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#3581 closed defect (fixed)
Label position asked for before label drawn (and various other errors)
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202008010351 (2020-08-01 03:51:48 UTC)
Description
I have multiple 2Dlabels in my session. When I select one of the group to move, I get this error and cannot move the label. I can only move the label if I close all the other labels.
Log:
UCSF ChimeraX version: 1.1.dev202008010351 (2020-08-01)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test_membrane_label.cxs
> format session
Log from Sat Aug 1 11:55:04 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie_withmaps.cxs
> format session
Log from Tue Jul 28 17:42:25 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
Log from Mon Jul 27 23:45:58 2020UCSF ChimeraX version: 1.1.dev202007121748
(2020-07-12)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.cxs
Log from Thu Jul 9 17:26:01 2020UCSF ChimeraX version: 1.0rc202005292300
(2020-05-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.cxs
> format session
Log from Thu Jul 9 09:23:52 2020UCSF ChimeraX version: 1.0rc202005292300
(2020-05-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.cxs
> format session
Log from Thu Jun 4 14:06:37 2020UCSF ChimeraX version: 1.0rc202005292300
(2020-05-29)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> format session
Log from Wed Jun 3 21:08:22 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> format session
Log from Wed Jun 3 17:08:59 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.cxs
> format session
Log from Tue May 19 13:09:11 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.cxs
> format session
Log from Mon May 18 23:49:34 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/prot_exterior.cxs
Log from Fri May 8 19:25:54 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/prot_exterior.cxs
Log from Sat Apr 18 17:23:14 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/prot_exterior.cxs
> format session
Log from Sat Apr 18 16:43:45 2020 Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/job653_refine3D_protzone_minus_strand1.mrc
Opened job653_refine3D_protzone_minus_strand1.mrc, grid size 512,512,512,
pixel 0.835, shown at level 0.00206, step 2, values float32
> volume #1 level 0.0025
> lighting full
> lighting full
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> toolshed show "Side View"
> view orient
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/job653_refine3D_strand1_minusdimer.mrc
Opened job653_refine3D_strand1_minusdimer.mrc, grid size 512,512,512, pixel
0.835, shown at level 1.09e-06, step 2, values float32
> set bgColor white
> volume #2 level 0.0006473
> volume #2 level 0.00025
> volume #2 level 0.0025
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/job653_refine3D_strand1_dimeronly.mrc
Opened job653_refine3D_strand1_dimeronly.mrc, grid size 512,512,512, pixel
0.835, shown at level 7.51e-08, step 2, values float32
> volume #3 level 0.002137
> volume #3 level 0.0025
> camera stero
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> camera stereo
Could not switch graphics mode. Graphics driver did not create OpenGL context.
> camera ortho
No help found for 'help:user/commands/'
> cofr
Center of rotation: 213.76 213.78 213.98 front center
> cofr #1
> turn x
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> turn y 1
> ui dockable false "Side View"
> volume #3 color #006600
> volume #3 color #339933
> volume #3 color #336633
> volume #3 color #669966
> volume #3 color #33cc00
> volume #3 color #339900
> volume #2 color #35b219
> volume #2 color #66ff66
> volume #2 color #99ff99
> volume #1 color #00ccff
> volume #1 color #33ccff
> volume #1 color #66ccff
> volume #1 color #33ffff
> volume #1 color #66ffff
> volume #1 color #006666
> volume #1 color #66ffff
> volume #1 color #33ffff
> volume #1 color #66ffff
> surface dust #1 size 5
> surface dust #2 size 5
> surface dust #3 size 5
> surface undust #2 size 5
Expected fewer arguments
> surface undust #2
> surface dust #2 size 5
> volume #1 level 0.0022
> volume #2 level 0.0022
> volume #3 level 0.0022
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> volume #1 color #669966
> volume #1 color #99ff99
> volume #1 color #003300
> volume #1 color #99ff00
> volume #1 color #66ff00
> volume #1 color #66cc00
> volume #1 color #66cc33
> volume #1 color #99ff66
> volume #1 color #66ff33
> volume #1 color #ccffcc
> volume #1 color #99cc99
> volume #1 color #ccffcc
> volume #1 color #99ff99
> volume #1 color #66cc99
> volume #1 color #33cc66
> volume #1 color #99ff33
> volume #1 color #99ff00
> volume #1 color #66ff00
> volume #1 color #99ff66
> volume #1 color #66ff33
> volume #1 color #99ff00
> volume #1 color #66ff00
> volume #1 color #99ff00
> volume #1 color #66cc00
> volume #3 color #8bff87
> volume #1 color #7dff74
> volume #2 color lime
> volume #2 color #00cc00
> volume #3 color #35b219
> volume #3 color #006600
> volume #1 color #7dff74f5
> volume #1 color #7dff74e4
> volume #1 color #7dff74dd
> volume #1 color #7dff74d9
> volume #1 color #7dff74ce
> volume #1 color #7dff74cb
> volume #1 color #7dff74c4
> volume #1 color #7dff74c1
> volume #1 color #7dff74be
> volume #1 color #7dff74b9
> volume #1 color #7dff74ae
> volume #1 color #7dff74a6
> volume #1 color #7dff74a3
> volume #1 color #7dff74a0
> volume #1 color #7dff7497
> volume #1 color #7dff7490
> volume #1 color #7dff74bf
> volume #1 color #7dff74b3
> volume #3 color #339933
> volume #3 color #006600
> volume #2 color #66ff66
> volume #2 color #339933
> volume #2 color #336633
> volume #2 color #669966
> volume #2 color #99cc99
> volume #1 color #7dff7499
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/exterior_view.png
> format png supersample 4 transparentBackground true
> volume #1 color #7dff7480
> volume #1 color #7cff7480
> volume #1 color #79ff7480
> volume #1 color #78ff7480
> volume #1 color #77ff7480
> volume #1 color #76ff7480
> volume #1 color #74ff7480
> volume #1 color #73ff7480
> volume #1 color #72ff7480
> volume #1 color #70ff7480
> volume #1 color #6fff7480
> volume #1 color #6cff7480
> volume #1 color #64ff7480
> volume #1 color #73ff7480
> volume #1 color #7dff7480
> volume #1 color #91ff7480
> volume #1 color #91ff6480
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/exterior_view.png
> format png supersample 4 transparentBackground true
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/prot_exterior.cxs
opened ChimeraX session
> volume #3 step 1
> volume #2 step 1
> volume #1 step 1
> volume #1 color #89c487
> volume #1 color #89c4874c
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/exterior_view.png
> format png supersample 4 transparentBackground true
> volume #1 color #89c48780
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/exterior_view.png
> format png supersample 4 transparentBackground true
> volume #1 color #89c487b3
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/exterior_view.png
> format png supersample 4 transparentBackground true
> volume #1 color #80ff07
> volume #1 color #ccff66
> volume #1 color #80ff07
> volume #1 color #89c487
> volume #1 color #89c487e6
> volume #2 color #80ff07
> volume #3 color #408002
> volume #3 color #108001
> volume #3 color #408002
> volume #3 color #108040
> volume #3 color #108001
> volume #3 color #006600
> volume #3 color #108001
> volume #2 color #21ff06
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/exterior_view.png
> format png supersample 4 transparentBackground true
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/Figures/filament/prot_exterior.cxs
opened ChimeraX session
> hide #!3 models
> show #!3 models
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/top_monomer_job653_refine3D.mrc
Opened top_monomer_job653_refine3D.mrc, grid size 512,512,512, pixel 0.835,
shown at level 7.96e-08, step 2, values float32
> hide #!3 models
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/bottom_monomer_job653_refine3D.mrc
Opened bottom_monomer_job653_refine3D.mrc, grid size 512,512,512, pixel 0.835,
shown at level 6.11e-07, step 2, values float32
> surface dust #1 size 5
> surface dust #2 size 5
> surface dust #4 size 5
> surface dust #5 size 5
> volume #4 color #108001
> volume #5 color #fc02ff
> volume #5 step 1
> volume #5 level 0.0022
> volume #4 level 0.002208
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/prot_exterior.cxs
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/exterior_view.png
> format png supersample 4 transparentBackground true
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/prot_exterior.cxs
opened ChimeraX session
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #3-5
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/job653_loophelix_1.mrc
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/job653_loophelix_2.mrc
Opened job653_loophelix_1.mrc, grid size 38,40,46, pixel 0.835,0.835,0.835,
shown at level 0.00357, step 1, values float32
Opened job653_loophelix_2.mrc, grid size 42,38,44, pixel 0.835,0.835,0.835,
shown at level 0.00359, step 1, values float32
> hide #!3 models
> show #!3 models
> volume #3 level 0.0025
> volume #4 level 0.0025
> volume #4 level 0.002
> volume #3 level 0.002
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/top_pmr.mrc
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/bottom_pmr.mrc
Opened top_pmr.mrc, grid size 512,512,512, pixel 0.835, shown at level 8e-07,
step 2, values float32
Opened bottom_pmr.mrc, grid size 512,512,512, pixel 0.835, shown at level
3.92e-08, step 2, values float32
> volume #5 level 0.0008619
> volume #5 step 1
> volume #5 level 0.0007
> volume #6 step 1
> volume #6 level 0.007
> volume #6 level 0.07
> volume #6 level 0.007
> volume #6 level 0.0007
> surface dust #1-7 size 5
> lighting full
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.cxs
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/job653_membraneish_cylinder.mrc
Opened job653_membraneish_cylinder.mrc, grid size 512,512,512, pixel 0.835,
shown at level 0.000516, step 2, values float32
> volume #7 step 1
> volume #7 color grey
> volume #7 level 0.0004337
> volume #7 level 0.0002
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.cxs
> toolshed show "Side View"
> surface dust #7 size 5
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.cxs
opened ChimeraX session
> surface dust #1-6 size 5
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 color #21ff06cc
> save
> /Users/hcnguyen/Documents/Frost_lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.png
> format png transparentBackground true
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/membrane_loophelixPMR.cxs
opened ChimeraX session
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/top_nadph.mrc
Opened top_nadph.mrc, grid size 26,12,24, pixel 0.835,0.835,0.835, shown at
level 0.00463, step 1, values float32
> volume #8 level 0.003937
> volume #8 level 0.003004
> lighting simple
> lighting simple
> camera pers
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> camera mono
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/bottom_nadph.mrc
Opened bottom_nadph.mrc, grid size 14,26,24, pixel 0.835,0.835,0.835, shown at
level 0.00425, step 1, values float32
> volume #8 color #ffff0a
> volume #8 color #ffff66
> volume #8 color #ffff0a
> volume #8 color #ffff66
> volume #8 color #ffff0a
> volume #9 color #ffff0a
> volume #9 level 0.003
> surface dust #1-9 size 5
> zoom
Pixel size at center of rotation is 0.477
> zoom
Pixel size at center of rotation is 0.477
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/maps/job653_membraneish_outerleaflet.mrc
Opened job653_membraneish_outerleaflet.mrc, grid size 512,512,512, pixel
0.835, shown at level 0.000119, step 2, values float32
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/maps/job653_sym_inner_leaftlet.mrc
Opened job653_sym_inner_leaftlet.mrc, grid size 512,512,512, pixel 0.835,
shown at level 0.000305, step 2, values float32
> hide #!7 models
> volume #11 step 1
> volume #11 level 0.0005
> volume #11 level 0.0008
> volume #11 level 0.0005
> volume #11 color #999999
> toolshed show "Side View"
> volume #10 color #999999
> volume #10 step 1
> volume #10 level 0.0001
> hide #!11 models
> hide #!10 models
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
opened ChimeraX session
> close #7
> show #!10 models
> show #!11 models
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/top_monomer_job653_refine3D.mrc
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/bottom_monomer_job653_refine3D.mrc
Opened top_monomer_job653_refine3D.mrc, grid size 72,82,66, pixel
0.835,0.835,0.835, shown at level 0.00381, step 1, values float32
Opened bottom_monomer_job653_refine3D.mrc, grid size 84,72,68, pixel
0.835,0.835,0.835, shown at level 0.00376, step 1, values float32
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> hide #!1 models
> view orient
> view orient
> view orient
> help help:user
> view orient
> view orient
> show #!1 models
> hide #!1 models
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> turn z 10
> view orient
> turn z 120
> turn z -120
> turn z 140
> turn z -140
> turn z 135
> turn y 180
> turn y 180
> view orient
> turn x 2 frames 45
> turn y 5
> turn y 5
> turn y 5
> turn y 5
> turn y 5
> turn y 5
> turn y 5
> turn y 5
> volume #12 level 0.002
> volume #7 level 0.002
> show #!1 models
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> zom #7,12 frames 25
Unknown command: zom #7,12 frames 25
> zoom #7,12 frames 25
Expected a number or a keyword
> view #7,12
> view name dimer
> view orient
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> surface dust #1-12 size 5
> cofr #1
> camera ortho
> view #7,12
> view name dimer
> view orient
> turn z 40
> view name topdown
> turn x 2 frames 45
> turn y 3 frames 120
executed script_movie.cxc
> view orient
> view
> view orient
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> surface dust #1-12 size 5
> cofr #1
> view orient
> turn z 40
> view name topdown
> camera ortho
> view #7,12
> view name dimer
> turn x 2 frames 45
executed script_movie.cxc
> view list
Named views: dimer, topdown
> view topdown
> turn z 40
> turn x 2 frames 45
> view topdown
> view topdown
> view orient
> view orient
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> view #1 orient
> hide #!1 models
> turn z 40
> turn z -40
> turn z -40
> turn z -1
> turn z -1
> turn z -1
> turn z -1
> turn z -1
> view #1 orient
No displayed objects specified.
> show #!1 models
> view #1 orient
> turn y 180
> hide #!1 models
> turn z 120
> turn z -120
> turn z -100
> turn z -20
> turn z -20
> turn z -5
> show #!1 models
> view name topdown
> turn x -2 frames 45
> view name exterior
> view dimer frames 45
> view delete dimer
> view topdown
> view exterior frames 10
> view #7,12
> view name dimer
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> view exterior
> view dimer frames 10
> transparency #7,12 50
> transparency #7,12 75
> transparency #7,12 100
> transparency #7,12 85
> transparency #7,12 0
> view #8,9
> view dimer
> view #8,9 pad -0.05
> view #8,9 pad -0.5
> view #8,9 pad -0.25
> hide #!7 models
> show #!7 models
> view #7,12 pad -0.25
> view #7,12 pad -0.75
> view #7,12
> hide #7,12
> view #5,6
> view #3-6
> view name mem_insert
> view list
Named views: dimer, exterior, mem_insert, topdown
> view dimer
> show #!12 models
> show #!7 models
> view dimer
> show #7,12
> toolshed show "Side View"
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> clip near 10
> view dimer
> clip near 100
> clip near -100
> clip near 80
> clip near 90
clip far plane is in front of near plane
> clip near -90
> clip near -80
> clip near 90
> clip near -90
> clip near 85
> clip near -85
> clip near 90
> view name clip_mem
> view dimer
> view clip_mem frames 10
> view dimer frames 40
> hide #7,12
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/top_LMG.mrc
Opened top_LMG.mrc, grid size 14,16,14, pixel 0.835,0.835,0.835, shown at
level 0.00178, step 1, values float32
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/bottom_LMG.mrc
Opened bottom_LMG.mrc, grid size 16,14,14, pixel 0.835,0.835,0.835, shown at
level 0.00164, step 1, values float32
> volume #13 level 0.001635
> volume #13 level 0.0012
> volume #13 level 0.0015
> volume #13 level 0.0016
> volume #13 level 0.002
> volume #13 level 0.0018
> volume #13 level 0.0017
> volume #14 level 0.0017
> volume #13 level 0.0018
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> surface dust #13-14 size 5
> surface undust #13-14
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> view mem_insert frames 30
> view dimer
> unhide #7,12
Unknown command: unhide #7,12
> show #7,12
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> view topdown
> view exterior frames 45
> view dimer frames 45
> view clip_mem frames 40
> view dimer
> crossfade
> hide #7,12
> wait 5
> crossfade 10
> hide #8-9
> wait 5
> show #8-9
> show #8-9
> show #7,12
> clip 10
Expected a keyword
> clip near 10
> clip near 10
> clip near 10
> clip near 10
> clip near 10
> clip near 10
> clip near 10
> clip near 10
> clip near 10
> clip near -90
> clip near 20
> view name clip20
> clip near 20
> view name clip40
> view clip20
> view clip40 frames 20
> view clip40
> view clip40
> clip near 20
> view name clip60
> clip near 20
> view name clip80
> view mem_insert
> view mem_insert
> view clip_mem
> view clip 80 frames 1
Invalid "clip" argument: Expected true or false (or 1 or 0)
> view clip80 frames 1
> view clip60 frames 1
> view clip40 frames 5
> view clip20 frames 5
> view dimer frames 5
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> view topdown
> volume #11 level 0.0006
> volume #11 level 0.001
> volume #11 level 0.0009
> volume #11 level 0.0008
> view exterior frames 45
> turn y 3 frames 120
> view dimer frames 45
> wait 2
> crossfade
> hide #7,12
> wait 5
> crossfade 10
> hide #8-9
> wait 5
> show all
> view topdown
> view exterior frames 45
> turn y 3 frames 120
> view dimer frames 45
> wait 2
> crossfade
> hide #7,12
> wait 5
> crossfade 10
> hide #8-9
> wait 5
> show all
> view topdown
> view exterior frames 45
> wait 1
> turn y 3 frames 120
> wait
> view dimer frames 45
> view exterior
> turn z 3 frames 120
> turn x 3 frames 120
> roll z 3 frames 20
> roll z -60
> stop
> turn z 3 frames 10 coordinateSystem #1
> turn z 3 frames -10 coordinateSystem #1
Invalid "frames" argument: Must be greater than 1or equal to
> view exterior
> turn z 3 frames 120 coordinateSystem #1
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> view topdown
> wait 1
> movie record supersample 3
> view exterior frames 45
> wait 1
> turn z 3 frames 120 coordinateSystem #1
> wait
> view dimer frames 45
> wait 2
> crossfade
> hide #7,12
> wait 2
> crossfade 20
> hide #8-9
> wait 5
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
executed script_movie.cxc
> show all
> view topdown
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> view topdown
> wait 2
> movie record supersample 3
> view exterior frames 90
> wait 5
> turn z 3 frames 120 coordinateSystem #1
> wait
> view dimer frames 90
> wait 5
> view clip_mem frames 40
> wait 5
> view dimer frames 40
> wait 5
> crossfade 60
> hide #7,12
> wait 2
> crossfade 30
> hide #8-9
> wait 5
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
executed script_movie.cxc
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> format cmd
> view topdown
> wait 2
> movie record supersample 3
> view exterior frames 90
> wait 10
> turn z 1 frames 360 coordinateSystem #1
> wait 10
> view dimer frames 360
> wait 10
> crossfade 60
> hide #7,12
> wait 2
> crossfade 30
> hide #8-9
> wait 5
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
executed script_movie.cxc
> view dimer
> show all
> view exterior
> view dimer frames 90
> view exterior
> view dimer frames 90
> crossfade 60
> hide #7,12
> wait 2
> show all
> show all
> crossfade
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> view topdown
> wait 2
> movie record supersample 3
> view exterior frames 90
> wait 10
> turn z 1 frames 360 coordinateSystem #1
> wait 10
> view exterior
> wait 1
> view dimer frames 90
> wait 10
> crossfade 60
> hide #7,12
> wait 10
> crossfade 30
> hide #8-9
> wait 10
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
executed script_movie.cxc
> view dimer
> show all
> view exterior
> view topdown
> view exterior frames 90
> wait 10
> turn z 1 frames 360 coordinateSystem #1
> wait 10
> view exterior
> wait 1
> view dimer frames 90
> wait 10
> crossfade 60
> hide #7,12
> wait 10
> crossfade 30
> hide #8-9
> wait 10
> view dimer
> show all
> show #8-9
> view exterior
> wait 1
> view dimer frames 90
> wait 10
> crossfade 60
> hide #7,12
> wait 10
> crossfade 30
> hide #8-9
> wait 10
> show #6-9
> show #!12 models
> show #12
> view topdown
> movie record supersample 3
> view exterior frames 90
> wait 10
> turn z 1 frames 360 coordinateSystem #1
> wait 10
> view exterior
> wait 10
> view dimer frames 90
> wait 10
> crossfade 60
> hide #7,12
> wait 10
> crossfade 30
> hide #8-9
> wait 10
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
> view topdown
> view topdown
> open2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> view topdown
> wait 2
> movie record supersample 3
> view exterior frames 90
> wait
> turn z 1 frames 360 coordinateSystem #1
> wait
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> view dimer frames 90
> wait
> crossfade 60
> hide #7,12
> wait
wait requires a frame count argument unless motion is in progress
> crossfade 30
> hide #8-9
> wait
wait requires a frame count argument unless motion is in progress
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
executed script_movie.cxc
> transparency #1 0
> view exterior
> transparency #2 0
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> show all
> save2
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
opened ChimeraX session
> view dimer
> view list
Named views: clip20, clip40, clip60, clip80, clip_mem, dimer, exterior,
mem_insert, topdown
> view mem_insert frames 10
> view clip_mem
> view dimer
> view clip_mem, frames 10
Expected an objects specifier or a view name or a keyword
> view clip_mem frames 10
> view dimer frames 10
> view clip20
> view clip40 view clip60; view clip80; view clip_mem
Expected an integer >= 1 or a keyword
> view clip20
> view clip40 view clip60; view clip80; view clip_mem
Expected an integer >= 1 or a keyword
> view clip 20
Invalid "clip" argument: Expected true or false (or 1 or 0)
> view clip20
> view clip40
> view clip60
> view clip80
> view clip80 10
> view clip20 10
> view dimer 10
> view clip_mem 60
> view dimer 60
> view clip80 60
> view dimer 5
> crossfade 60
> view clip80
> crossfade 1220
> view dimer
> crossfade 120
> view clip80
> view clip80
> view dimer
> ui mousemode right "move planes"
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> ui mousemode right clip
> ui tool show "Side View"
> view dimer
> view dimer
> view front 90
Expected an objects specifier or a view name or a keyword
> clip front 90
> clip front -90
> view dimer
> clip front 10
> clip off
> view dimer
> clip front 5 coordinateSystem #1
> view dimer
> clip back 5 coordinateSystem #1
> clip back off coordinateSystem #1
> clip front -10 coordinateSystem #1
> view dimer
> clip front -10 coordinateSystem #1
> clip front -100 coordinateSystem #1
> clip front -80 coordinateSystem #1
> clip front -40 coordinateSystem #1
> clip front -100 coordinateSystem #1
> clip front -200 coordinateSystem #1
> clip front -10 coordinateSystem #1
> clip front 0 coordinateSystem #1
> clip front 10 coordinateSystem #1
> clip front 100 coordinateSystem #1
> view dimer
> clip front on
Invalid "front" argument: Expected 'off' or a number
> hide #!11 models
> hide #!10 models
> volume all region 0,0,145,279,279,164
> volume all region 0,0,100,279,279,164
> volume all region 0,0,0,279,279,164
> volume all region 0,0,0,0,279,164
> volume all region 0,0,0,100,279,164
> volume all region 0,0,0,100,0,164
> volume all region 0,0,0,100,0,0
> volume all region 0,0,0,100,100,0
> volume all region 0,0,0,100,100,100
> volume all region 0,0,100,100,100,100
> volume all region 0,0,010,0,100,100
> volume all region 0,100,0,100,100,100
Volume region axis minimum values 0,100,0 must be less than or equal to axis
maximum values 100,0,100
> volume all region 0,0,0,0,0,0
Volume region axis minimum values 100,0,0 must be less than or equal to axis
maximum values 0,0,0
> volume all region 0,0,0,0,0,0
Volume region axis minimum values 0,10,0 must be less than or equal to axis
maximum values 10,0,10
Volume region axis minimum values 0,10,0 must be less than or equal to axis
maximum values 10,0,100
> volume all region 0,0,145,279,279,164
> volume all region 0,0,145,280,280,160
> view dimer
> volume all region 0,0,145,280,280,160
> ui mousemode right "move planes"
> volume #4 region 0,0,43,41,37,43
> volume #7 region 0,0,33,71,81,33
> volume all region 0,0,145,280,280,160
> volume all region 0,0,145,280,280,160
> volume all region 0,0,145,279,279,164
> volume all region 0,0,100,279,279,164
> volume initial
Expected a density maps specifier or a keyword
> volume region all
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> ui mousemode right "move planes"
> volume #1 region 0,0,0,511,511,511
> view dimer
> ui mousemode right clip
> ui mousemode right "move planes"
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,511,511
> ui mousemode right "crop volume"
> volume #1 region 0,0,0,511,511,511
> volume #1 region 0,0,0,511,509,511
> view dimer
> volume #1 region 0,0,0,511,511,511
> ui mousemode right select
> move x 10
> move x -10
> move z 10
> move z 10
> move z 10
> move z 10
> move z 10
> move z 10
> move z 10
> move z 10
> move z 10
> move z -1
> move z -1
> move z -1
> move z -1
> move z -1
> move z -1
> move z -1
> show #!10 models
> show #!11 models
> move z 1
> move z 1
> move z 1
> move z 1
> view list
Named views: clip20, clip40, clip60, clip80, clip_mem, dimer, exterior,
mem_insert, topdown
> view delete clip20
> view delete clip40
> view delete clip60
> view delete clip80
> view delete clip_mem
> view name slicethrough
> view dimer
> view slicethrough frames 10
> view dimer frames 10
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> volume #11 level 0.0007
> view licethrough frames 10
Expected an objects specifier or a view name or a keyword
> view slicethrough frames 10
> view dimer frames 10
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> show all
> view topdown
> wait 10
> movie record supersample 3
> view exterior frames 90
> wait 110
> turn z 2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 90
> wait 110
> view slicethrough frames 90
> wait 110
> view dimer frames 90
> wait 110
> crossfade 60
> hide #7,12
> wait 90
> crossfade 30
> hide #8-9
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/test_movie.mp4
> show all
executed script_movie.cxc
> volume #10 level 8e-05
> volume #10 level 5e-05
> volume #10 level 9e-05
> volume #6 level 0.0008
> volume #5 level 0.0008
> hide #!12 models
> show #!12 models
> hide #!12 models
> volume #6 level 0.001
> volume #6 level 0.008
> volume #6 level 0.0008
> show #!12 models
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> show all
> view topdown
> wait 10
> movie record supersample 3
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #7,12
> wait 90
> crossfade 30
> hide #8-9
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
> show all
executed script_movie.cxc
> volume #11 level 0.0005
> view topdown
> volume #11 level 0.0006
> view dimer
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_movie.cxc
> show all
> movie record supersample 3
> view topdown
> wait 20
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #7,12
> wait 90
> crossfade 30
> hide #8-9
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie.mp4
> show all
executed script_movie.cxc
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overal_movie.cxs
opened ChimeraX session
> camera ortho
> hide #!12 models
> hide #!7 models
> 2dlabels text NADPH #15 color gold size 26 x 0 y 0
Expected a keyword
> 2dlabels text NADPH color gold size 26 xpos 0 ypos 0
> hide #!15 models
> show #!15 models
> select #15
2 models selected
> view membrane_insert
Expected an objects specifier or a view name or a keyword
> view dimer
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "move label"
> close #15
> 2dlabels text NADPH color gold size 26 xpos 0.5 ypos 0.5
> 2dlabels #15.1 xpos 0.400 ypos 0.483
> 2dlabels #15.1 xpos 0.421 ypos 0.483
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 185, in undo
inst.undo()
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 388, in undo
self._update_owner(owner, attribute, old_value, option)
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 426, in _update_owner
setattr(e, attribute, v)
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 243, in __setattr__
super(Drawing, self).__setattr__(key, value)
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 223, in _model_set_position
if pos != self.position:
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 445, in _drawing_get_position
return self._positions[0]
TypeError: 'NoneType' object is not subscriptable
undo failed: 'NoneType' object is not subscriptable:
TypeError: 'NoneType' object is not subscriptable
File
"/Applications/ChimeraX-1.0-rc-2020.05.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 445, in _drawing_get_position
return self._positions[0]
See log for complete Python traceback.
> close #15
> 2dlabels text NADPH color gold size 32 xpos 0.421 ypos 0.483
> 2dlabels #15 bold
Missing "bold" keyword's argument
> 2dlabels #15 bold true
> 2dlabels #15 size 36
> 2dlabels #15.1 xpos 0.400 ypos 0.470
> hide #15
> show #15
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.cxs
> includeMaps true
opened ChimeraX session
> show all
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> 2dlabels #15 visibility false
> lighting full
> movie record supersample 1
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test.mp4 quality
> low
Movie saved to /Users/hcnguyen/.../movies/test.mp4
> show all
executed chimeraX_testing.cxc
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> 2dlabels #15 visibility false
> lighting full
> movie record supersample 1
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> crossfade 10
> hide #7,12
> 2dlabels #15 visibility true frames 30
> wait 30
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test.mp4 quality
> low
Movie saved to /Users/hcnguyen/.../movies/test.mp4
> show all
executed chimeraX_testing.cxc
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!12 models
> ui mousemode right "move label"
> 2dlabels #15.1 xpos 0.380 ypos 0.372
> 2dlabels #15.1 xpos 0.399 ypos 0.398
> 2dlabels #15.1 xpos 0.396 ypos 0.394
> view dimer
> 2dlabels #15 xpos 0.4 ypos 0.47
> 2dlabels #15 xpos 0.4 ypos 0.47 size 38
> 2dlabels #15.1 xpos 0.415 ypos 0.474
> close #15
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> lighting full
> movie record supersample 1
> view exterior
> wait 40
> crossfade 10
> hide #7,12
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> visibility true
> wait 30
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test.mp4 quality
> low
Movie saved to /Users/hcnguyen/.../movies/test.mp4
> show all
executed chimeraX_testing.cxc
> view slice_through
Expected an objects specifier or a view name or a keyword
> view slicethrough
> view dimer
> hide #!7 models
> hide #!9 models
> show #!9 models
> hide #!12 models
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> lighting full
> movie record supersample 1
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior
> wait 40
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 10
> hide #7,12
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> visibility true
> wait 30
> crossfade 10
> hide #8-9
> 2dlabels #15 visibility false
> wait 20
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test.mp4 quality
> low
Movie saved to /Users/hcnguyen/.../movies/test.mp4
> show all
executed chimeraX_testing.cxc
> close #15
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> lighting full
> movie record supersample 1
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 20
> view exterior
> wait 20
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 30
> wait 40
> crossfade 10
> hide #7,12
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> visibility true
> wait 30
> crossfade 10
> hide #8-9
> 2dlabels #15 visibility false
> wait 20
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test.mp4 quality
> low
Movie saved to /Users/hcnguyen/.../movies/test.mp4
> show all
executed chimeraX_testing.cxc
> hide #!7 models
> hide #!12 models
> ui mousemode right "move label"
> 2dlabels #15.1 xpos 0.365 ypos 0.722
> 2dlabels #15 visibility true
> 2dlabels #15.1 xpos 0.398 ypos 0.746
> 2dlabels #15.1 xpos 0.389 ypos 0.739
> 2dlabels #15.1 xpos 0.379 ypos 0.738
> 2dlabels #15.1 xpos 0.468 ypos 0.230
> 2dlabels #15.1 xpos 0.489 ypos 0.231
> 2dlabels #15.1 xpos 0.498 ypos 0.233
> 2dlabels #15 color cyan
> close #15
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> lighting full
> movie record supersample 1
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 30
> wait 40
> crossfade 10
> hide #7,12
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> visibility true frames 20
> wait 30
> crossfade 10
> hide #8-9
> 2dlabels #15 visibility false
> 2dlabels text Pchlide color cyan size 40 xpos 0.379 ypos 0.738 bold true
> visibility true frames 20
> 2dlabels text Pchlide color cyan size 40 xpos 0.498 ypos 0.223 bold true
> visibility true frames 20
> wait 30
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test.mp4 quality
> low
Movie saved to /Users/hcnguyen/.../movies/test.mp4
> show all
executed chimeraX_testing.cxc
> hide #!7 models
> hide #!12 models
> 2dlabels #15.3 xpos 0.499 ypos 0.235
> 2dlabels all visibility false
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_overall_movie.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> 2dlabels all visibility false
> lighting full
> movie record supersample 3
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #7,12
> 2dlabels #15 visibility true frames 90
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> visibility true frames 80
> wait 90
> crossfade 30
> hide #8-9
> 2dlabels #15 visibility false
> 2dlabels text Pchlide color cyan size 40 xpos 0.379 ypos 0.738 bold true
> visibility true frames 40
> 2dlabels text Pchlide color cyan size 40 xpos 0.499 ypos 0.235 bold true
> visibility true frames 40
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie_fulllight_labels.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie_fulllight_labels.mp4
> show all
executed script_overall_movie.cxc
> close #15.1-6
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> 2dlabels text Pchlide color cyan size 40 xpos 0.379 ypos 0.738 bold true
> 2dlabels text Pchlide color cyan size 40 xpos 0.499 ypos 0.235 bold true
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.cxs
> includeMaps true
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/chimeraX_testing.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> 2dlabels all visibility false
> lighting full
> movie record supersample 1
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #7,12
> 2dlabels #15.1 visibility true frames 80
> wait 90
> crossfade 30
> hide #8-9
> 2dlabels #15.1 visibility false
> 2dlabels #15.2 visibility true frames 40
> 2dlabels #15.3 visibility true frames 40
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test_labels.mp4
> quality low
Movie saved to /Users/hcnguyen/.../movies/test_labels.mp4
executed chimeraX_testing.cxc
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/script_overall_movie.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 5
> show all
> 2dlabels all visibility false
> lighting full
> movie record supersample 3
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #7,12
> 2dlabels #15.1 visibility true frames 60
> wait 90
> crossfade 30
> hide #8-9
> 2dlabels #15.1 visibility false
> 2dlabels #15.2 visibility true frames 40
> 2dlabels #15.3 visibility true frames 30
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie_fulllight_labels.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/overall_movie_fulllight_labels.mp4
> show all
executed script_overall_movie.cxc
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/overall_movie.cxs
opened ChimeraX session
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/maps/job773_bf97_local_helical.mrc
Opened job773_bf97_local_helical.mrc, grid size 384,384,384, pixel 1.11, shown
at level 0.00577, step 2, values float32
> hide #!15 models
> view list
Named views: dimer, exterior, mem_insert, slicethrough, topdown
> hide #!8 models
> hide #!9 models
> hide #!7 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!1 models
> hide #!2 models
> hide #!12 models
> volume #16 step 1
> surface dust #16 size 8
> lighting simple
> lighting simple
> show #!1 models
> hide #!1 models
> close #1
> show #!2 models
> hide #!2 models
> show #!2 models
> volume mask #16 surfaces #2 newMap true
Expected a keyword
> volume mask #16 surfaces #2
> hide #!11 models
> hide #!2 models
> hide #!10 models
> view #!1 clip false
No displayed objects specified.
> volume #1 level 0.003075
> show #!2 models
> hide #!2 models
> volume #1 level 0.00304
> hide #!1 models
> volume #1 level 0.00302
> volume #16 level 0.005714
> volume #16 level 0.005
> volume #16 level 0.004
> volume #1 level 9.546e-05
> close #1
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!2 models
> close #2-9,12
> rename #16 id #1
> rename #1 id #16
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_mid.cif
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_top.cif
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_bottom.cif
Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_mid.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_top.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_bottom.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for strand1_mid.cif #1
---
Chain | Description
A DA HA I LA Q V Z | No description available
Chain information for strand1_top.cif #2
---
Chain | Description
A DA E I M Q V Z | No description available
Chain information for strand1_bottom.cif #3
---
Chain | Description
DA E M Q V Z | No description available
> hide atoms
> show cartoons
> volume mask #16 nearAtoms #1-3 newMap true
Expected a keyword
> volume zone #16 nearAtoms #1-3 newMap true
> close #1-3
> rename #16 id #1
> rename #4 id #2
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/central_protomer_2.pdb
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/central_protomer_1.pdb
Chain information for central_protomer_2.pdb #3
---
Chain | Description
A | No description available
Chain information for central_protomer_1.pdb #4
---
Chain | Description
A | No description available
> select #4/A:332
22 atoms, 21 bonds, 1 model selected
> select up
267 atoms, 273 bonds, 1 model selected
> select up
4934 atoms, 4991 bonds, 1 model selected
> select up
9868 atoms, 9982 bonds, 14 models selected
> select down
4934 atoms, 4991 bonds, 1 model selected
> set bgColor black
> select clear
> select up
356 atoms, 358 bonds, 1 model selected
> select up
4934 atoms, 4991 bonds, 1 model selected
> select down
356 atoms, 358 bonds, 1 model selected
> select up
4934 atoms, 4991 bonds, 1 model selected
> select down
356 atoms, 358 bonds, 1 model selected
> select up
4934 atoms, 4991 bonds, 1 model selected
> select clear
> select up
162 atoms, 161 bonds, 1 model selected
> select up
4934 atoms, 4991 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select down
4933 atoms, 4990 bonds, 1 model selected
> select clear
> select clear
> select #4/A:500@N9A
1 atom, 1 model selected
> select clear
> select #4/A:500@PN
1 atom, 1 model selected
> select up
96 atoms, 104 bonds, 2 models selected
> volume zone #1 nearAtoms sele newMap True
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #1 nearAtoms sel newMap true
> rename #2 otherstrand
> rename #5 NADPHs
> hide #!5 models
> select clear
> select up
3 atoms, 1 bond, 2 models selected
> select up
90 atoms, 98 bonds, 2 models selected
> volume zone #1 nearAtoms sel newMap true
> rename #6 PMRs
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> select clear
> select up
229 atoms, 230 bonds, 1 model selected
> select up
4934 atoms, 4991 bonds, 1 model selected
> select down
229 atoms, 230 bonds, 1 model selected
> hide #!6 models
> select #4/A:600@MG
1 atom, 1 model selected
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> set bgColor white
> hide #!14 models
> hide #!13 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!14 models
> show #!13 models
> volume #13 level 0.001548
> volume #14 level 0.00145
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #4
4934 atoms, 4991 bonds, 2 pseudobonds, 2 models selected
> show #!3 models
> show #!4 models
> select clear
> select ::name="LMG"::name="NDP"::name="PMR"
232 atoms, 248 bonds, 4 pseudobonds, 4 models selected
> select ~sel
9636 atoms, 9734 bonds, 28 models selected
> ~select #2
9636 atoms, 9734 bonds, 24 models selected
> ~select #1
9636 atoms, 9734 bonds, 20 models selected
> ~select #5
9636 atoms, 9734 bonds, 18 models selected
> ~select #6
9636 atoms, 9734 bonds, 16 models selected
> ~select #10
9636 atoms, 9734 bonds, 13 models selected
> ~select #11
9636 atoms, 9734 bonds, 10 models selected
> ~select #13
9636 atoms, 9734 bonds, 8 models selected
> ~select #14
9636 atoms, 9734 bonds, 6 models selected
> ~select #15
9636 atoms, 9734 bonds, 2 models selected
> select #3
4934 atoms, 4991 bonds, 2 pseudobonds, 2 models selected
> set bgColor black
> select clear
> select #3/A:700@O3
1 atom, 1 model selected
> select up
9 atoms, 3 bonds, 2 models selected
> select up
232 atoms, 248 bonds, 2 models selected
> delete atoms sel
> delete bonds sel
> select clear
> select #3/A:108
19 atoms, 18 bonds, 1 model selected
> show #!2 models
> select clear
> select #3/A:373
20 atoms, 20 bonds, 1 model selected
> select up
46 atoms, 46 bonds, 1 model selected
> select up
4818 atoms, 4867 bonds, 1 model selected
> volume zone #1 nearAtoms sel
> volume unzone #1
> show #!1 models
> hide #!1 models
> volume zone #1 nearAtoms sel newMap true
> select clear
> select #4/A:381
10 atoms, 9 bonds, 1 model selected
> select up
36 atoms, 35 bonds, 1 model selected
> select up
4818 atoms, 4867 bonds, 1 model selected
> volume zone #1 nearAtoms sel newMap true
> close #3-4
> rename #7 top_protomer id #3
> rename #8 bottom_protomer id #4
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> hide #!3 models
> hide #!4 models
> hide #!2 models
> hide #!13 models
> hide #!14 models
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/Fig1_filament/membrane/loophelix_membrane.pdb
Chain information for loophelix_membrane.pdb #7
---
Chain | Description
E G | No description available
> select up
7 atoms, 3 bonds, 1 model selected
> select up
136 atoms, 144 bonds, 1 model selected
> delete atoms sel
> delete bonds sel
> select /G:328
7 atoms, 7 bonds, 1 model selected
> select up
124 atoms, 130 bonds, 1 model selected
> select up
283 atoms, 292 bonds, 1 model selected
> select up
566 atoms, 584 bonds, 1 model selected
> select down
283 atoms, 292 bonds, 1 model selected
> volume zone #1 nearAtoms sel newMap true
> select clear
> close #8
> show #!1 models
> hide #!1 models
> ui tool show "Fit in Map"
Fit molecule loophelix_membrane.pdb (#7) to map job773_bf97_local_helical.mrc
(#1) using 566 atoms
average map value = 0.00445, steps = 64
shifted from previous position = 1.38
rotated from previous position = 0.407 degrees
atoms outside contour = 242, contour level = 0.004
Position of loophelix_membrane.pdb (#7) relative to
job773_bf97_local_helical.mrc (#1) coordinates:
Matrix rotation and translation
0.99997995 -0.00058905 0.00630480 -1.33501561
0.00056865 0.99999460 0.00323802 -1.00669435
-0.00630667 -0.00323437 0.99997488 0.56426087
Axis -0.45507934 0.88672265 0.08139862
Axis point 91.64438703 0.00000000 229.30212847
Rotation angle (degrees) 0.40744989
Shift along axis -0.23919061
Fit molecule loophelix_membrane.pdb (#7) to map job773_bf97_local_helical.mrc
(#1) using 566 atoms
average map value = 0.004449, steps = 60
shifted from previous position = 0.0166
rotated from previous position = 0.0381 degrees
atoms outside contour = 245, contour level = 0.004
Position of loophelix_membrane.pdb (#7) relative to
job773_bf97_local_helical.mrc (#1) coordinates:
Matrix rotation and translation
0.99998236 -0.00031442 0.00593064 -1.33077894
0.00029805 0.99999615 0.00276033 -0.85887589
-0.00593148 -0.00275852 0.99997860 0.36201021
Axis -0.42136881 0.90568294 0.04676259
Axis point 61.74889279 0.00000000 238.79778490
Rotation angle (degrees) 0.37521631
Shift along axis -0.20019196
Fit molecule loophelix_membrane.pdb (#7) to map job773_bf97_local_helical.mrc
(#1) using 566 atoms
average map value = 0.00445, steps = 48
shifted from previous position = 0.0183
rotated from previous position = 0.0409 degrees
atoms outside contour = 244, contour level = 0.004
Position of loophelix_membrane.pdb (#7) relative to
job773_bf97_local_helical.mrc (#1) coordinates:
Matrix rotation and translation
0.99997937 -0.00054340 0.00640096 -1.36784906
0.00052263 0.99999459 0.00324671 -1.00026454
-0.00640269 -0.00324330 0.99997424 0.58394163
Axis -0.45088020 0.88950670 0.07405998
Axis point 92.93422392 0.00000000 230.17810304
Rotation angle (degrees) 0.41236412
Shift along axis -0.22975924
Fit molecule loophelix_membrane.pdb (#7) to map job773_bf97_local_helical.mrc
(#1) using 566 atoms
average map value = 0.00445, steps = 48
shifted from previous position = 0.00646
rotated from previous position = 0.0059 degrees
atoms outside contour = 245, contour level = 0.004
Position of loophelix_membrane.pdb (#7) relative to
job773_bf97_local_helical.mrc (#1) coordinates:
Matrix rotation and translation
0.99997944 -0.00046220 0.00639568 -1.38715055
0.00044104 0.99999443 0.00330943 -0.99870587
-0.00639718 -0.00330654 0.99997407 0.60584037
Axis -0.45846597 0.88650506 0.06259179
Axis point 95.83171120 0.00000000 232.35604157
Rotation angle (degrees) 0.41341168
Shift along axis -0.21147584
> show #!1 models
> view sel
> volume zone #1 nearAtoms sel newMap true
> view list
Named views: dimer, exterior, mem_insert, slicethrough, topdown
> view dimer
> volume #2 level 0.002953
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!4 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.000994
> close #8
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!7 models
> select clear
> select clear
> select /E:327
11 atoms, 11 bonds, 1 model selected
> select up
124 atoms, 130 bonds, 1 model selected
> select up
283 atoms, 292 bonds, 1 model selected
> volume zone #1 nearAtoms sel newMap true
> select clear
> select up
2 atoms, 1 bond, 1 model selected
> select up
10 atoms, 10 bonds, 1 model selected
> select up
73 atoms, 74 bonds, 1 model selected
> select up
283 atoms, 292 bonds, 1 model selected
> volume zone #1 nearAtoms sel newMap true
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #7
> show #!15 models
> show #!5 models
> show #!6 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> volume subtract #1 #2-6
volume subtract operation requires exactly two volumes
> rename #8 loophelix_top
> rename #9 loophelix_bottom
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_mid.cif
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_top.cif
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_bottom.cif
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/central_protomer_2.pdb
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/central_protomer_1.pdb
Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_mid.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_top.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/strand1_bottom.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for strand1_mid.cif #7
---
Chain | Description
A DA HA I LA Q V Z | No description available
Chain information for strand1_top.cif #12
---
Chain | Description
A DA E I M Q V Z | No description available
Chain information for strand1_bottom.cif #16
---
Chain | Description
DA E M Q V Z | No description available
Chain information for central_protomer_2.pdb #17
---
Chain | Description
A | No description available
Chain information for central_protomer_1.pdb #18
---
Chain | Description
A | No description available
> hide atoms
> show cartoons
> volume zone #1 nearAtoms #7,12,16-18 invert true
volume zone command currently does not support invert True with newMap False
> volume zone #1 nearAtoms #7,12,16-18 invert true newMap true
> hide #!19 models
> close #1
> show #!19 models
> rename #19 id #1
> rename #1 remainingstrands
> set bgColor white
> surface dust all size 8
> close #7,12,16-18
> 2dlabels all visibility false
> rename #3 protomer_B
> rename #4 protomer_A
> hide #!3 models
> hide #!4 models
> rename #8 loophelix_A
> rename #9 loophelix_B
> view topdown
> surface dust all size 10
> show all
> 2dlabels all visibility false
> view topdown
> view exterior
> view dimer
> view slicethrough
> view dimer
> hide #3,4
> volume #5 level 0.005
> volume #4 level 0.0035
> volume #4 level 0.004
> volume #14 level 0.00155
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> show #!3 models
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/script_sharpened_overall_movie.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 10
> show all
> 2dlabels all visibility false
> lighting full
> movie record supersample 3
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #3,4
> 2dlabels #15.1 visibility true frames 60
> wait 90
> crossfade 30
> hide #5
> 2dlabels #15.1 visibility false
> 2dlabels #15.2 visibility true frames 40
> 2dlabels #15.3 visibility true frames 30
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_movie_fulllight_labels.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/sharpened_movie_fulllight_labels.mp4
> show all
executed script_sharpened_overall_movie.cxc
> show #15.1 models
> hide #!8 models
> show #!8 models
> hide #!3 models
> hide #!4 models
> hide #15.1 models
> show #15.1 models
> show #15.1 models
> volume #2 level 0.004
> volume #4 level 0.005
> volume #3 level 0.005
> volume #8 level 0.005
> volume #9 level 0.005
> volume #1 level 0.005
> close #15.1-3
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!13 models
> hide #!14 models
> hide #!1 models
> hide #!2 models
> close #7
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> close #7
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold false
> close #7
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
opened ChimeraX session
> 2dlabels text NADPH color gold size 40 xpos 0.415 ypos 0.474 bold true
> 2dlabels text Pchlide color cyan size 40 xpos 0.379 ypos 0.738 bold true
> 2dlabels text Pchlide color cyan size 40 xpos 0.499 ypos 0.235 bold true
> view exterior
> show #!1 models
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> view dimer
> show #!3 models
> show #!4 models
> move y 10
> move y -10
> view dimer
> view dimer
> move y 1
> move y 4
> move y -10
> view dimer
> show #!5 models
> view dimer
> hide #!4 models
> hide #!3 models
> select #2
2 models selected
> select #3
2 models selected
> select #4
2 models selected
> select #5
2 models selected
> select #2
2 models selected
> view list
Named views: dimer, exterior, mem_insert, slicethrough, topdown
> view slicethrough
> show #!3 models
> show #!4 models
> view dimer
> show #!2 models
> hide #!3 models
> hide #!4 models
> show #!6 models
> view dimer
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/script_sharpened_overall_movie.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 10
> show all
> 2dlabels all visibility false
> lighting full
> movie record supersample 3
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #3,4
> 2dlabels #7.1 visibility true frames 60
> wait 90
> crossfade 30
> hide #5
> 2dlabels #7.1 visibility false
> 2dlabels #7.2 visibility true frames 40
> 2dlabels #7.3 visibility true frames 30
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_movie_fulllight_labels.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/sharpened_movie_fulllight_labels.mp4
> show all
executed script_sharpened_overall_movie.cxc
> select clear
> set bgColor white
> lighting simple
> hide #!1 models
> hide #!2 models
> hide all
> show #7.1 models
> hide #!7 models
> hide #7.1 models
> show #!5 models
> show #!3 models
> show #!4 models
> show #3-5
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/central_protomer_1_apo.pdb
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/central_protomer_2_apo.pdb
Chain information for central_protomer_1_apo.pdb #12
---
Chain | Description
A | No description available
Chain information for central_protomer_2_apo.pdb #15
---
Chain | Description
A | No description available
> hide #12 models
> show #12 models
> volume zone #4 nearAtoms #12
> volume zone #3 nearAtoms #15
> hide #12 models
> hide #15 models
> hide dust #3-4 size 10
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> surface dust #3-4 size 10
> hide #!5 models
> show #!5 models
> volume subtract #3 #5
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume subtract #4 #5
> close #3-4
> close #12,15
> show #!8 models
> show #8
> volume dust #16-17 size 10
Expected a density maps specifier or a keyword
> surface dust #16-17 size 10
> rename #16 protomer_A
> rename #16 #3
No name or id option specified for renaming
> rename #16 id #3
> rename #17 protomer_B
> rename #17 id #4
> select clear
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> view dimer
> show #!1 models
> show #!2 models
> show all
> hide all
> show #3,4,6
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume mask #3 #6 invertMask true
Missing required "surfaces" argument
> volume mask #3 surfaces #6 invertMask true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/maskcommand.py", line 44, in mask
fill_overlap, extend, model_id)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py", line 96, in masked_volume
volume)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py", line 157, in
surface_projection_coordinates
varray = tfrs.transform_points(vertices)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 136, in transform_points
cxyz = xyz.copy()
AttributeError: 'NoneType' object has no attribute 'copy'
AttributeError: 'NoneType' object has no attribute 'copy'
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 136, in transform_points
cxyz = xyz.copy()
See log for complete Python traceback.
> volume mask #3 surfaces #6 invertMask true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/maskcommand.py", line 44, in mask
fill_overlap, extend, model_id)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py", line 96, in masked_volume
volume)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mask/depthmask.py", line 157, in
surface_projection_coordinates
varray = tfrs.transform_points(vertices)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 136, in transform_points
cxyz = xyz.copy()
AttributeError: 'NoneType' object has no attribute 'copy'
AttributeError: 'NoneType' object has no attribute 'copy'
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 136, in transform_points
cxyz = xyz.copy()
See log for complete Python traceback.
> volume substract #3 #6
Expected a density maps specifier or a keyword
> volume subtract #3 #6
> volume subtract #4 #6
> surface dust all size 10
> close #3-4
> view dimer
> rename #15 protomer_A
> rename #12 protomer_B
> rename #12 id #4
> rename #15 id #3
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #8
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie.cxs
> open
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/script_sharpened_overall_movie.cxc
> surface dust #1-12 size 5
> camera ortho
> surface dust all size 10
> show all
> 2dlabels all visibility false
> lighting full
> movie record supersample 3
> view topdown
> wait
wait requires a frame count argument unless motion is in progress
> wait 40
> view exterior frames 90
> wait 110
> turn z -2 frames 180 coordinateSystem #1
> wait 220
> view exterior
> wait
wait requires a frame count argument unless motion is in progress
> wait 5
> view dimer frames 60
> wait 70
> view slicethrough frames 90
> wait 100
> view dimer frames 90
> wait 100
> crossfade 60
> hide #3,4
> 2dlabels #7.1 visibility true frames 60
> wait 90
> crossfade 30
> hide #5
> 2dlabels #7.1 visibility false
> 2dlabels #7.2 visibility true frames 40
> 2dlabels #7.3 visibility true frames 30
> wait 90
> movie encode
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_movie_fulllight_labels.mp4
> quality high
Movie saved to /Users/hcnguyen/.../movies/sharpened_movie_fulllight_labels.mp4
> show all
executed script_sharpened_overall_movie.cxc
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/sharpened_overall_movie/sharpened_overall_movie_withmaps.cxs
> includeMaps true
opened ChimeraX session
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!13 models
> hide #!14 models
> view topdown
> set bgColor black
> volume #10 level 8e-05
> volume #10 level 0.0001
> volume #10 level 0.001
> volume #10 level 0.0005
> volume #10 level 0.0007
> volume #10 level 0.002
> volume #10 level 0.005
> volume #10 level 0.001
> volume #10 level 0.0005
> hide #7.2 models
> lighting simple
> hide #7.3 models
> 2dlabels text "inner leaflet" color gray size 40 xpos 0.499 ypos 0.235 bold
> true
> select #7.4
1 model selected
> ui mousemode right "move label"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 252, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 632, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 632, in size
w,h = self._window_size
See log for complete Python traceback.
> ui mousemode right label
> label delete residues
> label delete residues
> label delete residues
> ui mousemode right "translate selected models"
> ui mousemode right "move label"
> select #7
5 models selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 252, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 632, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 632, in size
w,h = self._window_size
See log for complete Python traceback.
> ~select #7.4
4 models selected
> select #7.4
1 model selected
> close #7.4
> 2dlabels text "inner leaflet" color gray size 40 xpos 0.499 ypos 0.235 bold
> true
> close #7.4
> 2dlabels text "inner leaflet" color gray size 40 xpos 0.8 ypos 0.235 bold
> true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 252, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 632, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 632, in size
w,h = self._window_size
See log for complete Python traceback.
> save
> /Users/hcnguyen/Documents/Frost_Lab/POR/POR_Figures/movies/test_membrane_label.cxs
opened ChimeraX session
> close #7.4
> show #!1 models
> 2dlabels text "inner leaflet" color gray size 32 xpos 0.672 ypos 0.840 bold
> true
> close #7.4
> 2dlabels text "inner leaflet" color gray size 40 xpos 0.672 ypos 0.840 bold
> true
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
> select #7.4
1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
> select #7
5 models selected
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 635, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 535, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/movelabel.py", line 28, in mouse_down
self._label = label = label_under_window_position(self.session, x, y)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 262, in label_under_window_position
lw,lh = lbl.drawing.size
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
TypeError: cannot unpack non-iterable NoneType object
TypeError: cannot unpack non-iterable NoneType object
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 648, in size
w,h = self._window_size
See log for complete Python traceback.
> close #7.1-3
> 2dlabels #7.4 xpos 0.733 ypos 0.873
OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro10,1
Processor Name: Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
Boot ROM Version: 261.0.0.0.0
SMC Version (system): 2.3f36
Software:
System Software Overview:
System Version: macOS 10.13.6 (17G13035)
Kernel Version: Darwin 17.7.0
Time since boot: 11 days 3:17
Graphics/Displays:
Intel HD Graphics 4000:
Chipset Model: Intel HD Graphics 4000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0166
Revision ID: 0x0009
Automatic Graphics Switching: Supported
gMux Version: 3.2.19 [3.2.8]
Metal: Supported, feature set macOS GPUFamily1 v3
NVIDIA GeForce GT 650M:
Chipset Model: NVIDIA GeForce GT 650M
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Dynamic, Max): 1024 MB
Vendor: NVIDIA (0x10de)
Device ID: 0x0fd5
Revision ID: 0x00a2
ROM Revision: 3688
Automatic Graphics Switching: Supported
gMux Version: 3.2.19 [3.2.8]
Metal: Supported, feature set macOS GPUFamily1 v3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
2217:
Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus)
UI Looks like: 1680 x 1050 @ 60 Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: P148CHA003927
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple Mini DisplayPort To VGA Adapter
Automatically Adjust Brightness: No
Adapter Firmware Version: 1.03
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.0
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.2
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.dev202008010351
ChimeraX-CoreFormats: 1.0
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
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: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.2
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.5
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 47.3.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 4.3.3
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Label position asked for before label drawn (and various other errors) |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
comment:3 by , 5 years ago
There was an earlier traceback in the log "undo failed: 'NoneType' object is not subscriptable" from undoing the move of a model that had since been closed. That error was in the previous session with a May 2020 version of ChimeraX and has been fixed.
There was a third traceback in the log resulting from command "volume mask #3 surfaces #6 invertMask true". This was caused by surface #6 being empty. It appears that #6 was a volume and it had no surface probably because it had not been shown and the surface is only computed when it is shown. Fixed the error when masking to an empty surface.
Note:
See TracTickets
for help on using tickets.
Fixed.
The mouse mode for moving a 2D label gave an error when some label has been created but was never displayed. Initialization of window position was done when first displayed. Mouse mode incorrectly looked at undisplayed labels.