Bad silhouette edges

[sha4008@…]

The following bug report has been submitted:
Platform:        macOS-12.5-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Everytime I turn on Silhoutte on the surface of my pdb, i get black linesd all over inaddition to the border, I just want the border/outline. Can that be fixed?

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

Opened run_class001.mrc as #1, grid size 576,576,576, pixel 0.83, shown at
level 0.00778, step 1, values float32  
Log from Sat Aug 3 08:32:52 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

Opened run_class001.mrc as #1, grid size 576,576,576, pixel 0.83, shown at
level 0.00778, step 1, values float32  
Log from Fri Aug 2 18:15:39 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.cxs

Opened run_class001.mrc as #1, grid size 576,576,576, pixel 0.83, shown at
level 0.00852, step 1, values float32  
Opened run_class001.mrc as #3, grid size 576,576,576, pixel 0.83, shown at
level 0.00707, step 1, values float32  
Opened run_class001.mrc as #4, grid size 576,576,576, pixel 0.83, shown at
level 0.00623, step 1, values float32  
Log from Fri Aug 2 09:16:44 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.cxs

Opened run_class001.mrc as #1, grid size 576,576,576, pixel 0.83, shown at
level 0.00852, step 1, values float32  
Opened run_class001.mrc as #3, grid size 576,576,576, pixel 0.83, shown at
level 0.00624, step 1, values float32  
Log from Thu Aug 1 08:03:25 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/run_class001.mrc

Opened run_class001.mrc as #1, grid size 576,576,576, pixel 0.83, shown at
level 0.00426, step 4, values float32  

> set bgColor white

> volume #1 step 1

> open
> /Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/final/6v35onJ220-realspacerefine26-coot-5.pdb

Summary of feedback from opening
/Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/final/6v35onJ220-realspacerefine26-coot-5.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
22045 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 39 39 ALA H 2009 ALA H
2012 1 4  
Start residue of secondary structure not found: HELIX 40 40 SER H 2017 LEU H
2047 1 31  
Start residue of secondary structure not found: HELIX 41 41 GLU H 2104 THR H
2109 1 6  
Start residue of secondary structure not found: HELIX 42 42 ASN H 2123 LYS H
2138 1 16  
Start residue of secondary structure not found: HELIX 43 43 ILE H 2168 LYS H
2195 1 28  
39 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (2054 )  
Cannot find LINK/SSBOND residue CYS (2068 )  
Cannot find LINK/SSBOND residue CYS (2072 )  
Cannot find LINK/SSBOND residue CYS (2084 )  
Cannot find LINK/SSBOND residue CYS (2054 )  
11 messages similar to the above omitted  
  
Chain information for 6v35onJ220-realspacerefine26-coot-5.pdb #2  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> hide atoms

> show cartoons

> open
> /Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/run_class001.mrc

Opened run_class001.mrc as #3, grid size 576,576,576, pixel 0.83, shown at
level 0.00426, step 4, values float32  

> hide #!3 models

> volume #1 level 0.006022

> select #2/E,F,G,H

6200 atoms, 6356 bonds, 772 residues, 1 model selected  

> color sel cornflower blue

> hide #!1 models

> select #2/A,B,C,D

29237 atoms, 29940 bonds, 12 pseudobonds, 3657 residues, 2 models selected  

> color (#!2 & sel) dark gray

> select #2/E,F,G,H:24-43

208 atoms, 204 bonds, 32 residues, 1 model selected  

> color sel orange

> select clear

> show #!1 models

> color zone #1 near #2 distance 4.98

> volume #1 level 0.008225

> volume #1 level 0.008519

> volume #3 color #d6d6d6

> volume #3 color #d6d6d639

> volume #3 color #d6d6d638

> volume #3 step 1

> volume #3 level 0.006169

> select #2/E,F,G,H:24-43

208 atoms, 204 bonds, 32 residues, 1 model selected  

> ui tool show "Color Zone"

> color zone #3 near sel distance 4.98

> color zone #3 near sel distance 5.4

> color zone #3 near sel distance 3.69

[Repeated 1 time(s)]

> volume #3 color #ebebeb

> volume #3 color #d6d6d6

> volume #3 color #d6d6d638

> volume #3 level 0.006756

> color zone #3 near sel distance 3.69

> hide #!2 models

> ui tool show "Hide Dust"

> surface dust #3 size 4.98

> surface undust #3

> surface dust #3 size 3.45

> surface undust #3

> surface dust #3 size 1.93

> surface dust #3 size 1.87

> surface dust #3 size 1.51

[Repeated 1 time(s)]

> volume #3 level 0.006242

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.cxs

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.png
> width 3000 height 2230 supersample 4 transparentBackground true

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.cxs

——— End of log from Thu Aug 1 08:03:25 2024 ———

opened ChimeraX session  

> open
> /Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/run_class001.mrc

Opened run_class001.mrc as #4, grid size 576,576,576, pixel 0.83, shown at
level 0.00426, step 4, values float32  

> volume #4 step 1

> volume #4 level 0.005167

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 35212 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> volume #4 color #ffffff0a

> set silhouetteWidth 6.0

> show #!2 models

> select clear

> ui tool show "Color Zone"

> color zone #1 near #2 distance 4.98

> select #2/E,F,G,H:24-43

208 atoms, 204 bonds, 32 residues, 1 model selected  

> color zone #3 near sel distance 4.98

> select clear

> volume #4 level 0.00562

> volume #4 level 0.00615

> volume #3 level 0.007074

> set silhouetteWidth 1.0

> volume #4 level 0.006528

> volume #4 level 0.005847

> volume #4 level 0.006603

> set silhouetteWidth 6.0

> volume #4 level 0.006301

> volume #4 level 0.006452

> ui tool show "Hide Dust"

> surface dust #4 size 39.4

> surface dust #1 size 4.98

> hide #!2 models

> surface dust #3 size 1.51

> surface dust #3 size 1.53

> surface dust #3 size 2.21

> surface dust #3 size 2.1

> surface dust #3 size 11.56

> surface dust #4 size 43.49

> surface dust #4 size 26.91

> surface undust #4

> surface dust #4 size 26.91

> volume #4 level 0.006225

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.cxs

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.png
> width 3000 height 2672 supersample 4 transparentBackground true

> volume #4 level 0.006225

> set silhouetteWidth 8.0

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.png
> width 3000 height 2672 supersample 4 transparentBackground true

> set silhouetteWidth 6.0

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.png
> width 3000 height 2672 supersample 4 transparentBackground true

> surface dust #4 size 24.36

> surface dust #4 size 77.69

> surface dust #4 size 78.99

> surface dust #4 size 134.18

> surface dust #4 size 131.97

> surface dust #4 size 174.94

[Repeated 1 time(s)]

> surface dust #4 size 163.71

> surface dust #4 size 20.98

> volume #4 level 0.006225

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain2.png
> width 3000 height 2672 supersample 4 transparentBackground true

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/inactivatingchain.cxs

——— End of log from Fri Aug 2 09:16:44 2024 ———

opened ChimeraX session  

> close #3

> close #4

> graphics silhouettes false

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> open
> /Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/final/6v35onJ220-realspacerefine26-coot-6.pdb

Summary of feedback from opening
/Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/final/6v35onJ220-realspacerefine26-coot-6.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
22129 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 39 39 ALA H 2009 ALA H
2012 1 4  
Start residue of secondary structure not found: HELIX 40 40 SER H 2017 LEU H
2047 1 31  
Start residue of secondary structure not found: HELIX 41 41 GLU H 2104 THR H
2109 1 6  
Start residue of secondary structure not found: HELIX 42 42 ASN H 2123 LYS H
2138 1 16  
Start residue of secondary structure not found: HELIX 43 43 ILE H 2168 LYS H
2195 1 28  
39 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (2054 )  
Cannot find LINK/SSBOND residue CYS (2068 )  
Cannot find LINK/SSBOND residue CYS (2072 )  
Cannot find LINK/SSBOND residue CYS (2084 )  
Cannot find LINK/SSBOND residue CYS (2054 )  
11 messages similar to the above omitted  
  
Chain information for 6v35onJ220-realspacerefine26-coot-6.pdb #3  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> hide #!2 models

> show #!3 cartoons

> hide #!3 atoms

> close #2

> select #3/A,B,C,D

29237 atoms, 29932 bonds, 20 pseudobonds, 3657 residues, 2 models selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> color (#!3 & sel) dark gray

> select #3/E,F,G,H

6200 atoms, 6356 bonds, 772 residues, 1 model selected  

> color sel cornflower blue

> select #3/E,F,G,H:24-43

208 atoms, 204 bonds, 32 residues, 1 model selected  

> color sel orange

> select clear

> cartoon style #3 modeHelix tube sides 20

> show #!1 models

> color zone #1 near #3 distance 4.98

> volume #1 level 0.007785

> hide #!1 models

> select #3/A:328-336

75 atoms, 76 bonds, 9 residues, 1 model selected  

> select #3/A:328-336

75 atoms, 76 bonds, 9 residues, 1 model selected  

> color sel hot pink

> color sel magenta

> select #3/B:384-390

55 atoms, 54 bonds, 7 residues, 1 model selected  

> color sel forest green

> cartoon style thickness 1.0

> show #!1 models

> color zone #1 near sel & #3 distance 4.98

[Repeated 1 time(s)]

> select clear

> color zone #1 near #3 distance 4.98

> transparency 70

> ui tool show "Side View"

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/sideclosed.png
> width 3000 height 2097 supersample 4 transparentBackground true

[Repeated 1 time(s)]

> volume #1 color #ffffff1f

> volume #1 color #ffffff1b

> volume #1 color #ffffff35

> volume #1 color #ffffff36

> volume #1 color #ffffff7d

> transparency 80

> color zone #1 near #3 distance 4.98

> hide #!1 models

> surface #3

> ui tool show "Surface Zone"

> select #3/B:384-390

55 atoms, 54 bonds, 7 residues, 1 model selected  

> color (#!3 & sel) forest green

> select #3/A:328-336

75 atoms, 76 bonds, 9 residues, 1 model selected  

> color (#!3 & sel) magenta

> transparency (#!3 & sel) 70

> select clear

> transparency #3 70

> transparency #3 60

> transparency #3 40

> select #3/E,F,G,H:24-43

208 atoms, 204 bonds, 32 residues, 1 model selected  

> color (#!3 & sel) orange

> select clear

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/sideclosed.png
> width 3000 height 2097 supersample 4 transparentBackground true

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/sideclosed2.png
> width 3000 height 2097 supersample 4 transparentBackground true

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

——— End of log from Fri Aug 2 18:15:39 2024 ———

opened ChimeraX session  

> transparency #3 30

> transparency #3 90

> transparency #3 70

> dssp

[Repeated 1 time(s)]

> surface hidePatches #3

> select #3/A:300-328

226 atoms, 231 bonds, 29 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel rosy brown

> select #3/A,B,C,D:338-1056

19996 atoms, 20404 bonds, 8 pseudobonds, 2536 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel pale green

> select #3/B:384-390

55 atoms, 54 bonds, 7 residues, 1 model selected  

> select #3/A,B,C,D:338-1056

19996 atoms, 20404 bonds, 8 pseudobonds, 2536 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light green

> color (#!3 & sel) light sea green

> select clear

> select #3/B:384-390

55 atoms, 54 bonds, 7 residues, 1 model selected  

> color (#!3 & sel) forest green

> select #3/A,B,C,D:338-1056

19996 atoms, 20404 bonds, 8 pseudobonds, 2536 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel misty rose

> select #3/B:384-390

55 atoms, 54 bonds, 7 residues, 1 model selected  

> color (#!3 & sel) forest green

> select clear

> surface #3

> transparency #3 50

> transparency #3 60

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 641, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 147, in write  
self._f.write(buf)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write  
self._fp.write(compressed)  
OSError: [Errno 28] No space left on device  
  
OSError: [Errno 28] No space left on device  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write  
self._fp.write(compressed)  
  
See log for complete Python traceback.  
  
Cannot save
'/Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs':
[Errno 28] No space left on device  

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

——— End of log from Sat Aug 3 08:32:52 2024 ———

opened ChimeraX session  

> select #3/A,B,C,D:338-1056

19996 atoms, 20404 bonds, 8 pseudobonds, 2536 residues, 2 models selected  

> color (#!3 & sel) light gray

> select #3/B:384-390

55 atoms, 54 bonds, 7 residues, 1 model selected  

> color (#!3 & sel) forest green

> select clear

> transparency #3 50

> transparency #3 30

> transparency #3 70

> graphics silhouettes true color black width 5.5 depthJump 0.2

> surface style #3 mesh

> surface style #3 solid

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/sideclosed2.png
> width 3000 height 2097 supersample 4 transparentBackground true

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/side.cxs

> graphics silhouettes true color black width 5.5 depthJump 0.1

> graphics silhouettes true color black width 5.5 depthJump 0.4

> graphics silhouettes true color black width 5.5 depthJump 0.6

> graphics silhouettes true color black width 5.5 depthJump 0.3

> graphics silhouettes true color black width 5.5 depthJump 0.05

> transparency #3 90

> graphics silhouettes true color white width 5.5 depthJump 0.05

> graphics silhouettes true color black width 5.5 depthJump 0.05

> select clear

> surface hidePatches #3

> set silhouetteWidth 6.0

> set silhouetteWidth 9.0

> surface #3

> transparency #3 100

> graphics silhouettes false

> set silhouetteWidth 9.0

> surface hidePatches #3

> graphics silhouettes true

> surface #3

> graphics silhouettes false

> set silhouetteWidth 9.0

> graphics silhouettes true

> surface hidePatches #3

> open
> /Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/final/6v35onJ220-realspacerefine26-coot-6.pdb

Summary of feedback from opening
/Users/shubhangi/Desktop/CryoEM/BK/BKbeta2chimeracomplex05232023/job220/final/6v35onJ220-realspacerefine26-coot-6.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
22129 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 39 39 ALA H 2009 ALA H
2012 1 4  
Start residue of secondary structure not found: HELIX 40 40 SER H 2017 LEU H
2047 1 31  
Start residue of secondary structure not found: HELIX 41 41 GLU H 2104 THR H
2109 1 6  
Start residue of secondary structure not found: HELIX 42 42 ASN H 2123 LYS H
2138 1 16  
Start residue of secondary structure not found: HELIX 43 43 ILE H 2168 LYS H
2195 1 28  
39 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (2054 )  
Cannot find LINK/SSBOND residue CYS (2068 )  
Cannot find LINK/SSBOND residue CYS (2072 )  
Cannot find LINK/SSBOND residue CYS (2084 )  
Cannot find LINK/SSBOND residue CYS (2054 )  
11 messages similar to the above omitted  
  
Chain information for 6v35onJ220-realspacerefine26-coot-6.pdb #2  
---  
Chain | Description  
A B C D | No description available  
E F G H | No description available  
  

> hide atoms

> show cartoons

> color #2-3 white

> undo

> hide #!2 models

> hide #!3 models

> show #!2 models

> select #2

35437 atoms, 36288 bonds, 21 pseudobonds, 4429 residues, 2 models selected  

> color (#!2 & sel) light gray

> surface (#!2 & sel)

> transparency (#!2 & sel) 100

> hide sel cartoons

> show #!3 models

> hide #!2 models

> show #!2 models

> setattr M silhouette false #2

Expected a keyword  

> select clear

> setattr M silhouette false #2

Expected a keyword  

> setattr M silhouette false /#2

Expected a keyword  

> setattr M silhouette false

Unknown attribute target: 'M'  

> setattr silhouette false #2

Unknown attribute target: 'silhouette'  

> hide #!3 models

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true color black width 4.5 depthJump 0.05

> graphics silhouettes true color black width 4.5 depthJump 0.1

> graphics silhouettes true color black width 4.5 depthJump 0.5

> graphics silhouettes true color black width 5.5 depthJump 0.05

> graphics silhouettes true color black width 5.5 depthJump 0.2

> graphics silhouettes true color black width 5.5 depthJump 0.3

> graphics silhouettes true color black width 5.5 depthJump 0.4

> graphics silhouettes true color black width 5.5 depthJump 0.1

> show #!3 models

> set silhouetteWidth 6.0

> set silhouetteWidth 9.0

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/sideclosed2.png
> width 3000 height 2097 supersample 4 transparentBackground true

> hide #!2 models

> show #!2 models

> hide #!3 models

> graphics silhouettes true color black width 0.5 depthJump 0.4

> graphics silhouettes true color black width 1.5 depthJump 0.4

> set silhouetteWidth 6.0

> graphics silhouettes true color black width 5.5 depthJump 0.1

> graphics silhouettes true color black width 5.5 depthJump 0.15

> graphics silhouettes true color black width 5.5 depthJump 0.3

> graphics silhouettes true color black width 5.5 depthJump 0.25

> graphics silhouettes true color black width 5.5 depthJump 0.28

> graphics silhouettes true color black width 5.5 depthJump 0.29

> show #!3 models

> graphics silhouettes true color black width 5.5 depthJump 0.4

> graphics silhouettes true color black width 5.5 depthJump 0.2

> graphics silhouettes true color black width 5.5 depthJump 0.1

> graphics silhouettes true color black width 7.5 depthJump 0.1

> graphics silhouettes true color black width 9.5 depthJump 0.1

> save
> /Users/shubhangi/Desktop/manuscript/MANUSCRIPTFIGURES/closed/closeddetergent/sideclosed2.png
> width 3000 height 2097 supersample 4 transparentBackground true

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting full

[Repeated 1 time(s)]

> lighting simple

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 70424 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> transparency #2-3 80

> transparency #2-3 100

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> surface hidePatches #3

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> surface #3

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!2 models

> graphics silhouettes true color black width 9.5 depthJump 0.2

> graphics silhouettes false

> set silhouetteWidth 9.0

> graphics silhouettes true

> surface hidePatches #3

> set silhouetteWidth 9.0

> graphics silhouettes true color black width 9.5 depthJump 0.2

> graphics silhouettes true color black width 9.5 depthJump 0.1

> show #!2 models

> hide #!3 models

> graphics silhouettes true color green width 9.5 depthJump 0.2

> graphics silhouettes true color green width 5.5 depthJump 0.2

> show #!3 models

> graphics silhouettes true color balck width 9.5 depthJump 0.2

Invalid "color" argument: Invalid color name or specifier  

> graphics silhouettes true color black width 7.5 depthJump 0.1

> hide #!2 models

> show #!2 models




OpenGL version: 4.1 INTEL-18.8.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
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: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)
      OS Loader Version: 540.120.3~19

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5 days 1:15

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 Family: Supported, Metal GPUFamily macOS 2
      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: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Shubhangi Agarwal

[Eric Pettersen]

Asked and answered on the chimerax-users list