Cartoon pick: index is out of bounds

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.12.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.94 (2020-04-14)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/LPring_interactions-0.cxs

Log from Wed May 13 14:45:32 2020UCSF ChimeraX version: 0.94.dev202004140658
(2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/FlgHoligomerization.cxs

Log from Wed May 13 10:19:52 2020UCSF ChimeraX version: 0.94.dev202004140658
(2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/monoFlgH.cxs

Log from Tue May 12 21:20:06 2020UCSF ChimeraX version: 0.94.dev202004140658
(2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-0.cxs

Log from Tue May 12 16:34:18 2020UCSF ChimeraX version: 0.94.dev202004140658
(2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-0.cxs

Log from Tue May 12 15:56:41 2020UCSF ChimeraX version: 0.94.dev202004140658
(2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/PDB/LPring0511.pdb

Chain information for LPring0511.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | No description available  
a b c d e f g h i j k l m n o p q r s t u v w x y z | No description available  
  

> hide atoms

> show cartoons

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> open2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/PDB/LPring0511.pdb

Chain information for LPring0511.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z | No description available  
a b c d e f g h i j k l m n o p q r s t u v w x y z | No description available  
  

> hide atoms

> show cartoons

> hide #!2 models

> show #!2 models

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> select #1/A-Z

41314 atoms, 42172 bonds, 1 model selected  

> color sel spring green

> hide #!2 models

> color sel yellow green

> color sel lime green

> color sel lime

> select clear

> select #1/a-z

57928 atoms, 58344 bonds, 104 pseudobonds, 2 models selected  

> color sel cyan

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> select #1/A-Z:77-105,124-155

10998 atoms, 11024 bonds, 1 model selected  

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

> color sel royal blue

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel orange red

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel violet

> select clear

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel turquoise

> color sel yellow

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel deep sky blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel yellow

> select clear

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel pink

> color sel salmon

> color sel lime

> color sel sky blue

> color sel grey

> color sel plum

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel lightcoral

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-0.cxs

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel orange

> color sel #C90F4E

> color sel #B6D3A7

> color sel #FFE8AC

> color sel #06A2D1

> color sel #D1FF56

> select clear

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel green yellow

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-0.cxs

opened ChimeraX session  

> select #1:20-30,178-249

29718 atoms, 30134 bonds, 1 model selected  

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel red

> color sel dark red

> color sel pink

> color sel slate blue

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel orange

> color sel deep pink

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel sky blue

> color sel green

> color sel purple

> color sel hot pink

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel cyan

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel hot pink

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel slate blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel hot pink

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel slate blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel sky blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel gold

> color sel orange

> color sel orchid

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

> color sel magenta

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel deep skyblue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel coral

> color sel sandy brown

> color sel teal

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel lime

> color sel brown

> color sel red

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel yellow

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel slate blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel orange red

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel red

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel coral

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel purple

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel lime

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel dim grey

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel orange red

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel yellow

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-0.cxs

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel light grey

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel sea green

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel yellow

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel tomato

> color sel orange red

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel spring green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel blue

> color sel gray

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel deep pink

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel black

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel light cyan

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel orange

> color sel red

> select clear

> color sel orange

> color sel red

> color sel red

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel gold

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel indian red

> color sel light pink

> color sel purple

> color sel turquoise

> color sel khaki

> color sel light coral

> color sel light salmon

> color sel slate blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel red

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel lime

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel coral

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel pink

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel sky blue

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel red

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel magenta

> color sel lime

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel orange red

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel orange red

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel violet

> color sel red

> color sel purple

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel salmon

> select clear

> select #1/A-Z:106-123

3770 atoms, 3848 bonds, 1 model selected  

> color sel sky blue

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-0.cxs

opened ChimeraX session  

> select #1/A-Z:77-105,124-155

10998 atoms, 11024 bonds, 1 model selected  

> color sel spring green

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel lime green

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> select up

41314 atoms, 42172 bonds, 1 model selected  

> select down

10660 atoms, 10790 bonds, 1 model selected  

> color sel hot pink

> color sel pink

> color sel violet

> color sel plum

> color sel royal blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel red

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel purple

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel violet

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel grey

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-3.cxs

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel coral

> color sel orange red

> select clear

> color sel slate blue

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel slate blue

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-3.cxs

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel salmon

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel slate blue

> color sel sandy brown

> select clear

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel pink

> color sel deep pink

> color sel hot pink

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-3.cxs

> select #1/a-z

57928 atoms, 58344 bonds, 104 pseudobonds, 2 models selected  

> hide sel cartoons

> view orient

> turn x 90

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_11.jpg
> width 4000 height 4000 supersample 4

> show sel cartoons

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_12.jpg
> width 4000 height 4000 supersample 4

> select #1

99242 atoms, 100516 bonds, 104 pseudobonds, 2 models selected  

> hide sel cartoons

> show sel cartoons

> select #1/A-Z

41314 atoms, 42172 bonds, 1 model selected  

> hide sel cartoons

> select clear

> select #1/a-z:20-30,178-249,250-365

32162 atoms, 32292 bonds, 52 pseudobonds, 2 models selected  

> hide sel cartoons

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_13.jpg
> width 4000 height 4000 supersample 4

> select #1/a-z:20-30,178-249,250-365

32162 atoms, 32292 bonds, 52 pseudobonds, 2 models selected  

> show sel cartoons

> select clear

> select #1/a-z:250-365,178-249

29874 atoms, 30030 bonds, 52 pseudobonds, 2 models selected  

> hide sel cartoons

> show sel cartoons

> select #1/a-z:250-365,31-177

41392 atoms, 41626 bonds, 104 pseudobonds, 2 models selected  

> hide sel cartoons

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_14.jpg
> width 4000 height 4000 supersample 4

> select #1/a-z:20-30,178-249,31-177

42302 atoms, 42692 bonds, 52 pseudobonds, 2 models selected  

> select #1/a-z:250-365,31-177

41392 atoms, 41626 bonds, 104 pseudobonds, 2 models selected  

> show sel cartoons

> select #1/a-z:20-30,178-249,31-177

42302 atoms, 42692 bonds, 52 pseudobonds, 2 models selected  

> hide sel cartoons

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_15.jpg
> width 4000 height 4000 supersample 4

> show sel cartoons

> select clear

> show #!1 cartoons

> turn x 90

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_16.jpg
> width 4000 height 4000 supersample 4

> turn x 90

> turn x 90

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_17.jpg
> width 4000 height 4000 supersample 4

> turn x 90

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-3.cxs

> select #1/22-76

Nothing selected  

> select #1/22-76

Nothing selected  

> select #1:22-76

21606 atoms, 22048 bonds, 1 model selected  

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel purple

> select clear

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel fuchsia

> select clear

> select #1/A-Z:77-105,106-123

9126 atoms, 9230 bonds, 1 model selected  

> color sel green

> select clear

> select #1/A-Z:77-105,106-123

9126 atoms, 9230 bonds, 1 model selected  

> color sel light green

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel green

> select clear

> color sel lime green

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel lime green

> color sel teal

> color sel sea green

> select clear

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel light green

> select clear

> lighting shadows false

> select #1/A-Z:77-155

14768 atoms, 14924 bonds, 1 model selected  

> color sel light green

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel yellow green

> select clear

> select #1/A-Z:77-155

14768 atoms, 14924 bonds, 1 model selected  

> color sel sea green

> select clear

> select #1/A-Z:211-232

4784 atoms, 4914 bonds, 1 model selected  

> color sel sea green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel dodger blue

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel violet

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> select #1/a-z

57928 atoms, 58344 bonds, 104 pseudobonds, 2 models selected  

> color sel cyan

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel purple

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel magenta

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

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

> color sel royal blue

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel sky blue

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel yellow

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel orange

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel cyan

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel grey

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel light blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel dodger blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel sky blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel orange

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel blue

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel medium blue

> color sel deep sky blue

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel dodger blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel yellow

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel green

> select clear

> select #1/A-Z:77-155,211-232

19552 atoms, 19838 bonds, 1 model selected  

> color sel yellow green

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel salmon

> color sel light salmon

> select clear

> color sel salmon

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> color sel salmon

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel orange

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel magenta

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel lime

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel green

> select clear

> color sel spring green

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel spring green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel sea green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel yellow

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel gold

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel yellow

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel magenta

> select clear

> select #1/A-Z:156-210

10660 atoms, 10790 bonds, 1 model selected  

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel spring green

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel red

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel lime

> select clear

> select #1/A-Z:22-76

11102 atoms, 11466 bonds, 1 model selected  

> color sel blue

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel linen

> color sel antique white

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel silver

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel grey

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel cyan

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel light blue

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel pink

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel light cyan

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel magenta

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel deep sky blue

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

Unknown command: cyan  

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

> color sel cyan

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel sky blue

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel deep sky blue

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel deep sky blue

> color sel dodger blue

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel deep sky blue

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel aquamarine

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel cyan

> select clear

> select #1/a-z:31-177

25766 atoms, 26000 bonds, 52 pseudobonds, 2 models selected  

> color sel cyan

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel deep sky blue

> select clear

> select #1/a-z:20-30,178-249

16536 atoms, 16640 bonds, 1 model selected  

> color sel yellow

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel magenta

> select clear

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color sel light pink

> select clear

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> select #1/a-z:250-365

15626 atoms, 15626 bonds, 52 pseudobonds, 2 models selected  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel deep pink

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2-4.cxs

> view orient

> view orient

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_4.jpg
> width 4000 height 4000 supersample 4

> turn x 90

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_5.jpg
> width 4000 height 4000 supersample 4

> turn x 90

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_6.jpg
> width 4000 height 4000 supersample 4

> turn x 90

> turn x 90

> turn x 90

Expected an objects specifier or a keyword  

> select #1/B-Z,a-z

97653 atoms, 98894 bonds, 104 pseudobonds, 2 models selected  

> hide sel cartoons

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> style sel stick

Changed 15 atom styles  

> show sel atoms

> style sel stick

Changed 15 atom styles  

> color sel byhetero

> style sel sphere

Changed 15 atom styles  

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_7.jpg
> width 4000 height 4000 supersample 4

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_8.jpg
> width 4000 height 4000 supersample 4

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/monoFlgH.cxs

opened ChimeraX session  

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_8.jpg
> width 4000 height 4000 supersample 4

> select #1:22

598 atoms, 546 bonds, 1 model selected  

> color sel blue

> hide sel atoms

> select clear

> select #1/B

1589 atoms, 1622 bonds, 1 model selected  

> show sel cartoons

> select #1/B,C

3178 atoms, 3244 bonds, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select #1/Y,Z

3178 atoms, 3244 bonds, 1 model selected  

> show sel atoms

> show sel atoms

> hide sel atoms

> show sel cartoons

> select clear

> select #1/Y,Z,B,C

6356 atoms, 6488 bonds, 1 model selected  

> color sel white

> select clear

> select #1/Y,Z,B,C

6356 atoms, 6488 bonds, 1 model selected  

> color sel grey

> color sel lightgrey

> select clear

> select #1/Y,Z,B,C

6356 atoms, 6488 bonds, 1 model selected  

> transparency sel 50 cartoons

> select clear

> undo

> undo

> select clear

> select #1/Z

1589 atoms, 1622 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 1589 atom styles  

> color sel byhetero

> select clear

> select #1/A

1589 atoms, 1622 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 1589 atom styles  

> color sel byhetero

> select clear

> select #1/A:232

8 atoms, 7 bonds, 1 model selected  

> select #1/Y:221-232

109 atoms, 113 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 109 atom styles  

> color sel byhetero

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/FlgHoligomerization.cxs

Expected an objects specifier or a keyword  

> select #1/A:22,23,24/Z:214,215,218,221/Y:229,228,225,224

111 atoms, 110 bonds, 1 model selected  

> select clear

> hide #!1 atoms

> select #1/A:22,23,24/Z:214,215,218,221/Y:229,228,225,224

111 atoms, 110 bonds, 1 model selected  

> show sel atoms

> select clear

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

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

> color sel blue

> color sel byhetero

> select clear

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_9.jpg
> width 4000 height 4000 supersample 4

> toolshed show "Side View"

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_9.jpg
> width 4000 height 4000 supersample 4

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/FlgHoligomerization.cxs

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_9.jpg
> width 4000 height 4000 supersample 4

> select #1:X

Nothing selected  

> show #!1 cartoons

> hide #!1 cartoons

> show #!1 cartoons

> select #1:X

Nothing selected  

> show #!1 cartoons

> hide #!1 cartoons

> show #!1 cartoons

> hide #!1 cartoons

> select #1/A,B,C,X,Y,Z

9534 atoms, 9732 bonds, 1 model selected  

> show sel cartoons

> select #1/A,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

> color sel light grey

> undo

> select clear

> select #1/A,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

> color sel light grey

> select clear

> select #1/B,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

> color sel light grey

> select clear

> cartoon style

LPring0511.pdb #1  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  
LPring0511.pdb #2  
\- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow
scale=2  
\- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=12  
\- barbell parameters: sides=18 scale=0.5  

> select #1/A:22,23,24/Z:214,215,218,221/Y:229,228,225,224

111 atoms, 110 bonds, 1 model selected  

> size sel stickRadius 0.5

Changed 110 bond radii  

> size sel stickRadius 0.3

Changed 110 bond radii  

> size sel stickRadius 0.4

Changed 110 bond radii  

> size sel stickRadius 0.2

Changed 110 bond radii  

> size sel stickRadius 0.2

Changed 110 bond radii  

> size sel stickRadius 0.5

Changed 110 bond radii  

> size sel stickRadius 0.3

Changed 110 bond radii  

> size sel stickRadius 0.2

Changed 110 bond radii  

> size sel atomRadius 0.2

Changed 111 atom radii  

> size sel atomRadius 0.5

Changed 111 atom radii  

> size sel stickRadius 0.5

Changed 110 bond radii  

> size sel stickRadius 0.3

Changed 110 bond radii  

> color sel byhetero

> select clear

> select #1/B,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

> color sel grey

> color sel dimgrey

> color sel silver

> select clear

> select #1/A:22,23,24/Z:214,215,218,221/Y:229,228,225,224

111 atoms, 110 bonds, 1 model selected  

> color sel byhetero

> select clear

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> select #1/B,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

> graphics silhouettes true color red

> select clear

> graphics silhouettes true color black

> select #1/B,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

Expected a keyword  

Expected a keyword  

Expected a keyword  

Expected true or false or a keyword  

> select clear

> select #1/B,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

> graphics selection color black

Invalid "color" argument: Invalid color name or specifier  

> select #1/B,C,X,Y,Z

7945 atoms, 8110 bonds, 1 model selected  

Invalid "color" argument: Invalid color name or specifier  

> undo

> undo

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> color sel

> color sel blue

> color sel byhetero

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_9-0.jpg
> width 4000 height 4000 supersample 4

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> color sel orange

> color sel byhetero

> select #1/A:22@CA,CB

2 atoms, 1 bond, 1 model selected  

> color sel blue

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_9-0.jpg
> width 4000 height 4000 supersample 4

> select #1/A:22,23,24/Z:214,215,218,221/Y:229,228,225,224

111 atoms, 110 bonds, 1 model selected  

> hide sel atoms

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_14.jpg
> width 4000 height 4000 supersample 4

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_14.jpg
> width 4000 height 4000 supersample 4

> view orient

Unknown command: yutn x 90  

Unknown command: urn x 90  

> turn x 90

> turn x 90

> turn x 90

> turn x 90

> turn x 90

> turn y 180

> turn x 90

> turn x 90

> turn x 90

> turn x 90

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_14.jpg
> width 4000 height 4000 supersample 4

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/FlgHoligomerization.cxs

opened ChimeraX session  

> select #1/W

1589 atoms, 1622 bonds, 1 model selected  

> show sel cartoons

> color sel silver

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting flat

> lighting soft

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/FlgHoligomerization.cxs

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_14-0.jpg
> width 4000 height 4000 supersample 4

> lighting shadows true intensity 0.5

> lighting full

> lighting soft

> select #1/A:22

15 atoms, 14 bonds, 1 model selected  

> show sel atoms

> select clear

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/Fig2_8-1.jpg
> width 4000 height 4000 supersample 4

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/FlgHoligomerization.cxs

> select #1/a,b,c,z

8912 atoms, 8976 bonds, 16 pseudobonds, 2 models selected  

> show sel cartoons

> select #1/b

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> color sel sky blue

> color sel light blue

> lighting soft

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

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> select #1/b

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> color sel light sky blue

> color sel sky blue

> select #1/b

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> color sel sky blue

> select #1/c

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> color sel light green

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> lighting soft

> select #1/z

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> color sel plum

> select clear

> lighting soft

> lighting shadows true intensity 0.5

> lighting soft

> select #1/a:22

8 atoms, 7 bonds, 1 model selected  

> color sel yellow

> select clear

> hide #1.1 models

> select #1/C,X,W

4767 atoms, 4866 bonds, 1 model selected  

> hide sel cartoons

> select clear

> select #1/A,B,Y,Z,a,b,c,z

15268 atoms, 15464 bonds, 16 pseudobonds, 2 models selected  

> show sel atoms

> style sel stick

Changed 15268 atom styles  

> color sel byhetero

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/LPring_interactions.cxs

> select #1/z

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> surface sel

> color plum

> undo

> color sel plum

> select clear

> select #1/z

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> mlp sel

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

Unknown command: palette red-white-blue  

> mlp sel palette red-white-blue

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

> mlp sel palette cyan-white-maroon

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

> mlp sel palette grayscale

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

> mlp sel palette red-white-blue

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  
Fetching compressed palette red-green-blue from
http://www.colourlovers.com/api/palettes?keywords=red-green-
blue&format=json&numResults=100  
Could not find palette red-green-blue at COLOURlovers.com using keyword search  

> mlp sel palette lipophilicity

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

> select #1/b

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> mlp sel palette lipophilicity

Map values for surface "LPring0511.pdb_b SES surface": minimum -28.66, mean
-6.113, maximum 23.38  

> select clear

> mlp sel palette red-white-blue

mlp: no amino acids specified  

> select #1/b

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> mlp sel palette red-white-blue

Map values for surface "LPring0511.pdb_b SES surface": minimum -28.66, mean
-6.113, maximum 23.38  

> select clear

> select #1/a

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> mlp sel palette red-white-blue

Map values for surface "LPring0511.pdb_a SES surface": minimum -31.3, mean
-6.093, maximum 23.69  

> select #1/z

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> mlp sel palette red-white-blue

Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

> select #1/B,Y,Z

4767 atoms, 4866 bonds, 1 model selected  

> hide sel atoms

> select clear

> select #1/c

2228 atoms, 2244 bonds, 4 pseudobonds, 2 models selected  

> mlp sel palette red-white-blue

Map values for surface "LPring0511.pdb_c SES surface": minimum -29.55, mean
-6.09, maximum 23.32  

> select clear

> select #1/B,Y,Z

4767 atoms, 4866 bonds, 1 model selected  

> transparency sel 80 cartoons

> select clear

> select #1/a,b,c,z

8912 atoms, 8976 bonds, 16 pseudobonds, 2 models selected  

> mlp sel palette lipophilicity

Map values for surface "LPring0511.pdb_a SES surface": minimum -31.3, mean
-6.093, maximum 23.69  
Map values for surface "LPring0511.pdb_b SES surface": minimum -28.66, mean
-6.113, maximum 23.38  
Map values for surface "LPring0511.pdb_c SES surface": minimum -29.55, mean
-6.09, maximum 23.32  
Map values for surface "LPring0511.pdb_z SES surface": minimum -29.28, mean
-6.084, maximum 23.08  

> select #1/a,b,c,z:20-30,178-249

2544 atoms, 2560 bonds, 1 model selected  

> color sel yellow

> select clear

> select #1/a,b,c,z:31-177

3964 atoms, 4000 bonds, 8 pseudobonds, 2 models selected  

> color sel cyan

> select #1/a,b,c,z:250-365

2404 atoms, 2404 bonds, 8 pseudobonds, 2 models selected  

> color sel deep pink

> select clear

> select #1/a,b,c,z

8912 atoms, 8976 bonds, 16 pseudobonds, 2 models selected  

> hide sel surfaces

> select clear

> color #!1 byhetero

> hide #!1 atoms

> select #1/A:46-54,57,59,61-70,187,190,191

190 atoms, 189 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 190 atom styles  

> select
> #1/z:175-178,93,134,32,34-36,129,130,132/a:99,172,136,133,173,132,130,131/b:136,123,133,125,68,65,122,41,39,61,71,127,64,60/c:69,70,71,72,67,68

337 atoms, 319 bonds, 1 model selected  

> show sel atoms

> style sel stick

Changed 337 atom styles  

> color sel byhetero

> size sel stickRadius 0.3

Changed 319 bond radii  

> select #1/A:46-54,57,59,61-70,187,190,191

190 atoms, 189 bonds, 1 model selected  

> size sel stickRadius 0.3

Changed 189 bond radii  

> select clear

> select
> #1/z:175-178,93,134,32,34-36,129,130,132/a:99,172,136,133,173,132,130,131,129,37,38/b:136,123,133,125,68,65,122,41,39,61,71,127,64,60/c:69,70,71,72,67,68

356 atoms, 337 bonds, 1 model selected  

> show sel atoms

> size sel stickRadius 0.3

Changed 337 bond radii  

> lighting soft

> save2
> /home/tanjiaxing/Documents/1-2Flagella/Figures/HBB_PDB_0511/Fig2/LPring_interactions-0.cxs

opened ChimeraX session  

> size sel stickRadius 0.3

Changed 337 bond radii  

> select clear

> select #1/A:22-76/a,b,c,z

9339 atoms, 9417 bonds, 16 pseudobonds, 2 models selected  

> interfaces sel & ~solvent

8 buried areas: a b 3317, b c 3312, a z 3266, a c 487, b z 466, b A 457, a A
392, z A 374  

> select clear

> hide #!1 atoms

> show sel atoms

> style sel stick

Changed 363 atom styles  

> size sel stickRadius 0.3

Changed 345 bond radii  

> select clear

> size sel stickRadius 0.35

Changed 345 bond radii  

> size sel stickRadius 0.3

Changed 345 bond radii  

> size sel stickRadius 0.2

Changed 345 bond radii  

> size sel stickRadius 0.3

Changed 345 bond radii  

> select clear

> select #1/B,Z,Y

4767 atoms, 4866 bonds, 1 model selected  

> hide sel cartoons

> select clear

> select #1/a,z

4456 atoms, 4488 bonds, 8 pseudobonds, 2 models selected  

> transparency sel 80 cartoons

> transparency sel 50 cartoons

> select #1/A:47@CB/z:176@CG

2 atoms, 1 model selected  

> ui mousemode rightMode distance

> distance #1/z:176@CG #1/A:47@CB

Distance between LPring0511.pdb #1/z PRO 176 CG and /A ALA 47 CB: 4.228Å  

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> distance #1/A:50@OG #1/a:172@OE1

Distance between LPring0511.pdb #1/A SER 50 OG and /a GLU 172 OE1: 3.574Å  

> show #3.1 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #3

2 pseudobonds, 2 models selected  

> delete sel

> show #!3 models

> hide #!3 models

> select #3

2 pseudobonds, 2 models selected  

> delete sel

> select #3

2 pseudobonds, 2 models selected  

> delete sel

> distance #1/A:50@OG #1/a:172@OE1

Distance already exists; modify distance properties with 'distance style'  

> ui mousemode rightMode distance

> distance #1/A:50@OG #1/a:172@OE1

Distance already exists; modify distance properties with 'distance style'  

> show #!3 models

> hide #!3 models

> distance #1/A:48@ND2 #1/a:99@OE1

Distance between LPring0511.pdb #1/A ASN 48 ND2 and /a GLN 99 OE1: 4.233Å  

> ui mousemode rightMode distance

> distance #1/A:48@ND2 #1/a:99@OE1

Distance already exists; modify distance properties with 'distance style'  

> show #!3 models

> distance #1/A:48@ND2 #1/a:99@NE2

Distance between LPring0511.pdb #1/A ASN 48 ND2 and /a GLN 99 NE2: 4.285Å  

> distance #1/a:172@OE1 #1/z:32@NH2

Distance between LPring0511.pdb #1/a GLU 172 OE1 and /z ARG 32 NH2: 3.580Å  

Unknown command: seelct #1/z:178,177  

> hide #!1 atoms

> show #!1 atoms

> undo

> undo

Unknown command: seelct #1/z:178,177  

> select #1/z:178,177

16 atoms, 15 bonds, 1 model selected  

> hide sel atoms

> distance #1/z:34@OD1 #1/A:50@OG

Distance between LPring0511.pdb #1/z ASN 34 OD1 and /A SER 50 OG: 4.445Å  

> select #1/z:178,177,130

24 atoms, 22 bonds, 1 model selected  

> hide sel atoms

> distance delete

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 617, in
picked_object_on_segment  
p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 788, in first_intercept_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 986, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 586, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
IndexError: index 1487 is out of bounds for axis 0 with size 1423  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.43
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: C246-WU4
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
Cache Size: 12288 KB
Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:11a3]
	Kernel driver in use: nvidia

[Tom Goddard]

Was fixed April 21. Reporter is using April 14 build.