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Opened 12 months ago
Closed 8 months ago
#16164 closed defect (fixed)
ui view fourup: volume_viewer is None
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.9.dev202410220943 (2024-10-22 09:43:07 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9.dev202410220943 (2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/Fig3e-lipid.cxs
Opened emd_24252.map as #2, grid size 232,232,232, pixel 0.86, shown at level
1.65, step 1, values float32
Opened emd_24252.map copy as #4, grid size 232,232,232, pixel 0.86, shown at
level 5, step 1, values float32
Log from Tue Oct 22 18:06:10 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/3c-oct22.cxs
Log from Tue Oct 22 13:44:04 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/3c-oct22.cxs
Log from Tue Oct 22 13:05:33 2024UCSF ChimeraX version: 1.9.dev202410220943
(2024-10-22)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/Figure3c.cxs
Log from Fri Oct 18 14:51:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-session-oct17.cxs
Opened emd_24252.map as #2, grid size 232,232,232, pixel 0.86, shown at level
6.01, step 1, values float32
Log from Thu Oct 17 14:36:58 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residuesalias caps_off surface cap
> false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse command "mousemode alt right contour ;
> mousemode right clip ; mousemode alt left 'translate selected models' ;
> mousemode shift left 'rotate selected models' ; mousemode alt control left
> 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript //Users/aysenur/chimerax_startup.py
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7n98 fromDatabase pdb format mmcif
7n98 title:
Cryo-EM structure of MFSD2A [more info...]
Chain information for 7n98 #1
---
Chain | Description | UniProt
A | Sodium-dependent lysophosphatidylcholine symporter 1 | NLS1_MOUSE 1-534
> alias rainbow_rosie rainbow $1 palette
> #03256C:#277da1:#577590:#4d908e:#43aa8b:#90be6d:#f9c74f:#F9A64C:#F9844A:#F96347:#f94144:#9a031e
> rainbow_rosie #1
> open /Users/aysenur/Documents/PostDoc-Files/Manuscripts/MFSD2A_Review/Files-
> from-pdb/emd_24252.map
Opened emd_24252.map as #2, grid size 232,232,232, pixel 0.86, shown at level
3.37, step 1, values float32
> alias rainbow_rosie_map lighting soft; lighting multiShadow 512; show $1
> cartoons; hide $1 atoms; hide $1 surfaces; rainbow_rosie $1; volume $2 level
> $3; color zone $2 near $1 distance $4; surface zone $2 nearAtoms $1 distance
> $4 maxComponents $5
> alias rainbow_rosie_map #2
> volume #2 level 7.094
> volume #2 level 8.091
> volume #2 level 8.545
> volume #2 level 8.817
> volume #2 level 8.908
> fitmap #1 inMap #2
Fit molecule 7n98 (#1) to map emd_24252.map (#2) using 3625 atoms
average map value = 10.12, steps = 28
shifted from previous position = 0.0181
rotated from previous position = 0.0221 degrees
atoms outside contour = 1622, contour level = 8.9077
Position of 7n98 (#1) relative to emd_24252.map (#2) coordinates:
Matrix rotation and translation
0.99999993 -0.00033146 0.00018585 0.02421015
0.00033145 0.99999994 0.00006877 -0.03700841
-0.00018587 -0.00006871 0.99999998 0.01048885
Axis -0.17799526 0.48128046 0.85830461
Axis point 92.62022242 65.97631266 0.00000000
Rotation angle (degrees) 0.02212605
Shift along axis -0.01311809
> lighting soft
> lighting multiShadow 512
> hide #!2 models
> undo
> lighting full
> hide #!2 models
> show #!2 models
> lighting default
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume zone #2 nearAtoms #1/A range 2.5
> volume zone #2 nearAtoms #1/A range 2.2
> volume zone #2 nearAtoms #1/A range 2
> volume zone #2 nearAtoms #1/A range 2.5
[Repeated 1 time(s)]
> surface zone #2 nearAtoms #1/A distance 2.5 maxComponents 7
> color zone #2 near #1 distance 2.5
> hide #!2 models
> show #!2 models
> transparency #2 50
> coulombic protein surfaces #2 key true
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A :211
/A :217
/A :218
/A :219
/A :223
/A :224
/A :225
/A :226
/A :227
/A :228
/A :229
/A :231
/A :232
/A :233
/A :234
/A :235
/A :269
/A :270
/A :271
/A :272
/A :273
/A :274
/A :275
/A :276
/A :277
/A :278
/A :279
/A :281
/A :282
/A :283
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for surface #2.1: minimum, -8715.24, mean -4.44, maximum
1543.61
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> key border false
> key borderWidth 1.0
> key borderWidth 0.0
> key borderWidth 1.0
> key red-white-blue :-10 :0 :10
> ui mousemode right clip
> transparency #2 60
> transparency #2 50
> transparency #2 20
> transparency #2 30
> transparency #2 40
> hide #!2 models
> hide #3 models
No help found for 'help:user/commands/savepng.html'
> show #!2 models
> transparency #2 70
> transparency #2 45
> transparency #2 35
> transparency #2 40
> save /Users/aysenur/Desktop/myimage.png format png width 2048
> transparentBackground true
> transparency #2 0
> transparency #2 10
> transparency #2 20
> transparency #2 30
> save /Users/aysenur/Desktop/7n98electrostatic3.png format png width 2048
> transparentBackground true
> turn y 180
> undo
> turn y 180
> undo
> turn y 180
> save /Users/aysenur/Desktop/7n98electrostatic3y180.png format png width 2048
> transparentBackground true
> hide #!2 models
> show #!2 models
> undo
[Repeated 2 time(s)]
> hide #!2 models
> save /Users/aysenur/Desktop/7n98rainbowrosieribbon.png format png width 2048
> transparentBackground true
> show #!2 models
> hide #!2 target m
> show #!2 target m
> hide #1 target m
> turn x 90
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select :36-277
1776 atoms, 1823 bonds, 239 residues, 1 model selected
> cartoon hide sel
> surface hidePatches sel
> cartoon sel
> select add #1
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> select add #2
2 models selected
> show #1 models
> select subtract #2
Nothing selected
> transparency #2 0
> turn y 90
> turn x 90
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> undo
[Repeated 5 time(s)]
> hide #!2 models
> turn x 90
> undo
> turn x 90
> turn y 90
> undo
[Repeated 1 time(s)]
> turn y 90
> show #!2 models
> turn y 90
> turn x 90
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #1
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> select /A
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> hide #!2 models
> open /Users/aysenur/Documents/PostDoc-Files/Manuscripts/MFSD2A_Review/Files-
> from-pdb/7n98.pdb1
7n98.pdb1 title:
Cryo-em structure of MFSD2A [more info...]
Chain information for 7n98.pdb1 #4
---
Chain | Description
A | No description available
> hide #1 models
> select add #4
7250 atoms, 7452 bonds, 946 residues, 2 models selected
> select subtract #1
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> select #4/A
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> select ligand
Nothing selected
> surface #4
> select ligand
Nothing selected
> surface hidePatches #4
> hide #!4 models
> show #!2 models
> select ligand
Nothing selected
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #1
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> ui mousemode right label
> label #1/A:342
> label #1/A:338
> label #1/A:336
> label #1/A:335
> label #1/A:207
> label #1/A:204
> label #1/A:203
> label #1/A:202
> ui mousemode right select
> select clear
> select #1/A:335
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> show sel target ab
> select #1/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:203
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:202
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show #!2 models
> volume style surface
> volume hide
> volume show
> color zone #2 near #1 distance 5.16
Drag select of 2 residues, 2 emd_24252.map
> select clear
> volume #2 level 3.919
> volume #2 level 6.005
> undo
> select clear
> volume zone #2 nearAtoms #1/A range 2.5
> surface zone #2 nearAtoms #1/A distance 2.5 maxComponents 7
> volume #2 level 6.64
> hide #!2 models
> surface #1
> volume #2 level 2.377
> hide #!2 models
> volume #2 level 4.1
> select add #1
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> volume #2 level 6.277
> hide #!1 models
> select subtract #1
1 model selected
> volume #2 level 6.005
> hide #!2 models
> show #!1 models
> surface style #1 solid
> surface style #1 mesh
> select add #1
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> color sel bychain
> color sel byhetero
> hide sel surfaces
> show sel surfaces
> select subtract #1
1 model selected
> rainbow_rosie #1
> hide #!1 surfaces
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/7n98-session-oct17.cxs
——— End of log from Thu Oct 17 14:36:58 2024 ———
opened ChimeraX session
> ui mousemode right label
> label #1/A:203
[Repeated 1 time(s)]
> label #1/A:204
> label #1/A:81
[Repeated 3 time(s)]
> label #1/A:203
[Repeated 2 time(s)]
> label #1/A:252
> label delete residues
> alias select_Ndom select #1:39-278
> alias select_Cdom select #1:279-511
> select_Ndom
1781 atoms, 1828 bonds, 240 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> color sel cadet blue
> color sel steel blue
> color sel light slate gray
> color sel dark cyan
> color sel light sea green
> color sel royal blue
> color sel steel blue
> color sel cadet blue
> color sel steel blue
> select_Cdom
1844 atoms, 1896 bonds, 233 residues, 1 model selected
> color sel sandy brown
> ui mousemode right select
> select clear
> graphics silhouettes true
> hide #1.2 models
> show #1.2 models
> hide #!1 models
> show #!4 models
> select add #4
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> select subtract #4
1 model selected
> select add #4
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> graphics silhouettes false
> graphics silhouettes true
> lighting default
> lighting multiShadow 512
> ui mousemode right select
> select clear
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> alias select_disulfide #1:216,464
> alias select_disulfide select #1:216,464
> select_disulfide
12 atoms, 11 bonds, 2 residues, 1 model selected
> show atoms
> undo
> show sel atoms
> color sel pink
> ui tool show "Color Actions"
> color sel hot pink
> color sel dark violet
> color sel medium orchid
> color sel medium purple
> color sel pale violet red
> color sel light coral
> color sel violet
> color sel light pink
> color sel magenta
> color sel dark violet
> color sel medium slate blue
> color sel indigo
> color sel maroon
> color sel green yellow
> color sel chartreuse
> color sel medium spring green
> color sel cyan
> color sel rosy brown
> color sel magenta
> color sel dark violet
> color sel blue violet
> color sel medium orchid
> color sel orchid
> color sel pale violet red
> color sel violet
> color sel plum
> color sel deep pink
> color sel dark violet
> color sel blue violet
> color sel orchid
> color (#!1 & sel) byhetero
> select clear
> select #1/A:202@CB
1 atom, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> select #1/A:202@CG2
1 atom, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> select #1/A:202@OG1
1 atom, 1 residue, 1 model selected
> hide (#!1 & sel) target a
> select clear
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-twocolor-version.png format
> png width 2048 transparentBackground true
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/Figure3a.cxs
> turn x 90
> undo
> turn x 270
> undo
> turn x 90
> undo
> turn x 45
> undo
> turn x 70
> undo
> close #4
> close #2
> show #3 models
> hide #3 models
> close #3
> select #1
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> surface (#!1 & sel)
> coulombic sel
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/Figure3c.cxs
——— End of log from Fri Oct 18 14:51:32 2024 ———
opened ChimeraX session
> select add #1
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> select add #1.2
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> select add #1.2
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> select add #1.2
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> hide #!1.2 models
> view orient
> view
> view orient
[Repeated 1 time(s)]
> view
> ui tool show "Side View"
> show #1.2 models
> open 7n98
7n98 title:
Cryo-EM structure of MFSD2A [more info...]
Chain information for 7n98 #2
---
Chain | Description | UniProt
A | Sodium-dependent lysophosphatidylcholine symporter 1 | NLS1_MOUSE 1-534
> hide #!1 models
> hide #1.2 models
> surface #2
> select add #2
7250 atoms, 7452 bonds, 946 residues, 3 models selected
> clip front 0 position :ola
Invalid "position" argument: Center argument no objects specified
> clip front 0 position
Missing "position" keyword's argument
> close #2
> show #!1 models
> show #1.2 models
> color #1.2.1 #9f7f66eb
> color #1.2.1 #9f7f66af
> color #1.2.1 grey
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbf94
> color #1.2.1 #bfbfbfb1
> ui mousemode right select
> select clear
> hide #!1 models
> show #!1 models
> color #1.2.1 #858585ff
> color #1.2.1 #858585b0
> color #1.2.1 #858585bb
> hide #!1.2 models
> ui tool show "Side View"
> show #1.2 models
> color #1.2.1 #858585ff
> color #1.2.1 #858585cb
[Repeated 1 time(s)]
> ui mousemode right clip
> hide #!1.2 models
> show #1.2 models
> color #1.2.1 #858585ff
> color #1.2.1 #85858599
> color #1.2.1 #858585b3
> color #1.2.1 #858585cc
> ui mousemode right select
> select clear
> select add #1.2
3625 atoms, 473 residues, 2 models selected
> red-white-blue range -10,10
Unknown command: palette red-white-blue range -10,10
> redblue range -10,10
Unknown command: palette redblue range -10,10
>
Incomplete command: palette
> range
Unknown command: palette range
> rainbow
Unknown command: palette rainbow
> select subtract #1.2.1
3625 atoms, 473 residues, 2 models selected
> select add #1.2.1
3625 atoms, 473 residues, 3 models selected
> select subtract #1.2.1
3625 atoms, 473 residues, 2 models selected
> select add #1.2.1
3625 atoms, 473 residues, 3 models selected
> select subtract #1.2.1
3625 atoms, 473 residues, 2 models selected
> select add #1.2
3625 atoms, 473 residues, 3 models selected
> select add #1
3625 atoms, 3726 bonds, 473 residues, 3 models selected
> select subtract #1
1 model selected
> select add #1.2
3625 atoms, 473 residues, 2 models selected
> select subtract #1.2.1
3625 atoms, 473 residues, 2 models selected
> coulombic
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
> select add #1.2
3625 atoms, 473 residues, 3 models selected
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbfcc
> select clear
> select /A
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> hide #1.2.1 models
> show #1.2.1 models
> select add #1
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> select subtract #1
1 model selected
> hide #!1.2 models
> show #1.2 models
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbfe6
> select clear
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-electrostatic.png format
> png width 2048 transparentBackground true
> turn #1 y 180
Expected an axis vector or a keyword
> turn y 180
> hide #!1.2 models
> show #1.2 models
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbfe6
> turn y 180
[Repeated 1 time(s)]
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-electrostatic.png format
> png width 2048 transparentBackground true
> hide #!1.2 models
> show #1.2 models
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbfe6
> turn y 20
> undo
> turn y 340
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-electrostatic2.png format
> png width 2048 transparentBackground true
> color #1.2.1 #bfbfbfcc
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-electrostatic3.png format
> png width 2048 transparentBackground true
> ui tool show "Surface Color"
> select add #1.2
3625 atoms, 473 residues, 2 models selected
> color radial #1.2 palette -5,#ff0000:0,#ffffff:5,#0000ff
> color radial #1.2 palette -10,#ff0000:0,#ffffff:10,#0000ff center
> 100.41,96.934,103.41
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> key red-white-blue :-10 :0 :10
> ui mousemode right select
No map chosen for coloring
[Repeated 2 time(s)]
> hide #1.2.1 models
> show #1.2.1 models
> select subtract #1.2.1
3625 atoms, 473 residues, 2 models selected
> select add #1.2.1
3625 atoms, 473 residues, 3 models selected
> coulombic sel
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbfcc
> hide #2 models
> close #2
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/3c-oct22.cxs
——— End of log from Tue Oct 22 13:05:33 2024 ———
opened ChimeraX session
> coulombic sel
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color #1 #bfbfbfff
> coulombic sel
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color #1.2 #bfbfbfff
> color #1 #c9c9c9ff
> select add #1
3625 atoms, 3726 bonds, 473 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1.2
3625 atoms, 473 residues, 2 models selected
> coulombic sel
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color #1.2.1 #bfbfbfff
> ui mousemode right select
> select clear
> hide #!1.2 models
> ui tool show "Side View"
> select_Ndom
1781 atoms, 1828 bonds, 240 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sandy brown
> select_Cdom
1844 atoms, 1896 bonds, 233 residues, 1 model selected
> color sel steel blue
> graphics silhouettes false
> graphics silhouettes true
> select clear
> select_Cdom
1844 atoms, 1896 bonds, 233 residues, 1 model selected
> color sel sandy brown
> select_Ndom
1781 atoms, 1828 bonds, 240 residues, 1 model selected
> color sel steel blue
> select clear
> alias TM select #1:329-358
> alias TM8 select #1:329-358
> TM8
264 atoms, 273 bonds, 30 residues, 1 model selected
> select clear
> show #1.2 models
> select add #1.2
3625 atoms, 473 residues, 2 models selected
> coulombic sel
Coulombic values for 7n98_A SES surface #1.2: minimum, -29.14, mean -0.41,
maximum 13.77
To also show corresponding color key, enter the above coulombic command and
add key true
> color #1.2.1 #bfbfbfff
> color #1.2.1 #bfbfbf00
> TM8
264 atoms, 273 bonds, 30 residues, 1 model selected
> hide #1.2.1 models
> show #1.2.1 models
> color #1.2.1 #bfbfbfcc
> select clear
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/7n98-electrostatic-top-view.png
> format png width 2048 transparentBackground true
> TM8
264 atoms, 273 bonds, 30 residues, 1 model selected
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/3c-oct22.cxs
——— End of log from Tue Oct 22 13:44:04 2024 ———
opened ChimeraX session
> ui tool show "Side View"
> hide #!1.2 models
> ui mousemode right select
> select clear
> open /Users/aysenur/Documents/PostDoc-Files/Manuscripts/MFSD2A_Review/Files-
> from-pdb/emd_24252.map
Opened emd_24252.map as #2, grid size 232,232,232, pixel 0.86, shown at level
3.37, step 1, values float32
> volume #2 level 5.914
> volume #2 style mesh
> volume #2 level 3.647
> volume #2 level 8.363
> volume #2 level 7.638
> volume #2 level 5.733
> volume #2 style surface
> volume #2 step 2
> volume #2 step 4
> volume #2 step 2
> volume #2 step 1
> volume #2 level 16.25
> volume #2 level 7
> ui mousemode right "map eraser"
> volume erase #2 center 96.024,86.939,95.015 radius 13.417 outside true
Opened emd_24252.map copy as #4, grid size 232,232,232, pixel 0.86, shown at
step 1, values float32
> ui mousemode right translate
> hide #3 models
> volume #4 level 6.086
> volume #4 level 4.757
> volume #2 level 1.648
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #4 level 6.419
> volume #4 level 8
> volume #4 level 9
> volume #4 level 0.6108
> volume #4 level 1
> volume #4 level 3
> volume #4 level 4
> volume #4 level 5
> volume #4 level 6
> volume #4 level 5
> ui tool show "Segment Map"
Segmenting emd_24252.map copy, density threshold 5.000000
Showing 3 region surfaces
66 watershed regions, grouped to 3 regions
Showing emd_24252 copy.seg - 3 regions, 3 surfaces
> ui mousemode right select
> select #5.2
1 model selected
> select #4
2 models selected
> ui mousemode right translate
> ui mousemode right select
> select #4
2 models selected
> select #5.1
1 model selected
> select #5.1
1 model selected
> select #4
2 models selected
Select one or more regions to delete
> select #5.1
1 model selected
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/Fig3e-lipid.cxs
——— End of log from Tue Oct 22 18:06:10 2024 ———
opened ChimeraX session
Showing emd_24252 copy.seg - 3 regions, 3 surfaces
> ui mousemode right select
> select #5.3
1 model selected
> select #5.2
1 model selected
> select #4
2 models selected
> select #5.3
1 model selected
Segmenting emd_24252.map copy, density threshold 5.000000
Showing 3 region surfaces
66 watershed regions, grouped to 3 regions
Showing emd_24252 copy.seg - 3 regions, 3 surfaces
> select #3.2
1 model selected
> select #3.3
1 model selected
> select #4
2 models selected
> select #3.1
1 model selected
Segmenting emd_24252.map copy, density threshold 5.000000
Showing 3 region surfaces
66 watershed regions, grouped to 3 regions
Showing emd_24252 copy.seg - 3 regions, 3 surfaces
> hide #!4 models
> hide #3.3 models
> hide #3.2 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> ui mousemode right translate
> ui mousemode right select
> select #3.1
1 model selected
Segmenting emd_24252.map copy, density threshold 5.000000
Showing 3 region surfaces
66 watershed regions, grouped to 3 regions
Showing emd_24252 copy.seg - 3 regions, 3 surfaces
> hide #3.3 models
> hide #3.2 models
> select #3.1
1 model selected
> select #3.1
1 model selected
> select clear
> select #3.1
1 model selected
Ungrouped to 3 regions
> select #3.6
1 model selected
> select #3.4
1 model selected
> select #3.5
1 model selected
> select #3.4
1 model selected
Ungrouped to 6 regions
> select #3.9
1 model selected
> select #3.10
1 model selected
> select #3.8
1 model selected
> select #3.1
1 model selected
> select #3.7
1 model selected
> select #3.11
1 model selected
Ungrouped to 11 regions
> select #3.4
1 model selected
> select #3.12
1 model selected
> select #3.14
1 model selected
> select #3.13
1 model selected
> select #3.20
1 model selected
> select #3.16
1 model selected
> select #3.15
1 model selected
> select :202,335
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #:202,335
Expected an objects specifier or a keyword
> select #1:202,335
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/A:202,335
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> close #3
> show #!4 models
> hide #!4 models
> close #4
> show #!2 models
> hide #!2 models
> ui mousemode right translate
> select #1/A:202,335
15 atoms, 13 bonds, 2 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium orchid
> color (#!1 & sel) byhetero
> ui mousemode right select
> select clear
> show #!2 models
> volume #2 level 4
> volume #2 level 6
> ui mousemode right "map eraser"
> volume erase #2 center 99.265,98.471,95.005 radius 31.684 outside true
Opened emd_24252.map copy as #4, grid size 232,232,232, pixel 0.86, shown at
step 1, values float32
> matchmaker #2 to #1
No molecules/chains to match specified
> fitmap #2 inMap map #1
Invalid "inMap" argument: invalid density map specifier
Must specify one map, got 0
Must specify one map, got 0
Must specify one map, got 0
> fitmap #1 inMap #2
Fit molecule 7n98 (#1) to map emd_24252.map (#2) using 3625 atoms
average map value = 10.12, steps = 28
shifted from previous position = 0.00149
rotated from previous position = 0.0234 degrees
atoms outside contour = 956, contour level = 6
Position of 7n98 (#1) relative to emd_24252.map (#2) coordinates:
Matrix rotation and translation
0.99999997 -0.00020394 -0.00011062 0.04198597
0.00020397 0.99999993 0.00032003 -0.05135780
0.00011055 -0.00032006 0.99999994 0.00524849
Axis -0.80964473 -0.27975470 0.51595805
Axis point 0.00000000 43.64058740 175.27427230
Rotation angle (degrees) 0.02264856
Shift along axis -0.01691813
> volume erase #4 center 96.935,101.62,95.447 radius 15.463 outside true
> hide #3 models
> close #4
> show #!2 models
> fitmap #1 inMap #2
Fit molecule 7n98 (#1) to map emd_24252.map (#2) using 3625 atoms
average map value = 10.12, steps = 40
shifted from previous position = 0.00529
rotated from previous position = 0.00151 degrees
atoms outside contour = 954, contour level = 6
Position of 7n98 (#1) relative to emd_24252.map (#2) coordinates:
Matrix rotation and translation
0.99999997 -0.00021085 -0.00008982 0.03743141
0.00021088 0.99999993 0.00030538 -0.04994366
0.00008976 -0.00030540 0.99999995 0.01009362
Axis -0.79981183 -0.23516741 0.55226562
Axis point 0.00000000 55.84106121 173.27727482
Rotation angle (degrees) 0.02187688
Shift along axis -0.01261861
> show #3 models
> volume erase #2 center 117.86,101.42,61.281 radius 19.852
Opened emd_24252.map copy as #4, grid size 232,232,232, pixel 0.86, shown at
step 1, values float32
> volume erase #4 center 81.899,102.02,119.38 radius 19.852
> hide #3 models
> hide #2.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #3 models
> hide #3 models
> ui tool show "Side View"
> view
Segmenting emd_24252.map, density threshold 6.000000
Only showing 60 of 86 regions.
Showing 60 of 86 region surfaces
743 watershed regions, grouped to 86 regions
Showing emd_24252.seg - 86 regions, 60 surfaces
> ui mousemode right select
> select #5.54
1 model selected
> select #5.19
1 model selected
> select #5.41
1 model selected
Drag select of 1138, 8721 of 9144 triangles, 1120, 7038 of 8752 triangles,
1142, 5097 of 8008 triangles, 1136, 5070 of 7464 triangles, 1131, 1965 of 6704
triangles, 1139, 5613 of 7796 triangles, 1141, 2193 of 6644 triangles, 1125,
3023 of 7268 triangles, 1117, 2472 of 7752 triangles, 1075, 2542 of 5444
triangles, 1108, 2067 of 5260 triangles, 1127, 5318 of 5340 triangles, 1002,
909 of 4192 triangles, 1049, 699 of 4512 triangles, 1124, 55 of 3964
triangles, 1079, 3610 of 3892 triangles, 1126, 5087 of 5228 triangles, 920,
2555 of 3684 triangles, 1024, 1059, 1140, 3613 of 3752 triangles, 146
residues, 4 emd_24252.map copy
> select clear
Drag select of 1138, 8990 of 9144 triangles, 1120, 4215 of 8752 triangles,
1115, 510 of 8248 triangles, 1142, 2535 of 8008 triangles, 1136, 1131, 820 of
6704 triangles, 1139, 3129 of 7796 triangles, 1141, 4610 of 6644 triangles,
1125, 4117 of 7268 triangles, 1117, 4687 of 7752 triangles, 1075, 1108, 98 of
5260 triangles, 1127, 5288 of 5340 triangles, 1002, 3463 of 4192 triangles,
1049, 489 of 4512 triangles, 1119, 7005 of 8612 triangles, 1079, 459 of 3892
triangles, 1126, 5125 of 5228 triangles, 920, 3288 of 3684 triangles, 1024,
1679 of 2592 triangles, 1059, 1140, 376 of 3752 triangles, 135 residues, 4
emd_24252.map copy
Drag select of 1128, 7680 of 12736 triangles, 1122, 7525 of 9012 triangles,
1083, 1123, 1893 of 8664 triangles, 1110, 1414 of 7712 triangles, 1053, 1333
of 7656 triangles, 1104, 51 of 5876 triangles, 1114, 3813 of 5708 triangles,
910, 227 of 4800 triangles, 1109, 4748 of 4996 triangles, 948, 1134, 1116,
1132, 1433 of 2992 triangles, 3 atoms, 25 residues, 3 bonds, 4 emd_24252.map
copy
> select #4
2 models selected
> hide #!4 models
> select #5.44
1 model selected
> select #5.45
1 model selected
> select #5.15
1 model selected
> select #5.50
1 model selected
> select #5.19
1 model selected
> select #5.42
1 model selected
> select #5.38
1 model selected
> select #5.10
1 model selected
> select #5.56
1 model selected
> select #5.18
1 model selected
> select #5.32
1 model selected
> hide #!5 models
> show #!5 models
> select #5.49
1 model selected
> select #5.7
1 model selected
> select #5.59
1 model selected
> select #5.37
1 model selected
> select #5.42
1 model selected
> select #5.55
1 model selected
> select #5.15
1 model selected
> select #5.18
1 model selected
> select #5.43
1 model selected
> select #5.35
1 model selected
> select #5.22
1 model selected
> select #5.40
1 model selected
> select #5.53
1 model selected
> select #5.48
1 model selected
> select #5.54
1 model selected
Ungrouped to 3 regions, but did not show all surfaces, see Options
> show #5.15 models
> hide #5.15 models
> show #5.34 models
> hide #5.34 models
> show #5.56 models
> hide #5.56 models
> show #5.6 models
> hide #5.6 models
> select clear
> select #5.62
1 model selected
Grouped 1 regions
> undo
> select clear
> select #5.61
1 model selected
> select #5.54
1 model selected
> close #4
> close #5
> show #!2 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #2.1 models
> select #3
1 model selected
> ui mousemode right "map eraser"
> show #2.1 models
> volume erase #2 center 111.57,107.68,96.341 radius 11.971 outside true
Opened emd_24252.map copy as #4, grid size 232,232,232, pixel 0.86, shown at
step 1, values float32
> volume erase #4 center 106.29,112.19,87.203 radius 4.988
> hide #3 models
> view orient
> view
[Repeated 1 time(s)]
> ui mousemode right select
> select #4
2 models selected
Segmenting emd_24252.map, density threshold 6.000000
Only showing 60 of 86 regions.
Showing 60 of 86 region surfaces
743 watershed regions, grouped to 86 regions
Showing emd_24252.seg - 86 regions, 60 surfaces
Drag select of 1132, 1124, 6960 of 8752 triangles, 1110, 3088 of 8248
triangles, 1120, 5986 of 8008 triangles, 1117, 637 of 7608 triangles, 1135,
7077 of 7464 triangles, 1123, 5791 of 6704 triangles, 1125, 7385 of 7796
triangles, 1136, 277 of 6304 triangles, 1122, 4482 of 6644 triangles, 1113,
6797 of 7268 triangles, 1133, 4051 of 7752 triangles, 1042, 1140, 5202 of 5260
triangles, 1119, 931, 3995 of 4192 triangles, 1031, 2712 of 4512 triangles,
1114, 7596 of 8612 triangles, 1056, 1112, 1013, 995, 644 of 3512 triangles,
1102, 79 of 4376 triangles, 1062, 1290 of 3012 triangles, 1130, 28 of 4300
triangles, 946, 1104, 1137, 3506 of 3752 triangles, 205 residues
> select #5.8
1 model selected
Drag select of 1132, 8379 of 9144 triangles, 1124, 2330 of 8752 triangles,
1110, 242 of 8248 triangles, 1120, 3038 of 8008 triangles, 1135, 6525 of 7464
triangles, 1123, 1825 of 6704 triangles, 1125, 5112 of 7796 triangles, 1122,
2183 of 6644 triangles, 1113, 4890 of 7268 triangles, 1133, 912 of 7752
triangles, 1042, 1140, 2634 of 5260 triangles, 1119, 931, 1983 of 4192
triangles, 1114, 4279 of 8612 triangles, 1056, 2412 of 3892 triangles, 1112,
5121 of 5228 triangles, 1013, 3359 of 3684 triangles, 946, 1104, 1137, 1153 of
3752 triangles, 139 residues
> select #5.44
1 model selected
> select #5.16
1 model selected
Drag select of 1118, 7021 of 12736 triangles, 1109, 5613 of 9012 triangles,
1065, 6129 of 9144 triangles, 1127, 4982 of 4996 triangles, 967, 339 of 2900
triangles, 1107, 1134, 4 residues
Drag select of 1111, 1896 of 7904 triangles, 1129, 4986 of 8664 triangles,
1099, 79 of 6792 triangles, 1108, 3645 of 5672 triangles, 1115, 50 of 5708
triangles, 916, 1102 of 3388 triangles, 1128, 5136 of 5224 triangles, 25
residues
Drag select of 1136, 1116, 1959 of 6704 triangles, 1069, 4124 of 5876
triangles, 917, 1460 of 4800 triangles, 929, 3156 of 3672 triangles, 995, 54
of 3512 triangles, 1102, 306 of 4376 triangles, 1062, 2638 of 3012 triangles,
1082, 139 of 3288 triangles, 1131, 1088, 839, 1415 of 2012 triangles, 1098,
1849 of 1892 triangles, 1138, 89 of 2992 triangles, 92 residues, 4
emd_24252.map copy
> select clear
> select #5.59
1 model selected
> select #5.38
1 model selected
> select #5.41
1 model selected
> select #5.15
1 model selected
> select #5.32
1 model selected
> select #5.14
1 model selected
> select /A:348
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.30
1 model selected
> select clear
> select #5.30
1 model selected
> select #5.48
1 model selected
> select #5.7
1 model selected
> select clear
> select #5.7
1 model selected
> select #5.50
1 model selected
> select #5.45
1 model selected
> select #5.19
1 model selected
> select #5.23
1 model selected
> select #5.53
1 model selected
> select #5.37
1 model selected
> select #5.40
1 model selected
> select #5.43
1 model selected
> select #5.56
1 model selected
> select #4
2 models selected
> select clear
> select #4
2 models selected
> select clear
> select #5.55
1 model selected
> select #4
2 models selected
> select #5.19
1 model selected
> select #5.60
1 model selected
> select #5.25
1 model selected
> select #4
2 models selected
Ungrouped to 92 regions, but did not show all surfaces, see Options
> select #5.73
1 model selected
> select add #5
94 models selected
> select #4
2 models selected
> select #4
2 models selected
Ungrouped to 207 regions, but did not show all surfaces, see Options
> hide #!5 models
> select /A:317
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4
2 models selected
Segmenting emd_24252.map copy, density threshold 6.000000
Showing 2 region surfaces
42 watershed regions, grouped to 2 regions
Showing emd_24252 copy.seg - 2 regions, 2 surfaces
> select #5.1
1 model selected
Ungrouped to 4 regions
> select #5.5
1 model selected
> select #4
2 models selected
> select #5.4
1 model selected
> select #5.3
1 model selected
> select #5.6
1 model selected
> select #4
2 models selected
> select #5.2
1 model selected
> select #4
2 models selected
> select subtract #4
Nothing selected
> select add #5.6
1 model selected
Ungrouped to 4 regions
> select #5.7
1 model selected
> select #4
2 models selected
> select #5.8
1 model selected
> select #5.9
1 model selected
> select #4
2 models selected
> select add #5.7
3 models selected
Ungrouped to 2 regions
> select #5.10
1 model selected
> select #4
2 models selected
> select add #5.1
3 models selected
> select subtract #5.1
2 models selected
> select add #5
12 models selected
Ungrouped to 17 regions
> select #5.22
1 model selected
> select #4
2 models selected
> select #5.13
1 model selected
> select #5.11
1 model selected
Drag select of 10, 14 of 844 triangles, 1 residues
> select #5.20
1 model selected
> select #5.15
1 model selected
> select #4
2 models selected
> select #5.17
1 model selected
> select #5.18
1 model selected
> select #5.7
1 model selected
> select #5.21
1 model selected
> select #4
2 models selected
> select #4
2 models selected
> select #5.6
1 model selected
> select clear
> select #4
2 models selected
> select add #5
22 models selected
> select subtract #5.6
21 models selected
> select subtract #4
19 models selected
> select add #5
20 models selected
> select clear
> select #4
2 models selected
Ungrouped to 17 regions
> select #5.8
1 model selected
> select #5.35
1 model selected
> select #5.33
1 model selected
> select #5.35
1 model selected
> select #4
2 models selected
> select #5.9
1 model selected
> select #5.28
1 model selected
> select #5.23
1 model selected
> select #5.5
1 model selected
> select #5.36
1 model selected
> select #4
2 models selected
> select clear
[Repeated 1 time(s)]
> select #4
2 models selected
Ungrouped to 21 regions
> select #5.41
1 model selected
> select #5.21
1 model selected
> select #5.51
1 model selected
> select #4
2 models selected
> select #5.40
1 model selected
> select #5.34
1 model selected
> select #5.2
1 model selected
> select #5.16
1 model selected
> select #5.38
1 model selected
> select #4
2 models selected
> select #5.18
1 model selected
> select #5.37
1 model selected
> select #4
2 models selected
> select clear
> select #4
2 models selected
Ungrouped to 0 regions
> select clear
> select #4
2 models selected
Ungrouped to 0 regions
> select #5.48
1 model selected
> select #5.1
1 model selected
> select #4
2 models selected
Select one or more regions to delete
> select #5.39
1 model selected
> select #5.3
1 model selected
> select #5.17
1 model selected
> select #4
2 models selected
> select #5.12
1 model selected
> select #4
2 models selected
Ungrouped to 0 regions
> ui mousemode right translate
> ui mousemode right select
> select clear
> select #4
2 models selected
> select #5.46
1 model selected
> select #5.10
1 model selected
> select #5.22
1 model selected
> select #4
2 models selected
> select #5.42
1 model selected
> select #5.43
1 model selected
> select #5.49
1 model selected
> select #5.48
1 model selected
> select #5.50
1 model selected
> select #4
2 models selected
> select #4
2 models selected
> select clear
> select #4
2 models selected
> select #5.47
1 model selected
> select #4
2 models selected
Ungrouped to 0 regions
> select add #5.32
3 models selected
> select subtract #5.32
2 models selected
> select add #5.32
3 models selected
> select subtract #5.32
2 models selected
> select add #5.31
3 models selected
> select subtract #5.31
2 models selected
> select clear
> select add #5.32
1 model selected
> select subtract #5.32
Nothing selected
> select add #5.25
1 model selected
> select subtract #5.25
Nothing selected
> select add #5.6
1 model selected
> select subtract #5.6
Nothing selected
> select #4
2 models selected
> select #5.44
1 model selected
> select #4
2 models selected
> select #4
2 models selected
Ungrouped to 0 regions
> select #5.30
1 model selected
> select #4
2 models selected
Ungrouped to 0 regions
Segmenting emd_24252.map copy, density threshold 6.000000
Showing 2 region surfaces
42 watershed regions, grouped to 2 regions
Showing emd_24252 copy.seg - 2 regions, 2 surfaces
> select #5.1
1 model selected
Ungrouped to 4 regions
> select #5.4
1 model selected
> select #4
2 models selected
> select #5.2
1 model selected
> select #5.5
1 model selected
> select #5.3
1 model selected
> hide #!5 models
> hide #!4 models
> show #!5 models
> select #5.6
1 model selected
Ungrouped to 4 regions
> select #5.1
1 model selected
> select #5.8
1 model selected
> select #5.3
1 model selected
Ungrouped to 3 regions
> select #5.10
1 model selected
> select #5.11
1 model selected
> select #5.8
1 model selected
> select #5.9
1 model selected
> select #5.7
1 model selected
Ungrouped to 4 regions
> select #5.13
1 model selected
> select #5.3
1 model selected
> select #5.14
1 model selected
> select #5.9
1 model selected
> select #5.6
1 model selected
> select #5.12
1 model selected
> select #5.6
1 model selected
> select add #5.12
2 models selected
> select add #5.9
3 models selected
Grouped 3 regions
Ungrouped to 3 regions
> select #5.7
1 model selected
Ungrouped to 2 regions
> select #5.15
1 model selected
Ungrouped to 0 regions
> select #5.6
1 model selected
> select #5.9
1 model selected
Ungrouped to 0 regions
> select add #5.12
1 model selected
> select add #5.9
2 models selected
> select add #5.6
3 models selected
> select add #5.15
4 models selected
Grouped 4 regions
> select clear
> save /Users/aysenur/Documents/PostDoc-
> Files/Manuscripts/MFSD2A_Review/Figures/OFS/Fig3e-lipid.cxs
> ui mousemode right translate
> select #1/A:329-358
264 atoms, 273 bonds, 30 residues, 1 model selected
> ui mousemode right select
> select clear
> select /A
3625 atoms, 3726 bonds, 473 residues, 1 model selected
> hide sel cartoons
> select #1/A:177-227
346 atoms, 347 bonds, 51 residues, 1 model selected
> show sel cartoons
> select #1/A:329-358
264 atoms, 273 bonds, 30 residues, 1 model selected
> show sel cartoons
> select clear
> view
> select #5.6
1 model selected
> view sel
> select clear
> ui tool show Segmentations
> ui view fourup
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1360, in
_surfaceChosen
self._add_axis_to_volume_viewer(volume_viewer, v)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1360, in
_surfaceChosen
self._add_axis_to_volume_viewer(volume_viewer, v)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1360, in
_surfaceChosen
self._add_axis_to_volume_viewer(volume_viewer, v)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view fourup
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1360, in
_surfaceChosen
self._add_axis_to_volume_viewer(volume_viewer, v)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1360, in
_surfaceChosen
self._add_axis_to_volume_viewer(volume_viewer, v)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1360, in
_surfaceChosen
self._add_axis_to_volume_viewer(volume_viewer, v)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
AttributeError: 'NoneType' object has no attribute 'thresholds_panel'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1406, in
_add_axis_to_volume_viewer
tp = volume_viewer.thresholds_panel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir9,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 51 minutes, 1 second
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a51
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.15
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.3.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9.dev202410220943
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.5
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2
ChimeraX-Label: 1.1.11
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.2.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.7
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.54.1
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.1
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ui view fourup: volume_viewer is None |
comment:2 by , 8 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
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This was fixed on November 12 2024 in commit 7423e418edcc6194e5fbb99552b1d0c008fedcf6 -- try the release or the 1.10 daily builds.