Ribbon index error

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-14)
Description
(Describe the actions that caused this problem to occur here)

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

> open "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/Aaron_ATP.cxs"

Log from Thu Jun 4 10:50:46 2020UCSF ChimeraX version: 0.94.dev202004160103
(2020-04-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show Toolbar

> open2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/6WVK_HelD_ATP-model-1min.pdb"

Chain information for 6WVK_HelD_ATP-model-1min.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
  

> open2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/frame_000.pdb"

Chain information for frame_000.pdb #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
  

> open2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/frame_019.pdb"

Chain information for frame_019.pdb #3  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
  

> open2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/6WVK_HelD.pdb"

Chain information for 6WVK_HelD.pdb #4  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
  

> open2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/1qhh-moved.pdb"

1qhh-moved.pdb title:  
Structure of DNA helicase with adpnp [more info...]  
  
Chain information for 1qhh-moved.pdb #5  
---  
Chain | Description  
A | PCRA (subunit)  
B | PCRA (subunit)  
C | PCRA (subunit)  
D | PCRA (subunit)  
  
Non-standard residues in 1qhh-moved.pdb #5  
---  
ATP — adenosine-5'-triphosphate  
  

> open2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/2is4-moved.pdb"

2is4-moved.pdb title:  
Crystal structure of UVRD-DNA-adpnp ternary complex [more info...]  
  
Chain information for 2is4-moved.pdb #6  
---  
Chain | Description  
A B | DNA helicase II  
C D | 25-mer  
  
Non-standard residues in 2is4-moved.pdb #6  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
  

> hide atoms

> show cartoons

> hide #5 models

> hide #!6 models

> ui mousemode rightMode zoom

> hide #!4 models

> hide #!3 models

> hide #!2 models

> set bgColor white

> select ::name="ATP"

62 atoms, 66 bonds, 2 models selected  

> show sel atoms

> select #5

5291 atoms, 5285 bonds, 1 model selected  

> ~select #5

Nothing selected  

> select #5

5291 atoms, 5285 bonds, 1 model selected  

> ~select #5

Nothing selected  

> save2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/Aaron_ATP.cxs"

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  
Alignment identifier is 4  
Alignment identifier is 5  
Alignment identifier is 6  
Alignment identifier is 5.A  
Alignment identifier is 5.B  
Alignment identifier is 5.C  
Alignment identifier is 5.D  
Alignment identifier is 7  
Alignment identifier is 8  

> select #1/H#2/H#3/H#4/H

24519 atoms, 25045 bonds, 4 models selected  
Alignment identifier is 1  

> select clear

Seqview [ID: 1] region 4 chains [167-572] RMSD: 2.551  
  
Seqview [ID: 1] region 4 chains [604-605] RMSD: 3.586  
  

> show sel atoms

> style (#!1 & sel) stick

Changed 23 atom styles  

> color (#!1 & sel) byhetero

Seqview [ID: 1] region 4 chains [210] RMSD: 3.419  
  

> show sel atoms

> style (#!1 & sel) stick

Changed 8 atom styles  

> color (#!1 & sel) byhetero

Seqview [ID: 1] region 4 chains [214] RMSD: 2.919  
  

> show sel atoms

> style (#!1 & sel) stick

Changed 9 atom styles  

> color (#!1 & sel) byhetero

Seqview [ID: 1] region 4 chains [236-238] RMSD: 2.516  
  

> show sel atoms

> style (#!1 & sel) stick

Changed 22 atom styles  

> color (#!1 & sel) byhetero

Seqview [ID: 1] region 4 chains [713] RMSD: 3.366  
  

> show sel atoms

> style (#!1 & sel) stick

Changed 9 atom styles  

> color (#!1 & sel) byhetero

Seqview [ID: 1] region 4 chains [742] RMSD: 3.616  
  

> show sel atoms

> style (#!1 & sel) stick

Changed 11 atom styles  

> color (#!1 & sel) byhetero

> select clear

> save2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/Aaron_ATP.cxs"

> show #!2 models

> style #1-2 stick

Changed 56481 atom styles  

> color #1-2 byhetero

> show #!3 models

> style #1-3 stick

Changed 84706 atom styles  

> color #1-3 byhetero

> show #!4 models

> style #1-4 stick

Changed 112931 atom styles  

> color #1-4 byhetero

> hide #!4 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> view

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain D (#1) with frame_000.pdb,
chain D (#2), sequence alignment score = 5868.3  
RMSD between 1160 pruned atom pairs is 0.732 angstroms; (across all 1184
pairs: 0.811)  
  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain D (#1) with frame_019.pdb,
chain D (#3), sequence alignment score = 5844.3  
RMSD between 1178 pruned atom pairs is 0.634 angstroms; (across all 1184
pairs: 0.654)  
  

> lighting flat

> lighting shadows true intensity 0.5

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #1

28256 atoms, 28755 bonds, 6 pseudobonds, 2 models selected  

> select ::name="ATP"

62 atoms, 66 bonds, 2 models selected  

> show sel atoms

> select #1

28256 atoms, 28755 bonds, 6 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> view

> open2 "/Users/pjl984/OneDrive - The University of Newcastle/Cryo/HelD/Final
> Structures/HelD-RNAP/March 20/Aaron_final/All groups/Msm_HelD_RNAP.pdb"

Chain information for Msm_HelD_RNAP.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
H | No description available  
  

> open2 "/Users/pjl984/OneDrive - The University of Newcastle/Cryo/HelD/Final
> Structures/HelD-RNAP/March 20/Aaron_final/All groups/RNAP-delta-HelD.pdb"

Chain information for RNAP-delta-HelD.pdb #8  
---  
Chain | Description  
D | No description available  
E | No description available  
H | No description available  
U | No description available  
V | No description available  
X | No description available  
Y | No description available  
  

> select #7

27930 atoms, 28403 bonds, 1 model selected  

> select #8

28608 atoms, 29100 bonds, 1 model selected  

> hide sel target a

> show sel cartoons

> ~select #8

Nothing selected  

> select #7

27930 atoms, 28403 bonds, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> matchmaker #7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain D (#1) with Msm_HelD_RNAP.pdb,
chain D (#7), sequence alignment score = 3472.8  
RMSD between 566 pruned atom pairs is 1.132 angstroms; (across all 1122 pairs:
4.807)  
  

> matchmaker #8 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain D (#1) with RNAP-delta-
HelD.pdb, chain Y (#8), sequence alignment score = 5238.2  
RMSD between 501 pruned atom pairs is 1.267 angstroms; (across all 1127 pairs:
4.794)  
  

> save2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/Aaron_ATP.cxs"

opened ChimeraX session  

> select up

Nothing selected  

> select up

Nothing selected  

> select #1

28256 atoms, 28755 bonds, 6 pseudobonds, 2 models selected  

> select #1/H

6153 atoms, 6286 bonds, 1 model selected  

> select #1/A#2/A#3/A#4/A#5/A#6/A#7/A

14957 atoms, 15110 bonds, 12 pseudobonds, 9 models selected  

> delete atoms sel

> delete bonds sel

> select #1/B#2/B#3/B#4/B#5/B#6/B#7/B

15668 atoms, 15824 bonds, 18 pseudobonds, 9 models selected  

> delete atoms sel

> delete bonds sel

> select #1/C#2/C#3/C#4/C#5/C#6/C#7/C

44103 atoms, 44926 bonds, 25 pseudobonds, 12 models selected  

> delete atoms sel

> delete bonds sel

> select #1/D#2/D#3/D#4/D#5/D#6/D#7/D#8/D

48716 atoms, 49536 bonds, 33 pseudobonds, 11 models selected  

> delete atoms sel

> delete bonds sel

> select #1/E#2/E#3/E#4/E#7/E#8/E

3479 atoms, 3541 bonds, 6 models selected  

> delete atoms sel

> delete bonds sel

> select #1/F#2/F#3/F#4/F

1888 atoms, 1908 bonds, 4 models selected  

> delete atoms sel

> delete bonds sel

> select #8/U

1775 atoms, 1802 bonds, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #8/V

1745 atoms, 1771 bonds, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #8/X

8492 atoms, 8634 bonds, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #8/Y

8865 atoms, 9008 bonds, 1 model selected  

> delete atoms sel

> delete bonds sel

> save2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/Aaron_HelD_ATP.cxs"

Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
IndexError: index 716 is out of bounds for axis 0 with size 690  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  

> show #!2 models

> select up

Nothing selected  

Missing required "to" argument  

Missing or invalid "matchAtoms" argument: only initial part "#2" of atom
specifier valid  

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain H (#1) with frame_000.pdb,
chain H (#2), sequence alignment score = 3534  
RMSD between 654 pruned atom pairs is 1.153 angstroms; (across all 770 pairs:
1.786)  
  

> show #!3 models

> show #!4 models

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain H (#1) with frame_019.pdb,
chain H (#3), sequence alignment score = 3557.4  
RMSD between 735 pruned atom pairs is 1.003 angstroms; (across all 770 pairs:
1.513)  
  

> matchmaker #4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain H (#1) with 6WVK_HelD.pdb,
chain H (#4), sequence alignment score = 3528.6  
RMSD between 752 pruned atom pairs is 0.821 angstroms; (across all 770 pairs:
1.353)  
  

> matchmaker #7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6WVK_HelD_ATP-model-1min.pdb, chain H (#1) with Msm_HelD_RNAP.pdb,
chain H (#7), sequence alignment score = 564.2  
RMSD between 90 pruned atom pairs is 1.250 angstroms; (across all 620 pairs:
24.304)  
  

> view

> hide #!4 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> show #!4 models

> hide #7 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #7 models

> hide #7 models

> select ::name="ATP"

31 atoms, 33 bonds, 1 model selected  

> view sel

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #7 models

> hide #7 models

> save2 "/Users/pjl984/OneDrive - The University of
> Newcastle/Cryo/HelD/Analysis files/ATP binding/Aaron_HelD_ATP.cxs"

> ui mousemode rightMode zoom

> hide #8 models

> show #!2 models

> show #!3 models

> transparency #2 80

> transparency #3 80

> hide #!1 models

> view

> show #!1 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> select #4

6122 atoms, 6253 bonds, 1 model selected  

> select clear

> select #4

6122 atoms, 6253 bonds, 1 model selected  
Alignment identifier is 4.H  

> select clear

> color sel byhetero

> color sel byhetero

> color sel byhetero

> color sel byhetero

> color sel byhetero

> color sel byhetero

> color sel byhetero

> color sel byhetero

> select clear

> color sel #ead644ff

> select #4

6122 atoms, 6253 bonds, 1 model selected  

> ~select #4

Nothing selected  

> select #1

6153 atoms, 6286 bonds, 1 model selected  
Alignment identifier is 1.H  

> ~select #1

Nothing selected  

> color sel #00a0faff

> select #1

6153 atoms, 6286 bonds, 1 model selected  

> ~select #1

Nothing selected  

> select ::name="ATP"

31 atoms, 33 bonds, 1 model selected  

> view sel

> toolshed show "Side View"

> select #1

6153 atoms, 6286 bonds, 1 model selected  

> ~select #1

Nothing selected  

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> save /Users/pjl984/Desktop/image5.png supersample 3

> view

> save /Users/pjl984/Desktop/image6.png supersample 3

> select #4

6122 atoms, 6253 bonds, 1 model selected  

> show sel surfaces

> color sel #aa0a3cff

> ~select #4

1 model selected  

> hide #!1 models

> save /Users/pjl984/Desktop/image7.png supersample 3

> hide #!4 models

> show #!1 models

> select #1

6153 atoms, 6286 bonds, 1 model selected  

> show sel surfaces

> select clear

> save /Users/pjl984/Desktop/image8.png supersample 3

> select #1

6153 atoms, 6286 bonds, 1 model selected  

> ~select #1

1 model selected  

> show #!4 models

> hide #!1 models

> select #4

6122 atoms, 6253 bonds, 1 model selected  

> color sel #aa0a3cff

> color sel #aa0a3cf0

> color sel #aa0a3cde

> color sel #aa0a3ccd

> color sel #aa0a3cc8

> color sel #aa0a3cc0

> color sel #aa0a3cbb

> color sel #aa0a3cb9

> color sel #aa0a3cb1

> color sel #aa0a3caf

> color sel #aa0a3ca3

> color sel #aa0a3ca1

> color sel #aa0a3c94

> color sel #aa0a3c93

> color sel #aa0a3c8f

> show sel cartoons

> color sel #aa0a3c91

> color sel #aa0a3cea

> color sel #aa0a3cff

> select clear

> show #!1 models

> select ::name="ATP"

31 atoms, 33 bonds, 1 model selected  

> hide #!4 models

> view sel

> select clear

> show #!4 models

> select #4

6122 atoms, 6253 bonds, 3 models selected  

> hide sel surfaces

> show sel surfaces

> surface #4 transparency 80

> surface #4 transparency 60

> ~select #4

1 model selected  

> select #1

6153 atoms, 6286 bonds, 3 models selected  

> hide sel surfaces

> select clear

> select #1

6153 atoms, 6286 bonds, 3 models selected  

> show sel surfaces

> surface #4 transparency 60

> ~select #1

1 model selected  

> select #1

6153 atoms, 6286 bonds, 3 models selected  

> surface #4 transparency 60

> select #1/H

6153 atoms, 6286 bonds, 1 model selected  

> select #1

6153 atoms, 6286 bonds, 3 models selected  

> ~select #1

1 model selected  

> select #1

6153 atoms, 6286 bonds, 3 models selected  

> hide sel surfaces

> select clear

> select #4/H

6122 atoms, 6253 bonds, 1 model selected  

> hide sel surfaces

> select clear

> select ::name="ATP"

31 atoms, 33 bonds, 1 model selected  

> view sel

> select clear

> select #4/H

6122 atoms, 6253 bonds, 1 model selected  
Alignment identifier is 4.H  

> select clear

> color sel #ead644ff

> select clear

> save /Users/pjl984/Desktop/image9.png supersample 3

> save /Users/pjl984/Desktop/image10.png supersample 3

> show #7 models

> show #8 models

Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/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
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
IndexError: index 834 is out of bounds for axis 0 with size 770  
  
File
"/Users/pjl984/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 675, in first_intercept  
r = self._residues[tranges[n-1][0]]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.5.22
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.

[Tom Goddard]

Fixed 1.5 months ago.