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#3086 closed defect (fixed)

IndexError during ribbon pick

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Graphics	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-20)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.94.dev202004200102 (2020-04-20)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2 /Users/xwu/Desktop/1cqt.pdb

1cqt.pdb title:  
Crystal structure of A ternary complex containing an oca-B peptide, the oct-1
pou domain, and an octamer element [more info...]  
  
Chain information for 1cqt.pdb #1  
---  
Chain | Description  
A B | pou domain, class 2, transcription factor 1  
I J | pou domain, class 2, associating factor 1  
M O | DNA (5'- D(*TP*GP*TP*ap*TP*GP*CP*ap*ap*ap*TP*ap*ap*GP*G)-3')  
N P | DNA (5'- D(*ap*CP*CP*TP*TP*ap*TP*TP*TP*GP*CP*ap*TP*ap*C)-3')  
  

> style sphere

Changed 3649 atom styles  

> style stick

Changed 3649 atom styles  

> style sphere

Changed 3649 atom styles  

> style ball

Changed 3649 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 1183 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 1183 atom styles  

> nucleotides fill

> style nucleic stick

Changed 1183 atom styles  

> show cartoons

> hide atoms

> interfaces ~solvent

8 buried areas: A N 973, B O 865, A M 847, B P 750, O P 677, M N 649, A I 546,
B J 520  

> interfaces ~solvent

8 buried areas: A N 973, B O 865, A M 847, B P 750, O P 677, M N 649, A I 546,
B J 520  

> interfaces ~solvent

8 buried areas: A N 973, B O 865, A M 847, B P 750, O P 677, M N 649, A I 546,
B J 520  

> interfaces ~solvent

8 buried areas: A N 973, B O 865, A M 847, B P 750, O P 677, M N 649, A I 546,
B J 520  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> lighting simple

> lighting simple

> lighting simple

> lighting simple

> lighting flat

> lighting flat

> view

> view

> view

> view

> view orient

> view orient

> ui mousemode rightMode minimize

> ui mousemode rightMode minimize

> ui mousemode rightMode windowing

> ui mousemode rightMode windowing

> ui mousemode rightMode clip

> show target m

> show target m

> select #1.1

8 pseudobonds, 1 model selected  

> ~select #1.1

Nothing selected  

> select #1

3649 atoms, 3819 bonds, 8 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> ui mousemode rightMode "crop volume"

> ui mousemode rightMode select

> volume step 2

No volumes specified  

> volume step 1

No volumes specified  

> view orient

> volume projectionMode 2d-xyz

No volumes specified  

> volume projectionMode 2d-xyz

No volumes specified  

> volume projectionMode 3d

No volumes specified  

> volume projectionMode 3d

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting full

> nucleotides atoms

> style nucleic stick

Changed 1183 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 1183 atom styles  

> nucleotides fill

> style nucleic stick

Changed 1183 atom styles  

> nucleotides slab

> style nucleic stick

Changed 1183 atom styles  

> nucleotides tube/slab shape box

> nucleotides tube/slab shape box

> color bynucleotide

> color bynucleotide

> color bynucleotide

> nucleotides stubs

> nucleotides ladder

> hide surfaces

> show surfaces

> hide surfaces

> hide cartoons

> show cartoons

> hide atoms

> show atoms

> show atoms

> hide atoms

> style ball

Changed 3649 atom styles  

> style ball

Changed 3649 atom styles  

> style ball

Changed 3649 atom styles  

> style sphere

Changed 3649 atom styles  

> style sphere

Changed 3649 atom styles  

> style stick

Changed 3649 atom styles  

> style stick

Changed 3649 atom styles  

> hide cartoons

> show cartoons

> hide atoms

> show atoms

> show atoms

> show atoms

> hide atoms

> volume step 2

No volumes specified  

> select clear

> select clear

> volume appearance airways

No volumes specified  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> toolshed show "Cage Builder"

> toolshed show Toolbar

> select #1.2

310 atoms, 1 model selected  

> ~select #1.2

1 model selected  

> select #1

3649 atoms, 3819 bonds, 8 pseudobonds, 2 models selected  

> ~select #1

8 models selected  

> select #1.5

281 atoms, 1 model selected  

> ~select #1.5

1 model selected  

> select #1.4

293 atoms, 1 model selected  

> ~select #1.4

1 model selected  

> select #1.3

299 atoms, 1 model selected  

> ~select #1.3

1 model selected  

> select #1.9

184 atoms, 1 model selected  

> ~select #1.9

1 model selected  

> select #1.9

184 atoms, 1 model selected  

> ~select #1.9

1 model selected  

> select #1.8

179 atoms, 1 model selected  

> ~select #1.8

1 model selected  

> select #1.8

179 atoms, 1 model selected  

> select #1.9

184 atoms, 1 model selected  

> ~select #1.9

1 model selected  

> select #1.8

179 atoms, 1 model selected  

> ~select #1.8

1 model selected  

> hide #1.8 models

> hide #1.6 models

> hide #1.2 models

> hide #1.4 models

> hide #1.8 target m

> hide #1.8 target m

> hide #1.1 models

> hide #!1 models

> show #!1 models

> hide #1.3 models

> hide #1.5 models

> hide #1.7 models

> hide #1.9 models

> hide #!1 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> hide #!1 models

> show #1.2 models

> show #1.3 models

> hide #1.3 models

> hide #1.2 models

> select #1

3649 atoms, 3819 bonds, 8 pseudobonds, 2 models selected  

> ~select #1

8 models selected  

> select #1.2

310 atoms, 1 model selected  

> ~select #1.2

1 model selected  

> select #1.3

299 atoms, 1 model selected  

> ~select #1.3

1 model selected  

> select #1.3

299 atoms, 1 model selected  

> select #1.4

293 atoms, 1 model selected  

> select #1.5

281 atoms, 1 model selected  

> select #1.6

1061 atoms, 1 model selected  

> select #1.7

1042 atoms, 1 model selected  

> hide #1.7 target m

> show #1.7 models

> hide #1.7 models

> hide #!1 models

> show #!1 models

> show #1.1 models

> show #1.2 models

> show #1.3 models

> show #1.4 models

> show #1.5 models

> show #1.6 models

> show #1.7 models

> show #1.8 models

> show #1.9 models

> ~select #1.7

1 model selected  

> view ligand

No objects specified.  

> one molecucle

Unknown command: one molecucle  

> toolshed show "Basic Actions"

> select /A

1061 atoms, 1076 bonds, 2 pseudobonds, 2 models selected  

> select /A

1061 atoms, 1076 bonds, 2 pseudobonds, 2 models selected  

> select /A

1061 atoms, 1076 bonds, 2 pseudobonds, 2 models selected  

> select /A

1061 atoms, 1076 bonds, 2 pseudobonds, 2 models selected  

> toolshed show "Command Line Interface"

> toolshed show "Model Panel"

> toolshed show ViewDockX

No suitable models found for ViewDockX  

> select

3649 atoms, 3819 bonds, 8 pseudobonds, 2 models selected  
Drag select of 6 pseudobonds, 204 residues, 76 shapes  
Drag select of 4 pseudobonds, 154 residues, 73 shapes  
Drag select of 4 pseudobonds, 136 residues, 70 shapes  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 1 pseudobonds, 11 residues  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 16 atoms, 4 pseudobonds, 18 residues, 10 bonds, 11 shapes  

> select clear

Drag select of 16 atoms, 6 pseudobonds, 30 residues, 10 bonds, 11 shapes  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

Drag select of 5 atoms, 1 pseudobonds, 2 bonds  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

No visible atoms or bonds selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 362, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 466, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 623, in pause  
p = picked_object(x, y, self.view)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 613, in picked_object  
exclude = exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1002, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 619, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
IndexError: index 196 is out of bounds for axis 0 with size 186  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 684, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (7)

comment:1 by pett, 6 years ago

Component:	Unassigned → Graphics
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → IndexError during ribbon pick

comment:2 by Tom Goddard, 6 years ago

This error happened when the mouse was hovered over a ribbon that very likely residues had been deleted from without the ribbon being updated. Not clear how that can happen.

comment:3 by Tom Goddard, 6 years ago

Deleting a residue causes set_gc_ribbon() so ribbon should always be updated. Mouse pause is only checked after frame redraw so ribbon should be up to date. Could be that ribbon was updated by triangle ranges residue numbers go out of range due to some bug.

comment:4 by Tom Goddard, 6 years ago

Opening 1cqt, preset cylinders / stubs, drag select narrow horizontal rectangle, delete sel, now ctrl click residues picks wrong residue.

comment:5 by Tom Goddard, 6 years ago

I was able to reproduce this once by drag selecting thin horizontal rectangles and deleting them with ribbon (non tube). More commonly that procedure just picks the wrong residue but does not get a range error.

comment:6 by Tom Goddard, 6 years ago

Deleting a single residue in 1gcn single helix causes picking of wrong residues down stream.

comment:7 by Tom Goddard, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

Sorted triangle ranges was not reset so had value from first ribbon computation.

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