Picking: Singular matrix

[angela.fala@…]

The following bug report has been submitted:
Platform:        macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
numpy.linalg.LinAlgError: Singular matrix

File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")

See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/angela/Desktop/Structure/Ab_Asps.cxs format session

Log from Wed Aug 13 11:08:38 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/angela/Desktop/Structure/Ab_Asps.cxs format session

Log from Tue Jul 29 16:24:33 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/angela/Desktop/Structure/2024 Gyrase_last-coot7_NH.pdb" format
> pdb

Chain information for 2024 Gyrase_last-coot7_NH.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
  

> set bgColor white

> set bgColor #ffffff00

> hide atoms

> show cartoons

> select /A/B

8201 atoms, 8332 bonds, 2 pseudobonds, 1038 residues, 2 models selected  

> color sel bisque

> dssp

> select /C/D

2838 atoms, 2880 bonds, 2 pseudobonds, 358 residues, 2 models selected  

> color sel dark slate blue

> select /E/F/G/H

821 atoms, 917 bonds, 40 residues, 1 model selected  

> color sel goldenrod

> show sel atoms

> hide sel atoms

> show sel cartoons

> nucleotides sel tube/slab shape box

> show sel cartoons

> show sel atoms

> select /A:DK4

58 atoms, 63 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel orange red

> color sel byhetero

> select /A/B:513

4126 atoms, 4193 bonds, 1 pseudobond, 519 residues, 2 models selected  

> select /A/B:Asp

4375 atoms, 4411 bonds, 1 pseudobond, 550 residues, 2 models selected  

> select /A/B:Asp513

4118 atoms, 4186 bonds, 1 pseudobond, 518 residues, 2 models selected  

> select /C/D:513

1427 atoms, 1447 bonds, 1 pseudobond, 180 residues, 2 models selected  

> show sel atoms

> undo

> select /C:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /C:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

[Repeated 1 time(s)]

> style sel stick

Changed 8 atom styles  

> style sel ball

Changed 8 atom styles  

> color sel teal

> select /D:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 8 atom styles  

> color sel teal

> select clear

> select /A:DK4

58 atoms, 63 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 58 atom styles  

> select clear

> open 7z9c

7z9c title:  
E.coli gyrase holocomplex with 217 bp DNA and albicidin [more info...]  
  
Chain information for 7z9c #2  
---  
Chain | Description | UniProt  
A C | DNA gyrase subunit A | GYRA_ECOLI 2-875  
B D | DNA gyrase subunit B | GYRB_ECOLI 2-804  
E | DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3') |   
F | DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3') |   
G | DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3') |   
H | DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3') |   
  
Non-standard residues in 7z9c #2  
---  
BWH — albicidin  
MG — magnesium ion  
  

> hide #!1 models

> show #!1 models

> mmaker # to #1 show alignment true

> matchmaker # to #1 show alignment true

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> mmaker # to #1 showAlignment true

> matchmaker # to #1 showAlignment true

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> mmaker # to #1 show Alignment true

> matchmaker # to #1 show Alignment true

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> mmaker # to #1

> matchmaker # to #1

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> mmaker #2 to #1 show Alignment true

> matchmaker #2 to #1 showAlignment Alignment true

Invalid "showAlignment" argument: Expected true or false (or 1 or 0)  

> mmaker #2 to #1 showAlignment true

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 2024 Gyrase_last-coot7_NH.pdb, chain A (#1) with 7z9c, chain A
(#2), sequence alignment score = 1956.3  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 2024 Gyrase_last-coot7_NH.pdb
#1/A, 7z9c #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 441 pruned atom pairs is 0.933 angstroms; (across all 511 pairs:
1.677)  
  

> hide #!1 models

> hide #!2 atoms

> show #!2 cartoons

> color lavender

> color pale goldenrod

> color palegreen misty rose

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

> color misty rose

> color light salmon

[Repeated 1 time(s)]

> color light pink

> show #!1 models

> color #1/A/B bisque

> color #1/C/D dark slate blue

> color #1/D dark slate blue

> color #1/c dark slate blue

[Repeated 1 time(s)]

> color #1/C dark slate blue

> color #1/D dark slate blue

> color #1/B bisque

> select #1/A:DK4

58 atoms, 63 bonds, 1 residue, 1 model selected  

> color sel orange red

> style sel ball

Changed 58 atom styles  

> color sel byhetero

> select #2/JWH

Nothing selected  

> select #2/JWH

Nothing selected  

> show atoms

> undo

> select #2:JWH

Nothing selected  

> show atoms

> undo

> select #1/E/F/G/H

821 atoms, 917 bonds, 40 residues, 1 model selected  

> nucleotides sel tube/slab shape box

> show sel atoms

> color sel goldenrod rod

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

> color sel goldenrod

> select clear

> select #2/E/F/G/H

2029 atoms, 2183 bonds, 56 pseudobonds, 66 residues, 2 models selected  

> nucleotides sel tube/slab shape box

> show sel atoms

> select #2/JWH

Nothing selected  

> show atoms

> undo

> select #2/BWH

Nothing selected  

> show atoms

> undo

> dssp

[Repeated 2 time(s)]

> select #1/C:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel teal

> color sel byhetero

> select #1/D:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel teal

> color sel byhetero

> select clear

> select #2:BWH

62 atoms, 66 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel grey

> color sel byhetero

> style sel ball

Changed 62 atom styles  

> select clear

> select #2/B:500

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 12 atom styles  

> color sel byhetero

> select #2/D:500

12 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 12 atom styles  

> color sel byhetero

> select clear

> select #2/MG

Nothing selected  

> select #2:mg

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> color sel green

> color sel byhetero

> hide #!1 models

> select #2D:500

Expected an objects specifier or a keyword  

> select #2/D:500

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #2/B:500

12 atoms, 11 bonds, 1 residue, 1 model selected  

> delete sel H

Expected a keyword  

> delete H

> select #2/C:500

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete H

> show #!1 models

> view sel

[Repeated 1 time(s)]

> select clear

> view

> select #1/505-518

Nothing selected  

> select #1/D:505-518

104 atoms, 104 bonds, 14 residues, 1 model selected  

> select #1/D:507-516

71 atoms, 70 bonds, 10 residues, 1 model selected  

> select #2/A-D

14660 atoms, 14892 bonds, 10 pseudobonds, 1849 residues, 2 models selected  

> color sel khaki

> color sel tan

> select clear

> select #2:BWH

62 atoms, 66 bonds, 1 residue, 1 model selected  

> color sel grey

> style sel ball

Changed 62 atom styles  

> color sel byhetero

> select clear

> select #2/B:500

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select #2/D:500

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select #2/HOH

Nothing selected  

> select #2/MG

Nothing selected  

> select #2:MG

2 atoms, 2 residues, 1 model selected  

> show sel sphere

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

> show sel Sphere

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

> show sel atoms

> color sel green

> color sel lime

> color sel lawn green

> color sel lime

> select #2:HOH

10 atoms, 10 residues, 1 model selected  

> show sel atoms

> color sel red

> size #2:HOH stickRadius -0.2

Changed 0 bond radii  

> name frozen radius sel

> select radius

10 atoms, 10 residues, 1 model selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 1.26

Changed 10 atom radii  

> size sel atomRadius 1.2

Changed 10 atom radii  

> size sel atomRadius 1.18

Changed 10 atom radii  

> size sel atomRadius 1.16

Changed 10 atom radii  

> select clear

> select #2:MG

2 atoms, 2 residues, 1 model selected  

> ui tool show "Selection Inspector"

> size sel atomRadius 0.47

Changed 2 atom radii  

> size sel atomRadius 0.4

Changed 2 atom radii  

> select clear

> save /Users/angela/Desktop/Structure/Ab_7z9c_.cxs

> lighting full

[Repeated 2 time(s)]

> lighting soft

> lighting simple

> lighting soft

> lighting full

> select #1/D:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

6 hydrogen bonds found  

> hide #3 models

> ui tool show Distances

Exactly two atoms must be selected!  

> select #1/D:513,#2/MG

Expected an objects specifier or a keyword  

> select #1/D:513, #2/B:MG

Expected an objects specifier or a keyword  

> select #1/D:513 #2/B:MG

9 atoms, 7 bonds, 2 residues, 2 models selected  
Exactly two atoms must be selected!  

> select #1/D:513 OD2 #2/B:MG

Expected a keyword  

> select #1/D:513-OD2 #2/B:MG

1088 atoms, 1056 bonds, 139 residues, 2 models selected  

> select #1/D:513:OD2 #2/B:MG

9 atoms, 7 bonds, 2 residues, 2 models selected  

> select #1/D:513,OD2 #2/B:MG

9 atoms, 7 bonds, 2 residues, 2 models selected  

> select clear

> select add #1/D:513@OD2

1 atom, 1 residue, 1 model selected  

> select #2/B:901@MG

1 atom, 1 residue, 1 model selected  

> select add #1/D:513@OD2

2 atoms, 2 residues, 2 models selected  

> distance #2/B:901@MG #1/D:513@OD2

Distance between 7z9c #2/B MG 901 MG and 2024 Gyrase_last-coot7_NH.pdb #1/D
ASP 513 OD2: 1.874Å  

> save /Users/angela/Desktop/Structure/AB_7z9c_Asp_dist.png width 2000 height
> 1151 supersample 3 transparentBackground true

> select clear

> open 5cdq

5cdq title:  
2.95A structure of Moxifloxacin with S.aureus DNA gyrase and DNA [more
info...]  
  
Chain information for 5cdq #5  
---  
Chain | Description | UniProt  
A C R T | DNA gyrase subunit A | GYRA_STAAN 10-490  
B D S U | DNA gyrase subunit B,DNA gyrase subunit B | GYRB_STAAN 414-640  
E F V W | DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') |   
  
Non-standard residues in 5cdq #5  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MFX —
1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic
acid (moxifloxacin)  
MG — magnesium ion  
  
5cdq mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
83 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #5

22990 atoms, 23170 bonds, 157 pseudobonds, 3096 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> color sel gray

> select #5/MG

Nothing selected  

> view

> select #5:MG

14 atoms, 14 residues, 1 model selected  

> select #5:MG

14 atoms, 14 residues, 1 model selected  

> show sel atoms

> color sel green

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select clear

> hide #!2 models

> hide #!1 models

> hide #4.1 models

> hide #!4 models

> select ::name="HOH"

308 atoms, 308 residues, 2 models selected  

> show sel & #!5 atoms

> style sel & #!5 sphere

Changed 298 atom styles  

> color sel red

> color sel green

> size #5:HOH stickRadius -0.2

Changed 0 bond radii  

> show #!2 models

> hide #!2 models

> select HOH

Expected an objects specifier or a keyword  

> select #5:HOH

298 atoms, 298 residues, 1 model selected  

> color sel red

> size #5:HOH stickRadius -0.2

Changed 0 bond radii  

> size #5:HOH stickRadius -0.2

Changed 0 bond radii  

> select waters, resn HOH

Expected an objects specifier or a keyword  

> size #5:HOH atomRadius -0.2

Changed 298 atom radii  

> size #5:HOH atomRadius -0.2

Changed 298 atom radii  

> size #5:HOH atomRadius -0.1

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> select #5:MG

14 atoms, 14 residues, 1 model selected  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:HOH atomRadius -0.05

Changed 298 atom radii  

> size #5:MG atomRadius +0.2

Changed 14 atom radii  

> select clear

> select #5:Asp508

Nothing selected  

> select #5:508

32 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 32 atom styles  

> color sel byhetero

> select #5:510

32 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> style sel ball

Changed 32 atom styles  

> select clear

> show #!1 models

> show #!2 models

> mmaker #5 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 2024 Gyrase_last-coot7_NH.pdb, chain B (#1) with 5cdq, chain C
(#5), sequence alignment score = 1636.6  
RMSD between 404 pruned atom pairs is 0.884 angstroms; (across all 478 pairs:
1.624)  
  

> hide #!2 models

> select ::name="MFX"

174 atoms, 198 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel cyan

> color sel byhetero

> select clear

> select ::name="MFX"

174 atoms, 198 bonds, 6 residues, 1 model selected  

> style sel ball

Changed 174 atom styles  

> select clear

> size #5:MG atomRadius -0.2

Changed 14 atom radii  

> select #5:MG

14 atoms, 14 residues, 1 model selected  

> color sel lime

> size #5:HOH atomRadius -0.2

Changed 298 atom radii  

> size #5:HOH atomRadius -0.1

Changed 298 atom radii  

> select clear

> select #5:510

32 atoms, 28 bonds, 4 residues, 1 model selected  

> size stickRadius -0.2

Cannot reduce bond radius to <= 0  

> undo

> select #5:510

32 atoms, 28 bonds, 4 residues, 1 model selected  

> size stickRadius +0.2

Changed 51651 bond radii  

> select clear

> select #5:508

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #1:511

34 atoms, 30 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 34 atom styles  

> color sel byhetero

> color sel teal

> color sel byhetero

> select clear

> select #1:511

34 atoms, 30 bonds, 4 residues, 1 model selected  

> style sel stick

Changed 34 atom styles  

> select #1:513

32 atoms, 28 bonds, 4 residues, 1 model selected  

> style sel stick

Changed 32 atom styles  

> select #5:508

32 atoms, 28 bonds, 4 residues, 1 model selected  

> style sel stick

Changed 32 atom styles  

> select #5:510

32 atoms, 28 bonds, 4 residues, 1 model selected  

> style sel stick

Changed 32 atom styles  

> select clear

> select add #5/A:641@O

1 atom, 1 residue, 1 model selected  

> select add #5/E:2219@O

2 atoms, 2 residues, 1 model selected  

> select add #5/B:1114@O

3 atoms, 3 residues, 1 model selected  

> select add #5/A:617@O

4 atoms, 4 residues, 1 model selected  

> select add #5/A:615@O

5 atoms, 5 residues, 1 model selected  

> select add #5/B:1113@O

6 atoms, 6 residues, 1 model selected  

> select add #5/A:601@O

7 atoms, 7 residues, 1 model selected  

> select add #5/E:2209@O

8 atoms, 8 residues, 1 model selected  

> select add #5/F:2204@O

9 atoms, 9 residues, 1 model selected  

> select add #5/F:2215@O

10 atoms, 10 residues, 1 model selected  

> select add #5/F:2209@O

11 atoms, 11 residues, 1 model selected  

> select add #5/F:2205@O

12 atoms, 12 residues, 1 model selected  

> select add #5/A:616@O

13 atoms, 13 residues, 1 model selected  
Drag select of 1 residues  

> select subtract #5/B:582

Nothing selected  

> select add #5/F:2205@O

1 atom, 1 residue, 1 model selected  

> select add #5/A:617@O

2 atoms, 2 residues, 1 model selected  

> select add #5/F:2215@O

3 atoms, 3 residues, 1 model selected  

> select add #5/E:2209@O

4 atoms, 4 residues, 1 model selected  

> select add #5/A:615@O

5 atoms, 5 residues, 1 model selected  

> select add #5/A:641@O

6 atoms, 6 residues, 1 model selected  

> select add #5/E:2219@O

7 atoms, 7 residues, 1 model selected  

> select add #5/B:1109@O

8 atoms, 8 residues, 1 model selected  

> select add #5/E:2203@O

9 atoms, 9 residues, 1 model selected  

> select add #5/B:1113@O

10 atoms, 10 residues, 1 model selected  

> select add #5/E:2202@O

11 atoms, 11 residues, 1 model selected  

> select add #5/F:2204@O

12 atoms, 12 residues, 1 model selected  

> select add #5/F:2209@O

13 atoms, 13 residues, 1 model selected  

> select add #5/A:619@O

14 atoms, 14 residues, 1 model selected  

> select add #5/A:616@O

15 atoms, 15 residues, 1 model selected  

> select add #5/A:642@O

16 atoms, 16 residues, 1 model selected  

> select add #5/A:608@O

17 atoms, 17 residues, 1 model selected  

> select add #5/E:2216@O

18 atoms, 18 residues, 1 model selected  

> select add #5/F:2211@O

19 atoms, 19 residues, 1 model selected  

> select add #5/C:623@O

20 atoms, 20 residues, 1 model selected  

> select add #5/F:2216@O

21 atoms, 21 residues, 1 model selected  

> hide sel atoms

> select clear

> select add #1/D:513

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/D:512

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #1/D:511

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select add #1/D:510

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select add #5/B:510@CB

29 atoms, 24 bonds, 5 residues, 2 models selected  

> select add #5/B:509

34 atoms, 29 bonds, 6 residues, 2 models selected  

> select add #5/B:511

41 atoms, 35 bonds, 7 residues, 2 models selected  

> select add #5/B:512

49 atoms, 42 bonds, 8 residues, 2 models selected  

> select add #5/B:513

53 atoms, 45 bonds, 9 residues, 2 models selected  

> select add #1/A:601@C6

54 atoms, 45 bonds, 10 residues, 2 models selected  

> select add #5/B:1001@MG

55 atoms, 45 bonds, 11 residues, 2 models selected  

> select add #5/B:1116@O

56 atoms, 45 bonds, 12 residues, 2 models selected  

> select add #5/B:1111@O

57 atoms, 45 bonds, 13 residues, 2 models selected  

> select add #5/E:2101@C12

58 atoms, 45 bonds, 14 residues, 2 models selected  

> select subtract #1/A:601@C6

57 atoms, 46 bonds, 13 residues, 2 models selected  

> select add #5/B:514

62 atoms, 50 bonds, 14 residues, 2 models selected  

> select add #5/B:515

72 atoms, 60 bonds, 15 residues, 2 models selected  

> select add #5/B:516

80 atoms, 67 bonds, 16 residues, 2 models selected  

> select add #5/B:517

91 atoms, 77 bonds, 17 residues, 2 models selected  

> select add #5/B:518

98 atoms, 83 bonds, 18 residues, 2 models selected  

> select subtract #5/B:511

91 atoms, 81 bonds, 17 residues, 2 models selected  

> select subtract #5/B:510

90 atoms, 77 bonds, 16 residues, 2 models selected  

> select add #5/B:510

98 atoms, 84 bonds, 17 residues, 2 models selected  
Drag select of 1 residues  

> select add #5/B:513

98 atoms, 84 bonds, 17 residues, 2 models selected  

> select add #5/B:1107@O

99 atoms, 84 bonds, 18 residues, 2 models selected  

> select add #1/A:601@C6

100 atoms, 84 bonds, 19 residues, 2 models selected  

> select add #1/A:601@C11

101 atoms, 84 bonds, 19 residues, 2 models selected  

> select add #1/A:601@C12

102 atoms, 84 bonds, 19 residues, 2 models selected  

> select add #1/A:601@C15

103 atoms, 84 bonds, 19 residues, 2 models selected  

> select add #1/A:601@C18

104 atoms, 84 bonds, 19 residues, 2 models selected  

> select add #1/A:601@C17

105 atoms, 84 bonds, 19 residues, 2 models selected  

> select add #5/F:8

125 atoms, 105 bonds, 20 residues, 2 models selected  

> select add #5/F:7

146 atoms, 128 bonds, 21 residues, 2 models selected  

> select add #5/F:6

166 atoms, 149 bonds, 22 residues, 2 models selected  

> select add #1/F:13

187 atoms, 172 bonds, 23 residues, 2 models selected  

> select add #1/F:14

209 atoms, 196 bonds, 24 residues, 2 models selected  

> select subtract #5/B:510

201 atoms, 189 bonds, 23 residues, 2 models selected  

> select add #5/B:510

209 atoms, 196 bonds, 24 residues, 2 models selected  

> select add #5/B:511

216 atoms, 202 bonds, 25 residues, 2 models selected  

> select clear

> select add #5/B:1001@MG

1 atom, 1 residue, 1 model selected  

> select add #5/B:508@CG

2 atoms, 1 bond, 2 residues, 2 models selected  
Drag select of 14 atoms, 105 residues, 11 bonds, 5 pseudobonds  
Drag select of 74 atoms, 241 residues, 64 bonds, 7 shapes, 7 pseudobonds  

> select ~sel & ##selected

32770 atoms, 33245 bonds, 143 pseudobonds, 4267 residues, 6 models selected  

> select ~sel & ##selected

2080 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected  

> select up

2083 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected  

> select down

2080 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected  

> select ~sel & ##selected

32770 atoms, 33245 bonds, 148 pseudobonds, 4267 residues, 7 models selected  

> select ~sel & ##selected

2080 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected  

> select clear

> select add #5/B:1001@MG

1 atom, 1 residue, 1 model selected  

> select add #1/D:513@CG

2 atoms, 2 residues, 2 models selected  

> select add #5/B:508@CG

3 atoms, 3 residues, 2 models selected  
Drag select of 102 atoms, 386 residues, 80 bonds, 7 shapes, 11 pseudobonds  

> select up

3157 atoms, 3162 bonds, 11 pseudobonds, 412 residues, 3 models selected  

> select down

3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected  

> select down

3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected  

> select down

3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected  

> select up

3157 atoms, 3162 bonds, 11 pseudobonds, 412 residues, 3 models selected  

> select down

3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected  

> view sel

> select ~sel & ##selected

31712 atoms, 32155 bonds, 144 pseudobonds, 4126 residues, 6 models selected  

> hide sel atoms

> show sel atoms

> undo

[Repeated 1 time(s)]

> select clear

> select add #5/B:1001@MG

1 atom, 1 residue, 1 model selected  
Drag select of 92 atoms, 302 residues, 75 bonds, 1 shapes, 11 pseudobonds  

> select clear

> lighting full

> lighting soft

> lighting simple

> select add #5/A:611@O

1 atom, 1 residue, 1 model selected  

> select add #5/B:1106@O

2 atoms, 2 residues, 1 model selected  

> select add #5/B:1119@O

3 atoms, 3 residues, 1 model selected  

> select add #5/T:4632@O

4 atoms, 4 residues, 1 model selected  

> select add #5/F:2206@O

5 atoms, 5 residues, 1 model selected  

> select add #1/D:510

12 atoms, 6 bonds, 6 residues, 2 models selected  

> select add #1/D:509

20 atoms, 13 bonds, 7 residues, 2 models selected  

> select add #1/D:459

28 atoms, 20 bonds, 8 residues, 2 models selected  

> select add #1/D:439

36 atoms, 27 bonds, 9 residues, 2 models selected  

> select add #1/D:438

40 atoms, 30 bonds, 10 residues, 2 models selected  

> select add #1/D:437

49 atoms, 38 bonds, 11 residues, 2 models selected  

> select add #1/D:436

56 atoms, 44 bonds, 12 residues, 2 models selected  

> select add #5/A:28

62 atoms, 49 bonds, 13 residues, 2 models selected  

> select add #5/A:24

70 atoms, 56 bonds, 14 residues, 2 models selected  

> select add #5/A:27

78 atoms, 63 bonds, 15 residues, 2 models selected  

> select add #5/A:30

86 atoms, 70 bonds, 16 residues, 2 models selected  
Drag select of 2 residues  

> select add #5/A:32

111 atoms, 74 bonds, 19 residues, 2 models selected  

> select add #5/T:4618@O

112 atoms, 74 bonds, 20 residues, 2 models selected  

> select add #5/A:33

123 atoms, 84 bonds, 21 residues, 2 models selected  

> select add #5/A:34

128 atoms, 88 bonds, 22 residues, 2 models selected  

> select add #5/A:35

136 atoms, 95 bonds, 23 residues, 2 models selected  

> select add #5/A:31

143 atoms, 101 bonds, 24 residues, 2 models selected  

> select add #5/A:25

155 atoms, 113 bonds, 25 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select add #5/A:29

162 atoms, 119 bonds, 26 residues, 2 models selected  

> select add #1/D:458

169 atoms, 126 bonds, 27 residues, 2 models selected  

> select add #5/B:459

173 atoms, 129 bonds, 28 residues, 2 models selected  

> select add #5/B:458

184 atoms, 139 bonds, 29 residues, 2 models selected  

> hide sel cartoons

> select add #5/B:581

190 atoms, 144 bonds, 30 residues, 2 models selected  

> select add #5/B:580

202 atoms, 156 bonds, 31 residues, 2 models selected  

> select add #5/B:545

206 atoms, 159 bonds, 32 residues, 2 models selected  

> select add #5/B:544

213 atoms, 165 bonds, 33 residues, 2 models selected  

> select add #5/B:543

220 atoms, 172 bonds, 34 residues, 2 models selected  

> select add #1/D:440

226 atoms, 177 bonds, 35 residues, 2 models selected  

> select add #1/D:441

231 atoms, 181 bonds, 36 residues, 2 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up  
mouse_select(event, mode, self.session, self.view)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select  
pick = view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  

> select add #1/D:443

235 atoms, 184 bonds, 37 residues, 2 models selected  

> hide sel cartoons

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up  
mouse_select(event, mode, self.session, self.view)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select  
pick = view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up  
mouse_select(event, mode, self.session, self.view)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select  
pick = view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up  
mouse_select(event, mode, self.session, self.view)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select  
pick = view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  

> select ::name="DA"::name="DC"::name="DG"::name="DT"

3689 atoms, 4125 bonds, 93 pseudobonds, 184 residues, 5 models selected  

> nucleotides sel & #!1,5 tube/slab shape box

> show sel & #!1,5 atoms

> select clear

> select add #1/D:442

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide sel cartoons

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  

> select add #1/D:419

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #1/D:420

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select add #1/D:457

29 atoms, 25 bonds, 4 residues, 1 model selected  

> select add #1/D:456

37 atoms, 32 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> select clear

> select add #5/B:1114@O

1 atom, 1 residue, 1 model selected  

> select add #5/F:2217@O

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select clear

> select add #5/B:1115@O

1 atom, 1 residue, 1 model selected  

> select add #5/B:1103@O

2 atoms, 2 residues, 1 model selected  

> select add #5/A:601@O

3 atoms, 3 residues, 1 model selected  

> select add #5/E:2217@O

4 atoms, 4 residues, 1 model selected  

> hide sel atoms

> select add #5/B:460

13 atoms, 8 bonds, 5 residues, 1 model selected  

> hide sel cartoons

[deleted to fit within ticket limits]

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking  
self._mouse_pause()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause  
p = self.view.picked_object(x, y)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept  
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept  
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts  
p = d.first_intercept(xyz1, xyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept  
p = super().first_intercept(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children  
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse  
self._inverse = Place(m34.invert_matrix(self._matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix  
rinv[:, :] = matrix_inverse(r)  
^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv  
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
numpy.linalg.LinAlgError: Singular matrix  
  
numpy.linalg.LinAlgError: Singular matrix  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular  
raise LinAlgError("Singular matrix")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16T000R1D/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.41.12
      OS Loader Version: 10151.41.12

Software:

    System Software Overview:

      System Version: macOS 14.1.1 (23B81)
      Kernel Version: Darwin 23.1.0
      Time since boot: 9 days, 7 hours, 17 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        C27F390:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

[pett]

Duplicate of #18425