CliX: Could not determine home directory

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/admin/Desktop/1.cxs

Not registering illegal selector name "1"  

Not registering illegal selector name "1 "  

Not registering illegal selector name "~#/A"  

Not registering illegal selector name "~#1/A"  

Not registering illegal selector name "target ~#1?A"  

Log from Tue Sep 16 15:38:27 2025UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/admin/Desktop/3 课题工作/1 Dnd FGH/1 实验数据/2 结构建模/5
> 最终汇总/FGH-2S_DNA.pdb"

Chain information for FGH-2S_DNA.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E | No description available  
F | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
  

> open "/Users/admin/Desktop/3 课题工作/1 Dnd FGH/1 实验数据/2 结构建模/5 最终汇总/FGH-
> noS_DNA.pdb"

Chain information for FGH-noS_DNA.pdb #2  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E F | No description available  
H | No description available  
I | No description available  
  

> open "/Users/admin/Desktop/3 课题工作/1 Dnd FGH/1 实验数据/2 结构建模/5 最终汇总/FGH-
> allS_DNA.pdb"

Chain information for FGH-allS_DNA.pdb #3  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E | No description available  
F | No description available  
H J | No description available  
I K | No description available  
  

> open "/Users/admin/Desktop/3 课题工作/1 Dnd FGH/1 实验数据/2 结构建模/5 最终汇总/FGH-
> no_DNA.pdb"

Chain information for FGH-no_DNA.pdb #4  
---  
Chain | Description  
A B | No description available  
C D | No description available  
E | No description available  
F | No description available  
  

> rename #4 id #5

> rename #3 id #4

> rename #2 id #3

> rename #5 id #2

> delete /C/D/E/F/H/I/J/K/L/M

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> hide #4 models

> align #1 /B toAtoms #1 /A matchAtomNames true

RMSD between 8903 atom pairs is 2.827 angstroms  

> hide #1 atoms

> show #1 cartoons

> split

Split FGH-2S_DNA.pdb (#1) into 2 models  
Split FGH-allS_DNA.pdb (#4) into 2 models  
Split FGH-noS_DNA.pdb (#3) into 2 models  
Split FGH-no_DNA.pdb (#2) into 2 models  
Chain information for FGH-2S_DNA.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for FGH-2S_DNA.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for FGH-allS_DNA.pdb A #4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for FGH-allS_DNA.pdb B #4.2  
---  
Chain | Description  
B | No description available  
  
Chain information for FGH-noS_DNA.pdb A #3.1  
---  
Chain | Description  
A | No description available  
  
Chain information for FGH-noS_DNA.pdb B #3.2  
---  
Chain | Description  
B | No description available  
  
Chain information for FGH-no_DNA.pdb A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for FGH-no_DNA.pdb B #2.2  
---  
Chain | Description  
B | No description available  
  

> align #1 /B toAtoms #1 /A matchAtomNames true

RMSD between 8903 atom pairs is 2.827 angstroms  

> align #2 /A toAtoms #1 /A matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 8900 atom pairs is 2.878 angstroms  

> align #2 /A toAtoms #1 /A matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 8900 atom pairs is 2.878 angstroms  

> align #2 /B toAtoms #1 /A matchAtomNames true

Pairing dropped 3 atoms and 6 reference atoms  
RMSD between 8897 atom pairs is 3.760 angstroms  

> align #3 /B toAtoms #1 /A matchAtomNames true

Pairing dropped 2 atoms and 4 reference atoms  
RMSD between 8899 atom pairs is 2.904 angstroms  

> align #3 /A toAtoms #1 /A matchAtomNames true

Pairing dropped 1 atoms and 4 reference atoms  
RMSD between 8899 atom pairs is 3.659 angstroms  

> align #4 /A toAtoms #1 /A matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 8900 atom pairs is 3.882 angstroms  

> align #4 /B toAtoms #1 /A matchAtomNames true

RMSD between 8903 atom pairs is 2.716 angstroms  

> show #2.1 models

> show #2.2 models

> show #3.1 models

> show #3.2 models

> show #4.1 models

> show #4.2 models

> hide atoms

> show cartoons

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> hide #2.2 models

> hide #2.1 models

> hide #!2 models

> hide #1.2 models

> show #1.2 models

> ui tool show "Color Actions"

> color #1 #a141ffff

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel gray

> select clear

> show #2.1 models

> select add #2.1

8900 atoms, 9003 bonds, 551 residues, 1 model selected  

> color sel cyan

> select clear

> hide #2.1 models

> hide #!2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> show #!3 models

> show #3.1 models

> show #3.2 models

> show #!4 models

> show #4.1 models

> show #4.2 models

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 71210 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> hide #2.2 models

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> transparency #1B 10 C

Missing or invalid "percent" argument: Expected a number  

> transparency #1/B 10 cartoons

> transparency #1/B 20 cartoons

> transparency #1/B 90 cartoons

> transparency #1/B 50 cartoons

> set bgColor white

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> lighting shadows false

> graphics silhouettes true

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting full

> lighting soft

> lighting flat

[Repeated 2 time(s)]

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> select clear

> color #1.2 #6d3e9dff

> color #1.2 #6d3e9d86

> color #1.2 #6d3e9dff

> color #1.2 #673a94ff

> color #1.2 #683b95ff

> color #1.2 #683b9582

> select clear

> color #1.1 #80808081

> color #1.1 #80808082

> color #1.2 #683b95ff

> select clear

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #3.1 models

> hide #!3 models

> show #3.2 models

> hide #!2 models

> hide #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #!3 models

> hide #3.1 models

> show #1.1 models

> lighting full

> color #1.2 #bf80ffff

> color #1.1 #fefdff82

> color #1.1 #8c8c8dff

> select clear

> show #2.2 models

> color #1.1 #8c8c8d82

> show #!3 models

> color #1.1 #8c8c8dff

> color #1.1 #8c8c8d80

> show #!4 models

> show #4.1 models

> show #4.2 models

> show #3.1 models

> color #1.1 #8c8c8d80

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1.2

8903 atoms, 9006 bonds, 551 residues, 2 models selected  

> color #1.1 #8c8c8d85

Drag select of 11 residues  

> select clear

> color bfactor #1.1-2#2.2#3.1-2#4.1-2

62310 atoms, 3857 residues, atom bfactor range 33.4 to 361  

> hide #1.2 models

> hide #!2 models

> hide #2.2 models

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> color #1.1 #8c8c8dff

[Repeated 1 time(s)]

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color bfactor sel

8903 atoms, 551 residues, atom bfactor range 38.6 to 324  

> select clear

> save /Users/admin/Desktop/1.tif width 3860 height 2593 supersample 3
> transparentBackground true

> color #1.1 #818181ff

> color #1.1#!1 byelement

> ui tool show "Color Actions"

> color #1.1#!1 #818080ff

[Repeated 1 time(s)]

> color #1.1#!1 #7a7781ff

> color #1.1#!1 #706b81ff

> color #1.1#!1 #6e6881ff

> color #1.1#!1 #6b6581ff

> color #1.1#!1 #696281ff

> color #1.1#!1 #645d81ff

> color #1.1#!1 #635c81ff

> color #1.1#!1 #605881ff

> color #1.1#!1 #5b5381ff

> color #1.1#!1 #594f81ff

> color #1.1#!1 #574e81ff

> color #1.1#!1 #554c81ff

> color #1.1#!1 #544a81ff

> color #1.1#!1 #4e4581ff

[Repeated 1 time(s)]

> color #1.1#!1 #4c4281ff

> color #1.1#!1 #4b4281ff

> color #1.1#!1 #4b4181ff

> color #1.1#!1 #4a4181ff

> color #1.1#!1 #494081ff

> color #1.1#!1 #473c81ff

> color #1.1#!1 #433781ff

> color #1.1#!1 #433681ff

> color #1.1#!1 #433581ff

[Repeated 2 time(s)]

> color #1.1#!1 #443781ff

> color #1.1#!1 #473d81ff

> color #1.1#!1 #484081ff

[Repeated 1 time(s)]

> color #1.1#!1 #484181ff

> color #1.1#!1 #494181ff

> color #1.1#!1 #494282ff

> color #1.1#!1 #4d4589ff

> color #1.1#!1 #564d98ff

> color #1.1#!1 #665bb5ff

> color #1.1#!1 #7165c8ff

> color #1.1#!1 #796dd7ff

> color #1.1#!1 #8577ecff

> color #1.1#!1 #8a7bf4ff

> color #1.1#!1 #8e7ffbff

> color #1.1#!1 #8f80feff

> color #1.1#!1 #9081ffff

[Repeated 1 time(s)]

> color #1.1#!1 #8f80feff

> color #1.1#!1 #8a7bf3ff

> color #1.1#!1 #786bd5ff

> color #1.1#!1 #7266c9ff

> color #1.1#!1 #6f63c4ff

> color #1.1#!1 #6e63c3ff

> color #1.1#!1 #7266caff

> transparency #1/a 50 cartoons

> color purple

> color medium blue

> color dark orchid

> color slate blue

> color indigo

> color dark blue

> color medium blue

> color blue

> color medium slate blue

> color slate blue

> lighting full

> select ~sel & ##selected

Nothing selected  

> show #1.2 models

> color #1.2 #6a5acd87

> color #1.2 slateblue

[Repeated 1 time(s)]

> color #1.2 #404040ff

> color #1.2 grey

> select clear

> color #1.2 #80808081

> color #1.1 slateblue

> select clear

> show #!2 models

> show #2.1 models

> show #2.2 models

> show #!3 models

> show #3.1 models

> show #3.2 models

> show #4.1 models

> show #4.2 models

> color #1.1 grey

> color #2.1 grey

> color #2.2 grey

> color #3.1 grey

> color #3 grey models

> color #4.1 grey

> color #4.2 grey

> color medium slate blue

> undo

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel medium slate blue

> select clear

> color #1.2 #80808082

> color #2 #b2b2b287 models

> color #3.1 #80808084

> color #3.1 #80808085

> color #3.2 #80808087

> color #4.1 #80808082

> color #4.2 #80808088

> color #4.2 #80808087

> select clear

> color #1.1 mediumslateblue

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel medium slate blue

> select clear

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1.1

8903 atoms, 9006 bonds, 551 residues, 2 models selected  

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select all

71210 atoms, 72034 bonds, 4408 residues, 12 models selected  

> select subtract #1.1

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> color #1.2 grey

> color sel gray

> select clear

> lighting soft

> lighting full

> select clear

[Repeated 1 time(s)]

> save /Users/admin/Desktop/1.tif width 3860 height 3236 supersample 3
> transparentBackground true

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select all

71210 atoms, 72034 bonds, 4408 residues, 12 models selected  

> select subtract #1.1

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> hide #1.2#2.1-2#3.1-2#4.1-2 target m

> show #4.2 target m

> hide #1.1 target m

> show #1.1 target m

> hide #4.2 target m

> show #1.2 target m

> hide #1.1 target m

> show #2.1 target m

> hide #1.2 target m

> show #2.2 target m

> hide #2.1 target m

> show #3.1 target m

> hide #2.2 target m

> show #3.2 target m

> hide #3.1 target m

> undo

[Repeated 9 time(s)]

> show #1.2 models

> show #2.1 models

> show #2.2 models

> show #3.1 models

> show #3.2 models

> show #4.1 models

> show #4.2 models

> transparency sel 90 cartoons

> select clear

> color #1.1 mediumslateblue

> color #2 #b2b2b2ff models

> color #2 #b2b2b200 models

> color #3 #80808000 models

> color #4.1 #8080801a

> color #4.2 #80808000

> color #4.1 #80808000

> select clear

> transparency sel 20 cartoons

> select all

71210 atoms, 72034 bonds, 4408 residues, 12 models selected  

> select subtract #1.1

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> transparency sel 20 cartoons

> select clear

> select ~sel & ##selected

Nothing selected  

> view #1.1 clip false

[Repeated 1 time(s)]

> ui tool show Updates

> align #1 /A toAtoms #1 /A matchAtomNames true

RMSD between 8903 atom pairs is 0.000 angstroms  

> color #1.1 #7b68eefc

> color #4.2 #89928ecc

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

[Repeated 1 time(s)]

> nucleotides sel ladder

> cartoons

Unknown command: cartoons  

> transparency sel 20 surfaces

> transparency sel 80 surfaces

> transparency sel 100 surfaces

> select clear

> transparency sel 100 r

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

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> transparency sel 100 r

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

> material

Reflectivity: 0.8  
Specular reflectivity 0.3  
Specular exponent: 30  
Ambient reflectivity 0.8  
Transparent cast shadows: false  
Meshes cast shadows: false  

> material shiny

> material dull

> select clear

> material chimera

> select clear

> hide #1.2 models

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> material dull

> material shiny

> material shiny transparentCastShadows true

> material shiny transparentCastShadows true meshesCastShadows true

> material shiny transparentCastShadows true meshesCastShadows false

> lighting full

> lighting soft

> lighting simple

> lighting full

> material shiny transparentCastShadows true meshesCastShadows false

> material shiny transparentCastShadows true meshesCastShadows false
> exponent128

Expected a keyword  

> material shiny exponent128

Expected a keyword  

> material shiny exponent 18

> material shiny exponent 128

> material shiny exponent 18 specularReflectivity 1

> material shiny exponent 18 specularReflectivity 20

> material shiny exponent 18 specularReflectivity 1 reflectivity 5

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> material shiny exponent 18 specularReflectivity 1 reflectivity 1

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.1

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8
> reflectivity 10

Repeated keyword argument "reflectivity"  

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 10

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 0

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 0.8

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 1.8

> material shiny exponent 18 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 1.5

> material exponent 18 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 1.5

> material exponent 6 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 1.5

> material exponent 6 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 11.2

> material exponent 6 specularReflectivity 1 reflectivity 0.8
> ambientReflectivity 1.2

> lighting soft

> select clear

> lighting full

> lighting soft

> material exponent 6 specularReflectivity 1 reflectivity 0.6
> ambientReflectivity 1.2

> material exponent 6 specularReflectivity 0.8 reflectivity 0.6
> ambientReflectivity 1.2

> material exponent 6 specularReflectivity 0reflectivity 0.6
> ambientReflectivity 1.2

Invalid "specularReflectivity" argument: Expected a number  

> material exponent 6 specularReflectivity 0 reflectivity 0.6
> ambientReflectivity 1.2

> material exponent 1 specularReflectivity 0 reflectivity 0.6
> ambientReflectivity 1.2

> material exponent 1 specularReflectivity 0 reflectivity 0ambientReflectivity
> 1.2

Invalid "reflectivity" argument: Expected a number  

> material exponent 1 specularReflectivity 0 reflectivity 0
> ambientReflectivity 1.2

> materialdull exponent 1 specularReflectivity 0 reflectivity 0
> ambientReflectivity 1.2

Unknown command: materialdull exponent 1 specularReflectivity 0 reflectivity 0
ambientReflectivity 1.2  

> material dull exponent 1 specularReflectivity 0 reflectivity 0
> ambientReflectivity 1.2

> material dull exponent 1 specularReflectivity 0 reflectivity 0
> ambientReflectivity 0.8

> material dull exponent 1 specularReflectivity 0 reflectivity
> 10ambientReflectivity 0.8

Invalid "reflectivity" argument: Expected a number  

> material dull exponent 1 specularReflectivity 0 reflectivity 10
> ambientReflectivity 0.8

> material dull exponent 1 specularReflectivity 0 reflectivity 10
> ambientReflectivity 10

> material dull exponent 1 specularReflectivity 0 reflectivity 10
> ambientReflectivity 1.8

> material dull exponent 1 specularReflectivity 0 reflectivity 10
> ambientReflectivity 1.8 transparentCastShadows true

> material dull exponent 1 specularReflectivity 0 reflectivity 10
> ambientReflectivity 0.8 transparentCastShadows true

> show #1.2 models

> show #!2 models

> hide #!2 models

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> show #!2 models

> show #2.1 models

> show #2.2 models

> show #!3 models

> show #3.1 models

> show #3.2 models

> show #4.1 models

> show #4.2 models

> move z 10 models #1

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> move z 10 models #1。1

Invalid "models" argument: only initial part "#1" of atom specifier valid  

> move z 10 models #1.1

> select clear

> move z -10 models #1.1

[Repeated 1 time(s)]

> align #3 /A toAtoms #1/A matchAtomNames true

Pairing dropped 1 atoms and 4 reference atoms  
RMSD between 8899 atom pairs is 3.659 angstroms  

> align #2 /A toAtoms #1/A matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 8900 atom pairs is 2.878 angstroms  

> align #4 /A toAtoms #1/A matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 8900 atom pairs is 3.882 angstroms  

> align #4 /B toAtoms #1/A matchAtomNames true

RMSD between 8903 atom pairs is 2.716 angstroms  

> align #3 /B toAtoms #1/A matchAtomNames true

Pairing dropped 2 atoms and 4 reference atoms  
RMSD between 8899 atom pairs is 2.904 angstroms  

> align #2 /B toAtoms #1/A matchAtomNames true

Pairing dropped 3 atoms and 6 reference atoms  
RMSD between 8897 atom pairs is 3.760 angstroms  

> align #1 /B toAtoms #1/A matchAtomNames true

RMSD between 8903 atom pairs is 2.827 angstroms  

> select clear

> move z 10 models #1.1

> move z 5 models #1.1

> move z -5 models #1.1

[Repeated 1 time(s)]

> move z -3 models #1.1

> move z -2 models #1.1

> move z 2 models #1.1

> select clear

> move x 2 models #1.1

> select clear

> move y -1 models #1.1

> select clear

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> material default

> lighting soft

> lighting simple

> lighting soft

> lighting full

> ui tool show "Selection Inspector"

> name 1 1

"1": invalid atom specifier  

> name 1 #1

Not registering illegal selector name "1"  

> name "1 " #1

Not registering illegal selector name "1 "  

> name 好的 #1

> select 好的

Expected an objects specifier or a keyword  

> name F1 #1

> select F1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select subtract #1

Nothing selected  

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1

Nothing selected  

> color #1.1 #6b62b8fc

> lighting full

[Repeated 1 time(s)]

> lighting soft

> lighting full

> lighting simple

[Repeated 1 time(s)]

> color #1.1 #002cc5fc

> color #1.1 #5422c5fc

> color #1.1 #6c20c5fc

> color #1.1 #5d25c5fc

> color #1.1 #792ffffc

> color #1.1 #7940fffc

> color #1.1 #711bfffc

> save /Users/admin/Desktop/1.tif width 3860 height 3236 supersample 3
> transparentBackground true

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1.1

8903 atoms, 9006 bonds, 551 residues, 2 models selected  

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select clear

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select all

71210 atoms, 72034 bonds, 4408 residues, 12 models selected  

> select subtract #1.1

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> ui tool show "Color Actions"

> color sel white

> color sel light gray

> select clear

> save /Users/admin/Desktop/1.tif width 3860 height 3236 supersample 3
> transparentBackground true

> lighting full

[Repeated 1 time(s)]

> color light gray

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel slate blue

> color sel medium slate blue

> color sel slate blue

> select clear

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select all

71210 atoms, 72034 bonds, 4408 residues, 12 models selected  

> select subtract #1.1

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> name frozen ~#/A sel

Not registering illegal selector name "~#/A"  

> name frozen ~#1/A sel

Not registering illegal selector name "~#1/A"  

> undo

> select clear

> select all

71210 atoms, 72034 bonds, 4408 residues, 12 models selected  

> select subtract #1.1

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> name frozen ~#1/A sel

Not registering illegal selector name "~#1/A"  

> name frozen "target ~#1?A" sel

Not registering illegal selector name "target ~#1?A"  

> name frozen shangse sel

> select clear

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> color sel gainsboro

[Repeated 1 time(s)]

> color sel light gray

> color sel silver

> color sel dark gray

> select clear

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> transparency sel 20 cartoons

> transparency sel 80 cartoons

> transparency sel 30 cartoons

> select clear

> save /Users/admin/Desktop/1.tif width 3860 height 3236 supersample 3
> transparentBackground true

> move z -2 models #1.1

> select clear

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> transparency sel 100 cartoons

> select clear

> color #1.1 slateblue

> select clear

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel orange red

> color sel red

> color sel orange red

> color sel red

> color sel orange red

> color sel orange

> color sel yellow

> color sel lime

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> show #!2 models

> show #2.1 models

> show #2.2 models

> show #!3 models

> show #3.1 models

> show #3.2 models

> show #!4 models

> show #4.1 models

> show #4.2 models

> select clear

> hide #1.2 models

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> show #3.2 models

> hide #!4 models

> hide #3.2 models

> hide #!3 models

> hide #4.1 models

> hide #4.2 models

> color dark sea green

> show #1.2 models

> show #!2 models

> show #2.1 models

> show #2.2 models

> show #!3 models

> show #3.1 models

> show #3.2 models

> show #!4 models

> show #4.1 models

> show #4.2 models

> transparency sel 0 cartoons

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> transparency sel 0 cartoons

> select clear

> color gray

> select add #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel dark sea green

> select clear

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> graphics silhouettes true

> color light gray

> hide #!1 models

> hide #1.1 models

> hide #1.2 models

> hide #4.2 models

> hide #4.1 models

> hide #!4 models

> hide #3.2 models

> hide #3.1 models

> hide #!3 models

> hide #2.2 models

> hide #2.1 models

> show #!1 models

> show #1.1 models

> show #1.2 models

> show #2.1 models

> show #2.2 models

> show #!3 models

> show #3.1 models

> show #3.2 models

> show #!4 models

> show #4.1 models

> show #4.2 models

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> color sel light sea green

> select subtract #1.2

8903 atoms, 9006 bonds, 551 residues, 2 models selected  

> select subtract #1.1

1 model selected  

> color sel plum

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

17806 atoms, 18012 bonds, 1102 residues, 3 models selected  

> color sel plum

> select subtract #1

Nothing selected  

> hide #1.1 models

> hide #1.2 models

> show #1.1 models

> show #1.2 models

> transparency all 50 cartoons

> transparency all 30 cartoons

> transparency all 10 cartoons

> transparency all 0c

Missing or invalid "percent" argument: Expected a number  

> transparency all 0 cartoons

> select clear

> hide #1.2 models

> color #1.2 #dda0dd82

> color #1.2 plum

> toolshed show

Downloading bundle chimerax_clix-0.2.3-py3-none-any.whl  
/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/pkginfo/distribution.py:175: NewMetadataVersion: New metadata version
(2.4) higher than latest supported version: parsing as 2.3  
warnings.warn(NewMetadataVersion(self.metadata_version))  
Installed ChimeraX-clix (0.2.3)  

> transparency 70 #2,3

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

> transparency 70 #2,3 all

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

> transparency 70 #2,3 cartoons

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

> transparency 70 cartoons

> transparency #1 0 cartoons

> select clear

Downloading bundle chimerax_clix-0.2.3-py3-none-any.whl  
Bundle installation canceled  

> save /Users/admin/Desktop/1.cxs

——— End of log from Tue Sep 16 15:38:27 2025 ———

> view name session-start

opened ChimeraX session  

> toolshed show

> ui tool show clix

> ui tool show CliX

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> toolshed show

> ui tool hide "command line interface"

> ui tool show "Color Actions"

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> select ~sel & ##selected

Nothing selected  

> select shangse

62307 atoms, 63028 bonds, 3857 residues, 11 models selected  

> color sel light gray

> color sel gray

> select clear

> transparency shangse 40 cartoons

> transparency shangse 70 cartoons

> color gray

> color dim gray

> color black

> color dim gray

> select clear

> select 1#/a

Expected an objects specifier or a keyword  

> select #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  

> color sel slate blue

> select clear

> color medium slate blue

> select clear

> select #1.1

8903 atoms, 9006 bonds, 551 residues, 1 model selected  
Traceback (most recent call last):  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 174, in _on_text_changed  
self._update_completion_state(False)  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 98, in
_update_completion_state  
self._current_completion_state =
list_widget._get_completion_list(cursor.selectedText())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 169, in _get_completion_list  
if state := complete_path(last_word, current_command):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 8, in complete_path  
if completions := _complete_path_impl(last_word):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 26, in
_complete_path_impl  
_maybe_path = Path(last_word.lstrip("'").lstrip('"')).expanduser().absolute()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
RuntimeError: Could not determine home directory.  
  
RuntimeError: Could not determine home directory.  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 174, in _on_text_changed  
self._update_completion_state(False)  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 98, in
_update_completion_state  
self._current_completion_state =
list_widget._get_completion_list(cursor.selectedText())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 169, in _get_completion_list  
if state := complete_path(last_word, current_command):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 8, in complete_path  
if completions := _complete_path_impl(last_word):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 26, in
_complete_path_impl  
_maybe_path = Path(last_word.lstrip("'").lstrip('"')).expanduser().absolute()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
RuntimeError: Could not determine home directory.  
  
RuntimeError: Could not determine home directory.  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 174, in _on_text_changed  
self._update_completion_state(False)  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 98, in
_update_completion_state  
self._current_completion_state =
list_widget._get_completion_list(cursor.selectedText())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 169, in _get_completion_list  
if state := complete_path(last_word, current_command):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 8, in complete_path  
if completions := _complete_path_impl(last_word):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 26, in
_complete_path_impl  
_maybe_path = Path(last_word.lstrip("'").lstrip('"')).expanduser().absolute()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
RuntimeError: Could not determine home directory.  
  
RuntimeError: Could not determine home directory.  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 174, in _on_text_changed  
self._update_completion_state(False)  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 98, in
_update_completion_state  
self._current_completion_state =
list_widget._get_completion_list(cursor.selectedText())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/widgets/popups.py", line 169, in _get_completion_list  
if state := complete_path(last_word, current_command):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 8, in complete_path  
if completions := _complete_path_impl(last_word):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/admin/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/clix/algorithms/filepath.py", line 26, in
_complete_path_impl  
_maybe_path = Path(last_word.lstrip("'").lstrip('"')).expanduser().absolute()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
RuntimeError: Could not determine home directory.  
  
RuntimeError: Could not determine home directory.  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/pathlib.py",
line 1385, in expanduser  
raise RuntimeError("Could not determine home directory.")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac13,1
      Model Number: MJMV3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 18天7小时48分钟

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Redmi 238 NFS:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Redmi 238 NFS:
          Resolution: 1080 x 1920
          UI Looks like: 1080 x 1920 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: 90


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-clix: 0.2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    ChimeraX-Label: 1.1.14
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.9.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.4
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14