Restoring session: TypeError: 'builtin_function_or_method' object is not iterable

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.5-x86_64-i386-64bit
ChimeraX Version: 1.9rc202410300406 (2024-10-30 04:06:08 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410300406 (2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

restore_snapshot for "VolumeSurface" returned None  

Error opening map "/Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs": File
Figure4B.cxs, format mrc  
MRC header value nsymbt (1953526586) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "ClipCap" returned None  

[Repeated 1 time(s)]

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Fri Jun 13 18:23:36 2025UCSF ChimeraX version: 1.9rc202410300406
(2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
level 0.0923, step 2, values float32  
Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at level 0.0803, step 1, values float32  
Log from Wed Apr 16 19:31:19 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410300406 (2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb

Chain information for ZIKV-C11-sec-py.pdb #1  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> hide atoms

> show cartoons

Computing secondary structure  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /G:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /M:1-123

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /L:1-123

954 atoms, 979 bonds, 123 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /N:1-108

809 atoms, 827 bonds, 108 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /G:1-75

Nothing selected  

> select /G:1-75

Nothing selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> set bgColor white

> transparency 70

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb

Chain information for ZIKV-C11-sec-py.pdb #2  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> show cartoons

Computing secondary structure  

> hide atoms

> hide #2 models

> show target m

> hide target m

> show #1 models

> close #2

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> toolshed show

> ui tool show "Surface Color"

> ui tool show "Build Structure"

> select #2/D:1-502

Nothing selected  

> select #2/D:1-502

Nothing selected  

> select #2/E:1-502

Nothing selected  

> select #2/E:1-502

Nothing selected  

> select #2/F:1-502

Nothing selected  

> select #2/G:1-75

Nothing selected  

> select /E:1-502

Nothing selected  

> select /F:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> structure assign strand #1 /D:110-127

Unknown command: structure assign strand #1 /D:110-127  

> set bgColor black

> close

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb format pdb

Chain information for ZIKV-C11-sec-py.pdb #1  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> style stick

Changed 18627 atom styles  

> show cartoons

Computing secondary structure  

> hide atoms

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> remove /E

Unknown command: remove /E  

> delete /E

> delete /L

> delete /N

> delete /G

> delete /J

> delete /H

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> transparency sel 80

> surface sel

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff7g50

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel #ff7f50

> transparency (#!1 & sel) 80

> select /D:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #d2b48c

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> set bgColor white

> select all

11267 atoms, 11520 bonds, 1478 residues, 1 model selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> select /D:296-406

842 atoms, 860 bonds, 111 residues, 1 model selected  

> color sel #1e90ff

> select /F:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff0000

> select /F:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #ffd700

> select /F:296-406

842 atoms, 860 bonds, 111 residues, 1 model selected  

> color sel #0000ff

> delete /F:406-505

> delete /D:406-505

[Repeated 1 time(s)]

> select all

9851 atoms, 10076 bonds, 1284 residues, 1 model selected  

> select all

9851 atoms, 10076 bonds, 1284 residues, 1 model selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> select /D:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #daa520

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff4500

> lighting soft

> select /D:296-406

835 atoms, 853 bonds, 110 residues, 1 model selected  

> color sel #00bfff

> color sel #1e90ff

> select /E:1-52,132-193,280-296

Nothing selected  

> select /F:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff0000

> select /F:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #ffd700

> select /F:296-406

835 atoms, 853 bonds, 110 residues, 1 model selected  

> color sel #3232cd

> selece /M

Unknown command: selece /M  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M&I

Nothing selected  

> select /M&I

Nothing selected  

> select /M and I

Expected a keyword  

> select /M,I

1908 atoms, 1958 bonds, 246 residues, 1 model selected  

> color sel #40e0d0

> transparency (#!1 & sel) 80

> select /O,K

1618 atoms, 1654 bonds, 216 residues, 1 model selected  

> color sel #ff00ff

> transparency (#!1 & sel) 80

> ui tool show Contacts

> interfaces select /M & ::polymer_type>0 contacting /F & ::polymer_type>0
> areaCutoff 0 bothSides true

20 contacting residues  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> cartoon hide (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> color sel meganta

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel magenta

> undo

> select (/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)

107 atoms, 106 bonds, 12 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<6.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<6.5))

339 atoms, 330 bonds, 43 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> help help:user/selectcontacts.html

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> ribbon :I,M,J,N

> ribbon style tube

> cartoon style tube

Expected an atoms specifier or a keyword  

> ribscale 3 :I,M,J,N

Unknown command: ribscale 3 :I,M,J,N  

> surface :I,M,J,N

No atoms specified by :I,M,J,N  

> surface /I,M,J,N

> surfaceCategory outline

Unknown command: surfaceCategory outline  

> setattr s drawMode mesh :I,M,J,N

Expected a keyword  

> N

Unknown command: N  

> surfaceCategory outline

Unknown command: surfaceCategory outline  

> setattr s drawMode mesh /I,M,J,N

Expected a keyword  

> setattr s drawMode mesh /M

Expected a keyword  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting soft

> undo

[Repeated 5 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> select helix

540 atoms, 542 bonds, 68 residues, 1 model selected  

> show strand

> hide stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> undo

> cartoon (#!1 & sel)

> cartoon hide (#!1 & sel)

> cartoon (#!1 & sel)

> select strand

2938 atoms, 2920 bonds, 372 residues, 1 model selected  

> unselct

Unknown command: unselct  

> unselect

Unknown command: unselect  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> surface hidePatches (#!1 & sel)

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> transparency (#!1 & sel) 20

> transparency (#!1 & sel) 90

> lighting simple

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> surface hidePatches (#!1 & sel)

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> cartoon (#!1 & sel)

> surface (#!1 & sel)

> close #1

> open "/Users/yaminglu/Documents/1 Postdoc fellow/Zika/C11_4.26_zflip.mrc"

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> volume #1 level 0.08

> volume #1 change image level -0.01701,0 level 0.1224,0.8 level 0.2461,1

> surface dust #1 size 9.7

> volume #1 level 0.09

> surface dust #1 size 9.7

> vop gaussian #1 sdev 2.91

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> undo

Undo failed, probably because structures have been modified.  

> hide #!1 models

> show #!1 models

> close #2

> volume #1 style surface level 0.015

> vop radial #1 center 0,0,0

> volume radial #1 center 0,0,0

Expected a density maps specifier or a keyword  

> color sample default radius #1 map #2

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> hide #!1 models

> show #!1 models

> close #1

> open "/Users/yaminglu/Documents/1 Postdoc fellow/Zika/C11_4.26_zflip.mrc"
> format mrc

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> ui tool show "Color Zone"

> ui tool show "Surface Color"

> color radial #1.2 palette 230,#cccccc:235,#ffff33 center 388,388,387.03

> color radial #1.2 palette 230,#cccccc:240,#ffff33 center 388,388,387.03

> color radial #1.2 palette 230,#cccccc:250,#ffff33 center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 240,#cccccc:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff66 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc66 center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 240,#ffffff:250,#ffff99 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffd479 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffc79 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffb00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffcc00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffb00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#999933 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc66 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffcc00 center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#cccccc:260,#ccff66 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#ccff66 center
> 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#d9e000 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#edc200 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#edd500 center
> 388,388,387.03

> lighting soft

> graphics silhouettes false

> surface dust #1 size 9.7

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> volume #1 step 2

> volume #1 step 4

> lighting soft

> volume #1 change image level -0.01701,0 level 0.1224,0.8 level 0.2461,1

> volume #1 level 0.05734

> volume #1 step 2

> volume #1 level 0.0473

> volume #1 level 0.0673

> volume #1 level 0.0773

> volume #1 level 0.0873

> volume #1 level 0.0973

> volume #1 level 0.0923

> surface dust #1 size 9.7

> color radial #1.2 palette 225,#ffffff:235,#f5f5f5:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:240,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:245,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:250,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:250,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 230,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:245,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> volume gaussian #2 sDev 3

> volume gaussian #1 sDev 3

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!2 models

> show #!1 models

> volume gaussian #1 sDev 1

Opened C11_4.26_zflip.mrc gaussian as #3, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #3.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> volume gaussian #1 sDev 2

Opened C11_4.26_zflip.mrc gaussian as #4, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #4.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!3 models

> close #2

> close #3

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> volume gaussian #1 sDev 1.5

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> volume #2 level 0.0603

> volume #2 level 0.0703

> volume #2 level 0.0803

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!4 models

> close #4

> close #2

> show #!1 models

> volume gaussian #1 sDev 1.5

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> toolshed show

> hide dust #1 size 100

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> surface dust #1 size 20

> hide #!1 models

> show #!2 models

> surface dust #2 size 20

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> hide #!2 models

> show #!1 models

> color radial #1.2 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 3 time(s)]

> key white:240 #fafafa:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:240 #fafafa:240

> ui mousemode right translate

> color radial #1.2 palette 240,#ffffff:250,#f5e529 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#f5cf29 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#f5da29 center 388,388,387.03

> color radial #1.2 palette 245,#ffffff:250,#f5da29 center 388,388,387.03

> key white:245 #f5da29:250 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 245,#ffffff:250,#ffffff:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 230,#ffffff:240,#ffffff:255,#edd500 center
> 388,388,387.03

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:230 white:240

> key white:230 white:240 white:

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:230 white: #edd500:255

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key size 0.25000,0.04000

> key size 0.25000,0.03000

> key size 0.25000,0.02000

> key size 0.25000,0.03000

> ui mousemode right translate

> color radial #1.2 palette 230,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:230 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:200 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:235,#ffffff:260,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> key white:200 white:235 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:230,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:200 white:230 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:235,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 200,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:220 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key white:220 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> key size 0.25000,0.02000

> key size 0.25000,0.03000

> ui mousemode right translate

> show #!2 models

> hide #!1 models

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!2 models

> show #!1 models

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 22000 height 18410
> supersample 3 transparentBackground true

Image size 22000 x 18410 too large, exceeds maximum OpenGL render buffer size
16384  

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 16000 height 13389
> supersample 3 transparentBackground true

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 2400 height 2008
> supersample 3 transparentBackground true

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1-1.tif width 2400 height 2008
> supersample 3 transparentBackground true

> cd /Users/yaminglu/Desktop/ZIKV画图用

Current working directory is: /Users/yaminglu/Desktop/ZIKV画图用  

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.cxs

——— End of log from Wed Apr 16 19:31:19 2025 ———

opened ChimeraX session  

> open
> /Users/yaminglu/Desktop/ZIKV画图用/cryosparc_P21_J123_006_volume_map_sharp.mrc

Opened cryosparc_P21_J123_006_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 1.94, shown at level 0.345, step 2, values float32  

> volume #4 step 1

> volume #4 step 2

> volume #4 step 1

> surface dust #4 size 19.4

> close #2

> ui tool show "Surface Color"

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#b1f300 center
> 388,388,387.03

> ui tool show "Side View"

> key white:220 white:240 #b1f300:260 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> volume #1 level 0.03709

> ui tool show "Surface Color"

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#b1f300 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#65f300 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80f300 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80f321 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80e321 center
> 388,388,387.03

[Repeated 3 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#64c021 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#64dc21 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#84dc21 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9edc21 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9ec421 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 220,#ff6600:240,#ffcc33:260,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:200,#ffcc33:220,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:180,#ffcc33:200,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:180,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 100,#ff6600:150,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff6600:150,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff6600:150,#ffcc33:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:150,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:120,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> key red:50 #ff6600:120 #ffff33:190 white:230 #9ed121:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette
> 50,#ff0000:120,#ff6600:190,#ff6600:230,#ffcc33:260,#ffff33 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff6600:203,#ffcc33:210,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:203,#ffcc33:210,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:180,#ffcc33:200,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:180,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:150,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:230,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:180,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:235,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:190,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffff00:190,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffff00:180,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:180,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:200,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:195,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:195,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:200,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:225,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:230,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:235,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:200,#ffff00:235,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:180,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:170,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:160,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:150,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:140,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:90,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:110,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> lighting simple

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> volume #1 level 0.0341

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.tif width 2048 height 1389
> supersample 3 transparentBackground true

> ui tool show "Surface Color"

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9bd534
> center 388,388,387.03

[Repeated 3 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9adb16
> center 388,388,387.03

[Repeated 1 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#a7cd47
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#b2da4c
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#abd249
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#8ed245
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#97d248
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#95d23f
> center 388,388,387.03

[Repeated 4 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#f0f0f0:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#e8e8e8:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#dee0e0:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#d3d4d6:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#cccdcf:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ababad:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#d9d9d9:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#d1d1d1:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#c4c4c4:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-2.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:215,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:205,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:195,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:190,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.cxs

——— End of log from Fri Jun 13 18:23:36 2025 ———

opened ChimeraX session  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs format session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

restore_snapshot for "VolumeSurface" returned None  

Error opening map "/Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs": File
Figure4B.cxs, format mrc  
MRC header value nsymbt (1953526586) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "ClipCap" returned None  

[Repeated 1 time(s)]

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Fri Jun 13 18:23:36 2025UCSF ChimeraX version: 1.9rc202410300406
(2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
level 0.0923, step 2, values float32  
Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at level 0.0803, step 1, values float32  
Log from Wed Apr 16 19:31:19 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410300406 (2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb

Chain information for ZIKV-C11-sec-py.pdb #1  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> hide atoms

> show cartoons

Computing secondary structure  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /G:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /M:1-123

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /L:1-123

954 atoms, 979 bonds, 123 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /N:1-108

809 atoms, 827 bonds, 108 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /G:1-75

Nothing selected  

> select /G:1-75

Nothing selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> set bgColor white

> transparency 70

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb

Chain information for ZIKV-C11-sec-py.pdb #2  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> show cartoons

Computing secondary structure  

> hide atoms

> hide #2 models

> show target m

> hide target m

> show #1 models

> close #2

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> toolshed show

> ui tool show "Surface Color"

> ui tool show "Build Structure"

> select #2/D:1-502

Nothing selected  

> select #2/D:1-502

Nothing selected  

> select #2/E:1-502

Nothing selected  

> select #2/E:1-502

Nothing selected  

> select #2/F:1-502

Nothing selected  

> select #2/G:1-75

Nothing selected  

> select /E:1-502

Nothing selected  

> select /F:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> structure assign strand #1 /D:110-127

Unknown command: structure assign strand #1 /D:110-127  

> set bgColor black

> close

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb format pdb

Chain information for ZIKV-C11-sec-py.pdb #1  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> style stick

Changed 18627 atom styles  

> show cartoons

Computing secondary structure  

> hide atoms

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> remove /E

Unknown command: remove /E  

> delete /E

> delete /L

> delete /N

> delete /G

> delete /J

> delete /H

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> transparency sel 80

> surface sel

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff7g50

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel #ff7f50

> transparency (#!1 & sel) 80

> select /D:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #d2b48c

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> set bgColor white

> select all

11267 atoms, 11520 bonds, 1478 residues, 1 model selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> select /D:296-406

842 atoms, 860 bonds, 111 residues, 1 model selected  

> color sel #1e90ff

> select /F:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff0000

> select /F:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #ffd700

> select /F:296-406

842 atoms, 860 bonds, 111 residues, 1 model selected  

> color sel #0000ff

> delete /F:406-505

> delete /D:406-505

[Repeated 1 time(s)]

> select all

9851 atoms, 10076 bonds, 1284 residues, 1 model selected  

> select all

9851 atoms, 10076 bonds, 1284 residues, 1 model selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> select /D:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #daa520

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff4500

> lighting soft

> select /D:296-406

835 atoms, 853 bonds, 110 residues, 1 model selected  

> color sel #00bfff

> color sel #1e90ff

> select /E:1-52,132-193,280-296

Nothing selected  

> select /F:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff0000

> select /F:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #ffd700

> select /F:296-406

835 atoms, 853 bonds, 110 residues, 1 model selected  

> color sel #3232cd

> selece /M

Unknown command: selece /M  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M&I

Nothing selected  

> select /M&I

Nothing selected  

> select /M and I

Expected a keyword  

> select /M,I

1908 atoms, 1958 bonds, 246 residues, 1 model selected  

> color sel #40e0d0

> transparency (#!1 & sel) 80

> select /O,K

1618 atoms, 1654 bonds, 216 residues, 1 model selected  

> color sel #ff00ff

> transparency (#!1 & sel) 80

> ui tool show Contacts

> interfaces select /M & ::polymer_type>0 contacting /F & ::polymer_type>0
> areaCutoff 0 bothSides true

20 contacting residues  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> cartoon hide (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> color sel meganta

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel magenta

> undo

> select (/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)

107 atoms, 106 bonds, 12 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<6.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<6.5))

339 atoms, 330 bonds, 43 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> help help:user/selectcontacts.html

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> ribbon :I,M,J,N

> ribbon style tube

> cartoon style tube

Expected an atoms specifier or a keyword  

> ribscale 3 :I,M,J,N

Unknown command: ribscale 3 :I,M,J,N  

> surface :I,M,J,N

No atoms specified by :I,M,J,N  

> surface /I,M,J,N

> surfaceCategory outline

Unknown command: surfaceCategory outline  

> setattr s drawMode mesh :I,M,J,N

Expected a keyword  

> N

Unknown command: N  

> surfaceCategory outline

Unknown command: surfaceCategory outline  

> setattr s drawMode mesh /I,M,J,N

Expected a keyword  

> setattr s drawMode mesh /M

Expected a keyword  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting soft

> undo

[Repeated 5 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> select helix

540 atoms, 542 bonds, 68 residues, 1 model selected  

> show strand

> hide stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> undo

> cartoon (#!1 & sel)

> cartoon hide (#!1 & sel)

> cartoon (#!1 & sel)

> select strand

2938 atoms, 2920 bonds, 372 residues, 1 model selected  

> unselct

Unknown command: unselct  

> unselect

Unknown command: unselect  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> surface hidePatches (#!1 & sel)

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> transparency (#!1 & sel) 20

> transparency (#!1 & sel) 90

> lighting simple

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> surface hidePatches (#!1 & sel)

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> cartoon (#!1 & sel)

> surface (#!1 & sel)

> close #1

> open "/Users/yaminglu/Documents/1 Postdoc fellow/Zika/C11_4.26_zflip.mrc"

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> volume #1 level 0.08

> volume #1 change image level -0.01701,0 level 0.1224,0.8 level 0.2461,1

> surface dust #1 size 9.7

> volume #1 level 0.09

> surface dust #1 size 9.7

> vop gaussian #1 sdev 2.91

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> undo

Undo failed, probably because structures have been modified.  

> hide #!1 models

> show #!1 models

> close #2

> volume #1 style surface level 0.015

> vop radial #1 center 0,0,0

> volume radial #1 center 0,0,0

Expected a density maps specifier or a keyword  

> color sample default radius #1 map #2

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> hide #!1 models

> show #!1 models

> close #1

> open "/Users/yaminglu/Documents/1 Postdoc fellow/Zika/C11_4.26_zflip.mrc"
> format mrc

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> ui tool show "Color Zone"

> ui tool show "Surface Color"

> color radial #1.2 palette 230,#cccccc:235,#ffff33 center 388,388,387.03

> color radial #1.2 palette 230,#cccccc:240,#ffff33 center 388,388,387.03

> color radial #1.2 palette 230,#cccccc:250,#ffff33 center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 240,#cccccc:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff66 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc66 center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 240,#ffffff:250,#ffff99 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffd479 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffc79 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffb00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffcc00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffb00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#999933 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc66 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffcc00 center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#cccccc:260,#ccff66 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#ccff66 center
> 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#d9e000 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#edc200 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#edd500 center
> 388,388,387.03

> lighting soft

> graphics silhouettes false

> surface dust #1 size 9.7

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> volume #1 step 2

> volume #1 step 4

> lighting soft

> volume #1 change image level -0.01701,0 level 0.1224,0.8 level 0.2461,1

> volume #1 level 0.05734

> volume #1 step 2

> volume #1 level 0.0473

> volume #1 level 0.0673

> volume #1 level 0.0773

> volume #1 level 0.0873

> volume #1 level 0.0973

> volume #1 level 0.0923

> surface dust #1 size 9.7

> color radial #1.2 palette 225,#ffffff:235,#f5f5f5:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:240,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:245,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:250,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:250,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 230,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:245,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> volume gaussian #2 sDev 3

> volume gaussian #1 sDev 3

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!2 models

> show #!1 models

> volume gaussian #1 sDev 1

Opened C11_4.26_zflip.mrc gaussian as #3, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #3.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> volume gaussian #1 sDev 2

Opened C11_4.26_zflip.mrc gaussian as #4, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #4.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!3 models

> close #2

> close #3

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> volume gaussian #1 sDev 1.5

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> volume #2 level 0.0603

> volume #2 level 0.0703

> volume #2 level 0.0803

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!4 models

> close #4

> close #2

> show #!1 models

> volume gaussian #1 sDev 1.5

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> toolshed show

> hide dust #1 size 100

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> surface dust #1 size 20

> hide #!1 models

> show #!2 models

> surface dust #2 size 20

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> hide #!2 models

> show #!1 models

> color radial #1.2 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 3 time(s)]

> key white:240 #fafafa:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:240 #fafafa:240

> ui mousemode right translate

> color radial #1.2 palette 240,#ffffff:250,#f5e529 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#f5cf29 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#f5da29 center 388,388,387.03

> color radial #1.2 palette 245,#ffffff:250,#f5da29 center 388,388,387.03

> key white:245 #f5da29:250 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 245,#ffffff:250,#ffffff:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 230,#ffffff:240,#ffffff:255,#edd500 center
> 388,388,387.03

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:230 white:240

> key white:230 white:240 white:

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:230 white: #edd500:255

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key size 0.25000,0.04000

> key size 0.25000,0.03000

> key size 0.25000,0.02000

> key size 0.25000,0.03000

> ui mousemode right translate

> color radial #1.2 palette 230,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:230 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:200 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:235,#ffffff:260,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> key white:200 white:235 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:230,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:200 white:230 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:235,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 200,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:220 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key white:220 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> key size 0.25000,0.02000

> key size 0.25000,0.03000

> ui mousemode right translate

> show #!2 models

> hide #!1 models

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!2 models

> show #!1 models

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 22000 height 18410
> supersample 3 transparentBackground true

Image size 22000 x 18410 too large, exceeds maximum OpenGL render buffer size
16384  

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 16000 height 13389
> supersample 3 transparentBackground true

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 2400 height 2008
> supersample 3 transparentBackground true

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1-1.tif width 2400 height 2008
> supersample 3 transparentBackground true

> cd /Users/yaminglu/Desktop/ZIKV画图用

Current working directory is: /Users/yaminglu/Desktop/ZIKV画图用  

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.cxs

——— End of log from Wed Apr 16 19:31:19 2025 ———

opened ChimeraX session  

> open
> /Users/yaminglu/Desktop/ZIKV画图用/cryosparc_P21_J123_006_volume_map_sharp.mrc

Opened cryosparc_P21_J123_006_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 1.94, shown at level 0.345, step 2, values float32  

> volume #4 step 1

> volume #4 step 2

> volume #4 step 1

> surface dust #4 size 19.4

> close #2

> ui tool show "Surface Color"

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#b1f300 center
> 388,388,387.03

> ui tool show "Side View"

> key white:220 white:240 #b1f300:260 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> volume #1 level 0.03709

> ui tool show "Surface Color"

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#b1f300 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#65f300 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80f300 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80f321 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80e321 center
> 388,388,387.03

[Repeated 3 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#64c021 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#64dc21 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#84dc21 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9edc21 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9ec421 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 220,#ff6600:240,#ffcc33:260,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:200,#ffcc33:220,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:180,#ffcc33:200,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:180,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 100,#ff6600:150,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff6600:150,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff6600:150,#ffcc33:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:150,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:120,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> key red:50 #ff6600:120 #ffff33:190 white:230 #9ed121:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette
> 50,#ff0000:120,#ff6600:190,#ff6600:230,#ffcc33:260,#ffff33 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff6600:203,#ffcc33:210,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:203,#ffcc33:210,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:180,#ffcc33:200,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:180,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:150,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:230,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:180,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:235,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:190,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffff00:190,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffff00:180,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:180,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:200,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:195,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:195,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:200,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:225,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:230,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:235,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:200,#ffff00:235,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:180,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:170,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:160,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:150,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:140,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:90,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:110,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> lighting simple

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> volume #1 level 0.0341

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.tif width 2048 height 1389
> supersample 3 transparentBackground true

> ui tool show "Surface Color"

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9bd534
> center 388,388,387.03

[Repeated 3 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9adb16
> center 388,388,387.03

[Repeated 1 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#a7cd47
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#b2da4c
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#abd249
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#8ed245
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#97d248
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#95d23f
> center 388,388,387.03

[Repeated 4 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#f0f0f0:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#e8e8e8:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#dee0e0:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#d3d4d6:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#cccdcf:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ababad:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#d9d9d9:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#d1d1d1:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#c4c4c4:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-2.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:215,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:205,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:195,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:190,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.cxs

——— End of log from Fri Jun 13 18:23:36 2025 ———

opened ChimeraX session  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs format session

No such file/path: /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs format session

No such file/path: /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.cxs format session

No such file/path: /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.cxs  

> open "/Users/yaminglu/Desktop/ZIKV画图用/Figure5-Modeling IgG-1.cxs" format
> session

No such file/path: /Users/yaminglu/Desktop/ZIKV画图用/Figure5-Modeling IgG-1.cxs  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure1.cxs format session

No such file/path: /Users/yaminglu/Desktop/ZIKV画图用/Figure1.cxs  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs

Error opening map "/Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs": File
Figure4B.cxs, format mrc  
MRC header value nsymbt (1953526586) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

restore_snapshot for "VolumeSurface" returned None  

Error opening map "/Users/yaminglu/Desktop/ZIKV画图用/Figure4/Figure4B.cxs": File
Figure4B.cxs, format mrc  
MRC header value nsymbt (1953526586) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "ClipCap" returned None  

[Repeated 1 time(s)]

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9-rc2024.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9-rc2024.10.30.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Fri Jun 13 18:23:36 2025UCSF ChimeraX version: 1.9rc202410300406
(2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/yaminglu/Desktop/ZIKV画图用/Figure3-A.cxs

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
level 0.0923, step 2, values float32  
Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at level 0.0803, step 1, values float32  
Log from Wed Apr 16 19:31:19 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202410300406 (2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb

Chain information for ZIKV-C11-sec-py.pdb #1  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> hide atoms

> show cartoons

Computing secondary structure  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /G:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /M:1-123

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /L:1-123

954 atoms, 979 bonds, 123 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /N:1-108

809 atoms, 827 bonds, 108 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /G:1-75

Nothing selected  

> select /G:1-75

Nothing selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> select /H:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /J:1-75

600 atoms, 615 bonds, 75 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> set bgColor white

> transparency 70

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb

Chain information for ZIKV-C11-sec-py.pdb #2  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> show cartoons

Computing secondary structure  

> hide atoms

> hide #2 models

> show target m

> hide target m

> show #1 models

> close #2

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> dssp

Computing secondary structure  

> toolshed show

> ui tool show "Surface Color"

> ui tool show "Build Structure"

> select #2/D:1-502

Nothing selected  

> select #2/D:1-502

Nothing selected  

> select #2/E:1-502

Nothing selected  

> select #2/E:1-502

Nothing selected  

> select #2/F:1-502

Nothing selected  

> select #2/G:1-75

Nothing selected  

> select /E:1-502

Nothing selected  

> select /F:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> structure assign strand #1 /D:110-127

Unknown command: structure assign strand #1 /D:110-127  

> set bgColor black

> close

> open /Users/yaminglu/Desktop/ZIKV-C11-sec-py.pdb format pdb

Chain information for ZIKV-C11-sec-py.pdb #1  
---  
Chain | Description  
D E F | No description available  
G H J | No description available  
I L M | No description available  
K N O | No description available  
  

> style stick

Changed 18627 atom styles  

> show cartoons

Computing secondary structure  

> hide atoms

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /D:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E:1-502

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> select /E

3797 atoms, 3876 bonds, 502 residues, 1 model selected  

> remove /E

Unknown command: remove /E  

> delete /E

> delete /L

> delete /N

> delete /G

> delete /J

> delete /H

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> transparency sel 80

> surface sel

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff7g50

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel #ff7f50

> transparency (#!1 & sel) 80

> select /D:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #d2b48c

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> set bgColor white

> select all

11267 atoms, 11520 bonds, 1478 residues, 1 model selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> select /D:296-406

842 atoms, 860 bonds, 111 residues, 1 model selected  

> color sel #1e90ff

> select /F:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff0000

> select /F:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #ffd700

> select /F:296-406

842 atoms, 860 bonds, 111 residues, 1 model selected  

> color sel #0000ff

> delete /F:406-505

> delete /D:406-505

[Repeated 1 time(s)]

> select all

9851 atoms, 10076 bonds, 1284 residues, 1 model selected  

> select all

9851 atoms, 10076 bonds, 1284 residues, 1 model selected  

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> transparency (#!1 & sel) 80

> select /D:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #daa520

> select /D:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff4500

> lighting soft

> select /D:296-406

835 atoms, 853 bonds, 110 residues, 1 model selected  

> color sel #00bfff

> color sel #1e90ff

> select /E:1-52,132-193,280-296

Nothing selected  

> select /F:1-52,132-193,280-296

984 atoms, 996 bonds, 131 residues, 1 model selected  

> color sel #ff0000

> select /F:52-132,193-280

1309 atoms, 1340 bonds, 169 residues, 1 model selected  

> color sel #ffd700

> select /F:296-406

835 atoms, 853 bonds, 110 residues, 1 model selected  

> color sel #3232cd

> selece /M

Unknown command: selece /M  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M&I

Nothing selected  

> select /M&I

Nothing selected  

> select /M and I

Expected a keyword  

> select /M,I

1908 atoms, 1958 bonds, 246 residues, 1 model selected  

> color sel #40e0d0

> transparency (#!1 & sel) 80

> select /O,K

1618 atoms, 1654 bonds, 216 residues, 1 model selected  

> color sel #ff00ff

> transparency (#!1 & sel) 80

> ui tool show Contacts

> interfaces select /M & ::polymer_type>0 contacting /F & ::polymer_type>0
> areaCutoff 0 bothSides true

20 contacting residues  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> cartoon hide (#!1 & sel)

> surface hidePatches (#!1 & sel)

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> color sel meganta

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel magenta

> undo

> select (/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)

107 atoms, 106 bonds, 12 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<6.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<6.5))

339 atoms, 330 bonds, 43 residues, 1 model selected  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> help help:user/selectcontacts.html

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> ribbon :I,M,J,N

> ribbon style tube

> cartoon style tube

Expected an atoms specifier or a keyword  

> ribscale 3 :I,M,J,N

Unknown command: ribscale 3 :I,M,J,N  

> surface :I,M,J,N

No atoms specified by :I,M,J,N  

> surface /I,M,J,N

> surfaceCategory outline

Unknown command: surfaceCategory outline  

> setattr s drawMode mesh :I,M,J,N

Expected a keyword  

> N

Unknown command: N  

> surfaceCategory outline

Unknown command: surfaceCategory outline  

> setattr s drawMode mesh /I,M,J,N

Expected a keyword  

> setattr s drawMode mesh /M

Expected a keyword  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting soft

> undo

[Repeated 5 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> select helix

540 atoms, 542 bonds, 68 residues, 1 model selected  

> show strand

> hide stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> undo

> cartoon (#!1 & sel)

> cartoon hide (#!1 & sel)

> cartoon (#!1 & sel)

> select strand

2938 atoms, 2920 bonds, 372 residues, 1 model selected  

> unselct

Unknown command: unselct  

> unselect

Unknown command: unselect  

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> surface hidePatches (#!1 & sel)

> select ((/M & ::polymer_type>0 ) & ((/F & ::polymer_type>0 ) :<4.5)) | ((/F & ::polymer_type>0 ) & ((/M & ::polymer_type>0 ) :<4.5))

214 atoms, 208 bonds, 26 residues, 1 model selected  

> transparency (#!1 & sel) 20

> transparency (#!1 & sel) 90

> lighting simple

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> surface hidePatches (#!1 & sel)

> select /M

954 atoms, 979 bonds, 123 residues, 1 model selected  

> cartoon (#!1 & sel)

> surface (#!1 & sel)

> close #1

> open "/Users/yaminglu/Documents/1 Postdoc fellow/Zika/C11_4.26_zflip.mrc"

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> volume #1 level 0.08

> volume #1 change image level -0.01701,0 level 0.1224,0.8 level 0.2461,1

> surface dust #1 size 9.7

> volume #1 level 0.09

> surface dust #1 size 9.7

> vop gaussian #1 sdev 2.91

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> undo

Undo failed, probably because structures have been modified.  

> hide #!1 models

> show #!1 models

> close #2

> volume #1 style surface level 0.015

> vop radial #1 center 0,0,0

> volume radial #1 center 0,0,0

Expected a density maps specifier or a keyword  

> color sample default radius #1 map #2

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> hide #!1 models

> show #!1 models

> close #1

> open "/Users/yaminglu/Documents/1 Postdoc fellow/Zika/C11_4.26_zflip.mrc"
> format mrc

Opened C11_4.26_zflip.mrc as #1, grid size 800,800,800, pixel 0.97, shown at
step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> ui tool show "Color Zone"

> ui tool show "Surface Color"

> color radial #1.2 palette 230,#cccccc:235,#ffff33 center 388,388,387.03

> color radial #1.2 palette 230,#cccccc:240,#ffff33 center 388,388,387.03

> color radial #1.2 palette 230,#cccccc:250,#ffff33 center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 240,#cccccc:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff66 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc66 center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 240,#ffffff:250,#ffff99 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffd479 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffc79 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffb00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffcc00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffff00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#fffb00 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#999933 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc33 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#cccc66 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#ffcc00 center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#cccccc:260,#ccff66 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#ccff66 center
> 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#d9e000 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#edc200 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#f0f0f0:260,#edd500 center
> 388,388,387.03

> lighting soft

> graphics silhouettes false

> surface dust #1 size 9.7

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> volume #1 step 2

> volume #1 step 4

> lighting soft

> volume #1 change image level -0.01701,0 level 0.1224,0.8 level 0.2461,1

> volume #1 level 0.05734

> volume #1 step 2

> volume #1 level 0.0473

> volume #1 level 0.0673

> volume #1 level 0.0773

> volume #1 level 0.0873

> volume #1 level 0.0973

> volume #1 level 0.0923

> surface dust #1 size 9.7

> color radial #1.2 palette 225,#ffffff:235,#f5f5f5:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:240,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:235,#fafafa:245,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:235,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 225,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 225,#ffffff:250,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:250,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 240,#ffffff:245,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 230,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:245,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 235,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> volume gaussian #2 sDev 3

> volume gaussian #1 sDev 3

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!2 models

> show #!1 models

> volume gaussian #1 sDev 1

Opened C11_4.26_zflip.mrc gaussian as #3, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #3.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> volume gaussian #1 sDev 2

Opened C11_4.26_zflip.mrc gaussian as #4, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #4.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!3 models

> close #2

> close #3

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> volume gaussian #1 sDev 1.5

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> volume #2 level 0.0603

> volume #2 level 0.0703

> volume #2 level 0.0803

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!4 models

> close #4

> close #2

> show #!1 models

> volume gaussian #1 sDev 1.5

Opened C11_4.26_zflip.mrc gaussian as #2, grid size 800,800,800, pixel 0.97,
shown at step 1, values float32  

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> toolshed show

> hide dust #1 size 100

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> surface dust #1 size 20

> hide #!1 models

> show #!2 models

> surface dust #2 size 20

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> hide #!2 models

> show #!1 models

> color radial #1.2 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

[Repeated 3 time(s)]

> key white:240 #fafafa:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:240 #fafafa:240

> ui mousemode right translate

> color radial #1.2 palette 240,#ffffff:250,#f5e529 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#f5cf29 center 388,388,387.03

> color radial #1.2 palette 240,#ffffff:250,#f5da29 center 388,388,387.03

> color radial #1.2 palette 245,#ffffff:250,#f5da29 center 388,388,387.03

> key white:245 #f5da29:250 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 245,#ffffff:250,#ffffff:255,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 230,#ffffff:240,#ffffff:255,#edd500 center
> 388,388,387.03

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:230 white:240

> key white:230 white:240 white:

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key white:230 white: #edd500:255

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key white:230 white:240 #edd500:255 showTool true

> ui mousemode right "color key"

> key size 0.25000,0.04000

> key size 0.25000,0.03000

> key size 0.25000,0.02000

> key size 0.25000,0.03000

> ui mousemode right translate

> color radial #1.2 palette 230,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:230 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:200 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:235,#ffffff:260,#edd500 center
> 388,388,387.03

[Repeated 1 time(s)]

> key white:200 white:235 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:230,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:200 white:230 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette 200,#ffffff:235,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 200,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> key white:220 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key white:220 white:240 #edd500:260 showTool true

> ui mousemode right "color key"

> key size 0.25000,0.02000

> key size 0.25000,0.03000

> ui mousemode right translate

> show #!2 models

> hide #!1 models

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#edd500 center
> 388,388,387.03

> color radial #2.1 palette 240,#ffffff:240,#fafafa:255,#edd500 center
> 388,388,387.03

> hide #!2 models

> show #!1 models

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 22000 height 18410
> supersample 3 transparentBackground true

Image size 22000 x 18410 too large, exceeds maximum OpenGL render buffer size
16384  

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 16000 height 13389
> supersample 3 transparentBackground true

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.tif width 2400 height 2008
> supersample 3 transparentBackground true

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1-1.tif width 2400 height 2008
> supersample 3 transparentBackground true

> cd /Users/yaminglu/Desktop/ZIKV画图用

Current working directory is: /Users/yaminglu/Desktop/ZIKV画图用  

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure1.cxs

——— End of log from Wed Apr 16 19:31:19 2025 ———

opened ChimeraX session  

> open
> /Users/yaminglu/Desktop/ZIKV画图用/cryosparc_P21_J123_006_volume_map_sharp.mrc

Opened cryosparc_P21_J123_006_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 1.94, shown at level 0.345, step 2, values float32  

> volume #4 step 1

> volume #4 step 2

> volume #4 step 1

> surface dust #4 size 19.4

> close #2

> ui tool show "Surface Color"

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#b1f300 center
> 388,388,387.03

> ui tool show "Side View"

> key white:220 white:240 #b1f300:260 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> volume #1 level 0.03709

> ui tool show "Surface Color"

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#b1f300 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#65f300 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80f300 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80f321 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#80e321 center
> 388,388,387.03

[Repeated 3 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#64c021 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#64dc21 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#84dc21 center
> 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9edc21 center
> 388,388,387.03

> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9ec421 center
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> color radial #1.2 palette 220,#ffffff:240,#ffffff:260,#9ed121 center
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> color radial #1.2 palette
> 220,#ff6600:240,#ffcc33:260,#ffff33:240,#ffffff:260,#9ed121 center
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> color radial #1.2 palette
> 150,#ff6600:200,#ffcc33:220,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:180,#ffcc33:200,#ffff33:240,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 150,#ff6600:180,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 100,#ff6600:150,#ffcc33:200,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
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> 388,388,387.03

> color radial #1.2 palette
> 50,#ff6600:150,#ffcc33:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
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> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:120,#ff6600:190,#ffff33:230,#ffffff:260,#9ed121 center
> 388,388,387.03

> key red:50 #ff6600:120 #ffff33:190 white:230 #9ed121:260 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color radial #1.2 palette
> 50,#ff0000:120,#ff6600:190,#ff6600:230,#ffcc33:260,#ffff33 center
> 388,388,387.03

> color radial #1.2 palette
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> center 388,388,387.03

> color radial #1.2 palette
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> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:180,#ffcc33:200,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:145,#ff6600:160,#ff9900:180,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:150,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:190,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:240,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:230,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:182,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:180,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:235,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffcc33:190,#ffff33:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffff00:190,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:180,#ffff00:180,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:180,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:200,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:195,#ffff00:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:195,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:200,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
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> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:230,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:160,#ffff00:235,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:200,#ffff00:235,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:120,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:180,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
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> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:160,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:150,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:140,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 50,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:90,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:110,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9ed121
> center 388,388,387.03

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> key red:80 #ff6600:100 #ff9900:130 yellow:200 white:220 white:235
> #9ed121:250 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> lighting simple

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> lighting soft

> lighting full

[Repeated 1 time(s)]

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> volume #1 level 0.0341

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.tif width 2048 height 1389
> supersample 3 transparentBackground true

> ui tool show "Surface Color"

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9bd534
> center 388,388,387.03

[Repeated 3 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#9adb16
> center 388,388,387.03

[Repeated 1 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#a7cd47
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#b2da4c
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#abd249
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#8ed245
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#97d248
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ffffff:250,#95d23f
> center 388,388,387.03

[Repeated 4 time(s)]

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#f0f0f0:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#e8e8e8:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#dee0e0:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#d3d4d6:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#cccdcf:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-1.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#ffffff:235,#ababad:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#d9d9d9:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#d1d1d1:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

[Repeated 2 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#c4c4c4:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

[Repeated 1 time(s)]

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#c7c8ca:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B-2.tif width 2048 height 1389
> supersample 3 transparentBackground true

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:215,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:205,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:195,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:190,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> color radial #1.2 palette
> 80,#ff0000:100,#ff6600:130,#ff9900:200,#ffff00:220,#b7b7b7:235,#b8b9bb:250,#95d23f
> center 388,388,387.03

> save /Users/yaminglu/Desktop/ZIKV画图用/Figure3B.cxs

——— End of log from Fri Jun 13 18:23:36 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 INTEL-23.0.26
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: en_US.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 Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
      OS Loader Version: 583~1350

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 17小时45分钟

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          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
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    biopython: 1.85
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    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: 2.16.1
    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: 14.1.11
    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: 1.4.0
    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: 1.9rc202410300406
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-crai: 0.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    ChimeraX-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-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    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: 3.2.2
    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-Umap: 1.0
    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
    cripser: 0.0.15
    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
    fsspec: 2025.5.0
    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
    mpmath: 1.3.0
    mrcfile: 1.5.4
    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
    pyelftools: 0.31
    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
    sympy: 1.14.0
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    torch: 2.2.0
    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

[Tom Goddard]

Fixed on April 15, 2025, fix in ChimeraX 1.10. Error restoring session when volume surface not restored and the surface was being colored by surface color tool.