.119 ypos 0.504
> 2dlabels #34.11 xpos 0.045 ypos 0.167
> fly p6
> 2dlabels text a/b color dark goldenrod
> 2dlabels visibility false
> 2dlabels #34.18 visibility false
> 2dlabels #34.18 visibility true
> 2dlabels #34.18 xpos 0.538 ypos 0.025
> 2dlabels text WHA color cadet blue
> 2dlabels #34.19 xpos 0.247 ypos 0.071
> 2dlabels text Rbx1 color gold
> 2dlabels #34.20 xpos 0.403 ypos 0.781
> 2dlabels text N8 color deep pink
> 2dlabels #34.21 xpos 0.266 ypos 0.877
> 2dlabels text CSN2 color light sky blue
> 2dlabels #34.22 xpos 0.156 ypos 0.194
> 2dlabels text CSN4 color medium orchid
> 2dlabels #34.23 xpos 0.816 ypos 0.250
> 2dlabels #34.23 xpos 0.797 ypos 0.760
> 2dlabels text 4HB color dark slate blue
> 2dlabels #34.24 xpos 0.164 ypos 0.354
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 visibility true
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.18 #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 visibility true
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> fly p5
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 visibility true
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.18 #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 visibility true
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> view p4 60
> wait 120
> fly p5
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.18 #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 visibility true
> coordset #31-33
> wait 60
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> close #34.18-24
> 2dlabels text WHB color dodger blue
> fly p5
> 2dlabels #34.18 xpos 0.159 ypos 0.681
> fly p6
> 2dlabels text a/b color dark goldenrod
> 2dlabels #34.19 xpos 0.578 ypos 0.194
> fly p6
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels #34.19 xpos 0.578 ypos 0.188
[Repeated 1 time(s)]
> 2dlabels #34.19 xpos 0.552 ypos 0.054
> 2dlabels text WHA color cadet blue
> 2dlabels #34.18 xpos 0.148 ypos 0.550
> 2dlabels #34.20 xpos 0.200 ypos 0.065
> hide #34.18 models
> 2dlabels text WHA color cadet blue
> 2dlabels #34.21 xpos 0.387 ypos 0.379
> close #34.21
> 2dlabels text Rbx1 color gold
> 2dlabels #34.21 xpos 0.403 ypos 0.792
> 2dlabels text N8 color deep pink
> 2dlabels #34.22 xpos 0.264 ypos 0.877
> 2dlabels text CSN2 color light sky blue
> 2dlabels #34.23 xpos 0.139 ypos 0.233
> 2dlabels text CSN4 color medium orchid
> 2dlabels #34.24 xpos 0.769 ypos 0.777
> 2dlabels text 4HB color dark slate blue
> 2dlabels #34.25 xpos 0.116 ypos 0.421
> 2dlabels text WHB color dodger blue
> 2dlabels #34.26 xpos 0.134 ypos 0.548
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> 2dlabels visibility false
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> wait 60
> 2dlabels text 4HB color dark slate blue
> close #34.27
> 2dlabels text Rbx1 color gold
> 2dlabels #34.27 xpos 0.736 ypos 0.288
> 2dlabels text WHB color dodger blue
> 2dlabels #34.28 xpos 0.275 ypos 0.079
> 2dlabels #34.28 xpos 0.261 ypos 0.069
> 2dlabels text CSN5 color orange
> 2dlabels #34.29 xpos 0.111 ypos 0.348
> 2dlabels text CSN6 color pink
> 2dlabels #34.30 xpos 0.777 ypos 0.704
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> 2dlabels #34.27 #34.28 #34.29 #34.30 visibility true
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> wait 60
> 2dlabels text Kelch color light sea green
> 2dlabels #34.31 xpos 0.756 ypos 0.169
> 2dlabels text Kelch color pale turquoise
> 2dlabels #34.32 xpos 0.167 ypos 0.056
> 2dlabels text CSN1 color tomato
> 2dlabels #34.33 xpos 0.183 ypos 0.825
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> 2dlabels text removing state color white
Expected a keyword
> 2dlabels text removing-state color white
> 2dlabels #34.34 xpos 0.028 ypos 0.883
> 2dlabels text before-removal color white
> 2dlabels #34.34 xpos 0.017 ypos 0.740
> 2dlabels #34.35 xpos 0.014 ypos 0.892
> 2dlabels #34.35 xpos 0.017 ypos 0.890
> 2dlabels arrow
No 2D arrows in session
> ui mousemode right label
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
[Repeated 2 time(s)]
> 2dlabels arrow start .6,.6 end .5 .5 color white
Invalid "end" argument: Need exactly 2 ','-separated numbers
> 2dlabels arrow start .6,.6 end .5 ,.5 color white
> label delete residues
> ui mousemode right "move label"
> 2dlabels arrow #35.1 start 0.508,0.677
> 2dlabels arrow #35.1 end 0.509,0.508
> 2dlabels arrow #35.1 end 0.170,0.796
> 2dlabels arrow #35.1 start 0.170,0.873
> 2dlabels visibility false
> 2dlabels arrow visibility false
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels #34.34 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> 2dlabels visibility false
> 2dlabels #34.35 visibility true
> wait 60
> 2dlabels #34.34 visibility true
> 2dlabels arrow #35 visibility true
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 60
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
Can't find font for arrow
> open /home/zgchen/data/KCRI/movie/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> 2dlabels #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 visibility true
> wait 120
> 2dlabels visibility false
> 2dlabels #34.9 visibility true
> roll y 1 360
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> 2dlabels #34.10 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X gold
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 #34.18 visibility
> true
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 #34.25 #34.26 visibility
> true
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> 2dlabels #34.27 #34.28 #34.29 #34.30 visibility true
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> 2dlabels #34.31 #34.32 #34.33 visibility true
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels #34.34 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> 2dlabels visibility false
> 2dlabels #34.35 visibility true
> wait 60
> 2dlabels #34.34 visibility true
> 2dlabels arrow #35 visibility true
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
executed removing.cxc
> 2dlabels visibility false
> 2dlabels arrow visibility false
> save /home/zgchen/data/KCRI/movie/CSN/CSN_movie_0819.cxs
——— End of log from Mon Aug 22 13:56:21 2022 ———
opened ChimeraX session
> 2dlabels arrow visibility false
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels visibility false
> 2dlabels arrow visibility false
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> wait 60
> 2dlabels #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 visibility true
> wait 120
> 2dlabels visibility false
> 2dlabels #34.9 visibility true
> roll y 1 360
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> 2dlabels #34.10 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X gold
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 #34.18 visibility
> true
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 #34.25 #34.26 visibility
> true
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> 2dlabels #34.27 #34.28 #34.29 #34.30 visibility true
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> 2dlabels #34.31 #34.32 #34.33 visibility true
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels #34.34 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> 2dlabels visibility false
> 2dlabels #34.35 visibility true
> wait 60
> 2dlabels #34.34 visibility true
> 2dlabels arrow #35 visibility true
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
executed removing.cxc
Can't find font for arrow
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels visibility false
> 2dlabels arrow visibility false
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> movie record supersample 4 size 1280,960
> graphics rate maxFrameRate 80
> wait 60
> 2dlabels #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 visibility true
> wait 120
> 2dlabels visibility false
> 2dlabels #34.9 visibility true
> roll y 1 360
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> 2dlabels #34.10 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X gold
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 #34.18 visibility
> true
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 #34.25 #34.26 visibility
> true
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> 2dlabels #34.27 #34.28 #34.29 #34.30 visibility true
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> 2dlabels #34.31 #34.32 #34.33 visibility true
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels #34.34 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> 2dlabels visibility false
> 2dlabels #34.35 visibility true
> wait 60
> 2dlabels #34.34 visibility true
> 2dlabels arrow #35 visibility true
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> movie encode E:\cryo-EM\KCRI\PAPER\9_movies\CSN\movie.mov quality highest
Output directory does not exist: E:\cryo-EM\KCRI\PAPER\9_movies\CSN
> open D:/CryoEM/KCRI/PAPER/9_movies/CSN/removing.cxc
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels visibility false
> 2dlabels arrow visibility false
> windowsize 640 480
> ~ribbon # *
> hide #!4,18-21 models
> ribbon #5
> fly p3
> movie record supersample 4 size 1280,960
> graphics rate maxFrameRate 80
> wait 60
> 2dlabels #34.1 #34.2 #34.3 #34.4 #34.5 #34.6 #34.7 #34.8 visibility true
> wait 120
> 2dlabels visibility false
> 2dlabels #34.9 visibility true
> roll y 1 360
> wait
> wait 60
> color # * white
> ribbon #26
> view p4 60
> coordset #26
> wait 60
> 2dlabels #34.10 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> view p5 60
> wait 60
> color /B:1-414 light sky blue
> color /D:1-362 medium orchid
> color /V: 381-463 dark slate blue
> color /V: 464-572 dark goldenrod
> color /V: 573-679 cadet blue
> color /V: 680-768 dodger blue
> color /X gold
> color /N deep pink target c
> ~ribbon # *
> ribbon #3,5,27 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> 2dlabels visibility false
> 2dlabels #34.11 #34.12 #34.13 #34.14 #34.15 #34.16 #34.17 #34.18 visibility
> true
> ~ribbon # *
> ribbon #31-33 /N/X /B:1-414 /D:1-362 /V:381-768
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> view p6 60
> wait 60
> 2dlabels visibility false
> 2dlabels #34.19 #34.20 #34.21 #34.22 #34.23 #34.24 #34.25 #34.26 visibility
> true
> coordset #31-33
> wait 120
> coordset #31-33
> wait 60
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5,28 /N/X /B:1-414 /D:1-362 /V:381-768
> wait 60
> view p4 60
> wait 120
> view p7 60
> wait 60
> color /E:1-252 orange
> color /F:1-214 pink
> ~ribbon # *
> ribbon #29 /V:381-768 /X
> ribbon #5 /E:1-252 /F:1-214
> 2dlabels #34.27 #34.28 #34.29 #34.30 visibility true
> wait 60
> ~ribbon #5
> ribbon #31-33 /E:1-252 /F:1-214
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ribbon #3,5,28
> ~ribbon #3,5 /N/X /B:1-414 /D:1-362 /E:1-252 /F:1-214 /V:381-768
> ribbon #30 /B:1-414 /D:1-362
> wait 60
> view p4 60
> wait 60
> view p8 60
> wait 60
> color /U light sea green
> color /S pale turquoise
> color /A tomato
> ~ribbon # *
> ribbon #3 /U:264-605 /S:264-605
> ribbon #5 /A:1-463
> 2dlabels #34.31 #34.32 #34.33 visibility true
> wait 60
> ~ribbon #3,5
> ribbon #31-33 /U:264-605 /S:264-605 /A:1-463
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> 2dlabels visibility false
> ~ribbon # *
> ribbon #28-30
> wait 60
> view p4 60
> wait 60
> color /V yellow green
> color /U light sea green
> color /S pale turquoise
> color /T wheat
> color /W,X gold
> color /A tomato
> color /B light sky blue
> color /C medium slate blue
> color /D medium orchid
> color /E orange
> color /F pink
> color /G cornflower blue
> color /H dark sea green
> color /N deep pink target c
> color /O gold target c
> color #1,9-17/H,K,J,G,I,L chocolate
> color #1,9-17/M,N,O,P,Q,R lime green
> color #1,9-17/A,B,C,D,E,F olive
> 2dlabels #34.34 visibility true
> wait 60
> ~ribbon # *
> ribbon #3,5,27
> 2dlabels visibility false
> 2dlabels #34.35 visibility true
> wait 60
> 2dlabels #34.34 visibility true
> 2dlabels arrow #35 visibility true
> ~ribbon # *
> ribbon #31-33
> coordset #31-33
> wait 120
> coordset #31-33
> wait 120
> movie encode D:\CryoEM\KCRI\PAPER\9_movies\CSN\movie.mov quality highest
Movie saved to \D:CryoEM\\...\CSN\movie.mov
executed removing.cxc
> save D:/CryoEM/KCRI/PAPER/9_movies/CSN/CSN_movie_0819.cxs
——— End of log from Mon Aug 22 17:28:01 2022 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 472.19
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82K8
OS: Microsoft Windows 10 家庭中文版 (Build 19044)
Memory: 16,498,810,880
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Documentation |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash computing ribbons |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Appears it was in the C++ ribbon_extrusions() code called by _ribbon_geometry(). The log shows it crashed when the selection was cleared. That should not recompute the ribbon, so that is mysterious. The error is "Python aborted" rather than a segmentation fault.
Don't see any clues that would indicate what caused the crash.