Read PDB file: 'utf-8' codec can't decode byte

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/paulienpenne/Desktop/bèta streng.cxs" format session

Log from Sat Oct 29 18:56:22 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/paulienpenne/Desktop/tetrapeptide MWPT.cxs" format session

Log from Sat Oct 29 18:24:49 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/paulienpenne/Desktop/tetrapeptide MWPT.cxs" format session

Log from Thu Oct 27 00:22:32 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Build Structure"

> build start peptide "custom built" MWPT -119.0,113.0 -119.0,113.0
> -119.0,113.0 -119.0,113.0 rotLib Dunbrack chainId A

Chain information for custom built #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="MET"

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

> ui mousemode right label

> label #1/A:1

> label #1/A:2

> label #1/A:4

[Repeated 2 time(s)]

> select ::name="MET"::name="PRO"::name="THR"::name="TRP"

37 atoms, 39 bonds, 4 residues, 1 model selected  

> label delete residues

> select clear

> label #1/A:4

> ui mousemode right label

[Repeated 1 time(s)]

> ui mousemode right select

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select subtract /A:3@CA

Nothing selected  

> select clear

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> addh

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A THR 4  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
35 hydrogens added  
  

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:1@CG

1 atom, 1 residue, 1 model selected  

> select /A:1@CG

1 atom, 1 residue, 1 model selected  

> select /A:1@CB

1 atom, 1 residue, 1 model selected  

> select /A:1@CA

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> save /Users/paulienpenne/Desktop/image11.png supersample 3

> select ::name="MET"

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui mousemode right label

> label #1/A:1

> label #1/A:2

> label #1/A:3

> label #1/A:4

> save /Users/paulienpenne/Desktop/image12.png supersample 3

> select /A

72 atoms, 74 bonds, 4 residues, 1 model selected  

> color sel hot pink

> select ::name="MET"::name="PRO"::name="THR"::name="TRP"

72 atoms, 74 bonds, 4 residues, 1 model selected  

> select ::name="MET"

19 atoms, 18 bonds, 1 residue, 1 model selected  

> label delete residues

[Repeated 1 time(s)]

> select clear

> undo

[Repeated 4 time(s)]

> select clear

> select /A:1@CA

1 atom, 1 residue, 1 model selected  

> ui mousemode right "move label"

> ui mousemode right label

> label #1/A:1

> label #1/A:2

> label #1/A:3

> label #1/A:4

> select clear

> save /Users/paulienpenne/Desktop/image13.png supersample 3

> set bgColor white

> save /Users/paulienpenne/Desktop/image14.png supersample 3

> label #1/A:4,3

[Repeated 1 time(s)]

> select up

2 atoms, 1 bond, 2 residues, 1 model selected  

> select /A:4@C

1 atom, 1 residue, 1 model selected  

> label #1/A:4

[Repeated 1 time(s)]

> style sel sphere

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> undo

[Repeated 2 time(s)]

> label #1/A:2

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 15 atom styles  

> undo

> style sel sphere

Changed 0 atom styles  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> undo

> select clear

> label #1/A:4

[Repeated 2 time(s)]

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> select clear

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> select /A:1@CA

1 atom, 1 residue, 1 model selected  

> style sel stick

Changed 1 atom style  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select down

1 bond, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

72 atoms, 74 bonds, 4 residues, 1 model selected  

> select down

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel magenta

> undo

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel magenta

> label #1/A:3

> label #1/A:4

> select ~sel

70 atoms, 68 bonds, 4 residues, 2 models selected  

> style sel sphere

Changed 70 atom styles  

> undo

> select clear

> label #1/A:3

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 14 atom styles  

> style sel sphere

Changed 14 atom styles  

> style sel sphere

Changed 14 atom styles  

> undo

[Repeated 2 time(s)]

> color sel magenta

> undo

> select ~sel

58 atoms, 58 bonds, 3 residues, 2 models selected  

> style sel sphere

Changed 58 atom styles  

> undo

> select clear

> label #1/A:3

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel orange

> color sel magenta

> select ~sel

70 atoms, 68 bonds, 4 residues, 2 models selected  

> style sel sphere

Changed 70 atom styles  

> ui mousemode right "bond rotation"

[Repeated 1 time(s)]

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> torsion /A:3@O,C,CA,N -67.00

> ui mousemode right "bond rotation"

> select /A:3@CB

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> select clear

[Repeated 3 time(s)]

> ui mousemode right "bond rotation"

[Repeated 1 time(s)]Drag select of 1 bonds  

> select clear

> ui mousemode right "bond rotation"

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> select clear

> ui mousemode right "bond rotation"

> torsion /A:3@O,C,CA,N -67.00

> select /A:3@N

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

[Repeated 1 time(s)]

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> select /A:4@C

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> select /A

72 atoms, 74 bonds, 4 residues, 1 model selected  

> ui mousemode right "bond rotation"

> select clear

> select /A:3@N

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> select /A:1@SD

1 atom, 1 residue, 1 model selected  

> undo

> hide sel bonds

> undo

> ui mousemode right "bond rotation"

[Repeated 1 time(s)]

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> select down

1 bond, 1 model selected  

> select down

1 bond, 1 model selected  

> select clear

> ui mousemode right "clip rotate"

[Repeated 1 time(s)]

> ui mousemode right "bond rotation"

[Repeated 3 time(s)]

> torsion /A:3@O,C,CA,N -67.00

> undo

[Repeated 3 time(s)]

> redo

> undo

[Repeated 3 time(s)]

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

[Repeated 1 time(s)]

> show sel atoms

> show sel cartoons

> hide sel cartoons

> ui mousemode right "bond rotation"

Drag select of 2 atoms  
Drag select of 2 atoms, 1 bonds  

> torsion /A:3@O,C,CA,N -62.16

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N 68.11

> torsion /A:3@O,C,CA,N 83.06

> torsion /A:3@O,C,CA,N -87.86

[Repeated 9 time(s)]

> ui mousemode right "bond rotation"

> torsion /A:3@O,C,CA,N -87.86

> ui mousemode right "bond rotation"

[Repeated 2 time(s)]

> torsion /A:3@O,C,CA,N -87.86

> ui mousemode right "bond rotation"

[Repeated 3 time(s)]

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> torsion /A:3@O,C,CA,N -87.86

> ui mousemode right "bond rotation"

[Repeated 2 time(s)]

> torsion /A:3@O,C,CA,N -87.86

> ui mousemode right "bond rotation"

[Repeated 1 time(s)]

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select down

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 14 bonds, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> select /A:3@O

1 atom, 1 residue, 1 model selected  

> select clear

> ui mousemode right "bond rotation"

> torsion /A:3@O,C,CA,N -87.86

> ui mousemode right "bond rotation"

> save "/Users/paulienpenne/Desktop/tetrapeptide MWPT.cxs"

——— End of log from Thu Oct 27 00:22:32 2022 ———

opened ChimeraX session  

> style sel ball

Changed 0 atom styles  

> select /A:3@CB

1 atom, 1 residue, 1 model selected  

> select /A:3@CB

1 atom, 1 residue, 1 model selected  

> select clear

> style ball

Changed 72 atom styles  

> style ball

Changed 72 atom styles  

> style ball

Changed 72 atom styles  

> addh

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A THR 4  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
0 hydrogens added  
  

> close session

> ui tool show "Build Structure"

> build start peptide "custom built" MWPT -119.0,113.0 -119.0,113.0
> -119.0,113.0 -119.0,113.0 rotLib Dunbrack

Chain information for custom built #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="MET"

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

> ui mousemode right label

[Repeated 1 time(s)]

> select ::name="MET"

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

> ui mousemode right label

> label #1/A:1

> label delete residues

[Repeated 1 time(s)]

> label #1/A:1

> select clear

> select /A:1@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> addh

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A THR 4  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
35 hydrogens added  
  

> save /Users/paulienpenne/Desktop/image15.png supersample 3

> select clear

> select /A

72 atoms, 74 bonds, 4 residues, 1 model selected  

> hide target m

> close

> hide # target m

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

> close #

Expected a models specifier or a keyword  

> hide # target m

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

> undo

> build start peptide "custom built" MWPT -119.0,113.0 -119.0,113.0
> -119.0,113.0 -119.0,113.0 rotLib Dunbrack

Chain information for custom built #1  
---  
Chain | Description  
A | No description available  
  

> select ::name="MET"

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

> ui mousemode right label

> label #1/A:1

> select clear

> label #1/A:1

> select clear

> select /A:1@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:4@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> addh

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A THR 4  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
35 hydrogens added  
  

> select /A:3@CA

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel magenta

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select down

1 bond, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel hot pink

> color sel magenta

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> style sel ball

Changed 1 atom style  

> select /A:2@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select ~sel

72 atoms, 74 bonds, 4 residues, 2 models selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select ~sel

70 atoms, 68 bonds, 4 residues, 2 models selected  

> style sel sphere

Changed 70 atom styles  

> ui mousemode right "bond rotation"

> torsion /A:3@O,C,CA,N -66.54

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N 124.55

> torsion /A:3@O,C,CA,N -64.78

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N -64.55

> torsion /A:3@O,C,CA,N -74.20

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N -114.68

[Repeated 2 time(s)]

> torsion /A:3@O,C,CA,N -100.85

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N -78.89

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N 174.46

> torsion /A:3@O,C,CA,N 174.92

> torsion /A:3@O,C,CA,N -109.32

> torsion /A:3@O,C,CA,N 169.99

> torsion /A:3@O,C,CA,N 171.00

> torsion /A:3@O,C,CA,N -176.77

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N -178.20

> torsion /A:3@O,C,CA,N -10.18

> torsion /A:3@O,C,CA,N 166.35

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> select /A:3@N

1 atom, 1 residue, 1 model selected  

> select /A:4@N

1 atom, 1 residue, 1 model selected  

> select /A:3@N

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  

> select clear

[Repeated 1 time(s)]

> select /A:1@HA

1 atom, 1 residue, 1 model selected  

> select /A:1@HA

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:1@HA

1 atom, 1 residue, 1 model selected  

> select /A:1@HA

1 atom, 1 residue, 1 model selected  

> select /A:1@HA

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:1@HE3

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> save /Users/paulienpenne/Desktop/image16.png supersample 3

> save "/Users/paulienpenne/Desktop/tetrapeptide MWPT.cxs"

——— End of log from Sat Oct 29 18:24:49 2022 ———

opened ChimeraX session  

> torsion /A:3@O,C,CA,N 166.35

[Repeated 1 time(s)]

> torsion /A:3@O,C,CA,N 2.09

> torsion /A:3@O,C,CA,N 17.69

> save /Users/paulienpenne/Desktop/image17.png supersample 3

> close session

> ui tool show "Build Structure"

No peptide sequence entered  

> build start peptide "custom built" KRLAEMLENVQHILEA -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack chainId alpha-bèta

Chain information for custom built #1  
---  
Chain | Description  
alpha-bèta | No description available  
  

> select //chain_id='alpha-bèta':11

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

> select clear

> select //chain_id='alpha-bèta'

132 atoms, 132 bonds, 16 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> addh

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain alpha-bèta;
guessing termini instead  
Chain-initial residues that are actual N termini: //chain_id='alpha-bèta' LYS
1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: //chain_id='alpha-bèta' ALA 16  
Chain-final residues that are not actual C termini:  
12 hydrogen bonds  
139 hydrogens added  
  

> select clear

> save /Users/paulienpenne/Desktop/image18.png supersample 3

> save /Users/paulienpenne/Desktop/alpha-helix.cxs

> close session

> ui tool show "Build Structure"

> build start peptide "custom built" KRLAEMLENVQHILEA -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib
> Dunbrack chainId Bèta

Chain information for custom built #1  
---  
Chain | Description  
Bèta | No description available  
  

> build start peptide #1 KRLAEMLENVQHILEA -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack

> close session

> ui tool show "Build Structure"

> build start peptide "custom built" KRLAEMLENVQHILEA -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib
> Dunbrack chainId bèta

Chain information for custom built #1  
---  
Chain | Description  
bèta | No description available  
  

> select /bèta

Expected an objects specifier or a keyword  

> select /bèta:10

Expected an objects specifier or a keyword  

> build start peptide #1 KRLAEMLENVQHILEA -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0
> -139.0,135.0 -139.0,135.0 -139.0,135.0 -139.0,135.0 rotLib Dunbrack

Drag select of 26 atoms, 5 residues, 28 bonds  

> select clear

> select /bèta

Expected an objects specifier or a keyword  

> select /bèta:7

Expected an objects specifier or a keyword  

> select /A

132 atoms, 132 bonds, 16 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /bèta

Expected an objects specifier or a keyword  

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="GLN"::name="GLU"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="VAL"

132 atoms, 132 bonds, 16 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

Drag select of 11 atoms, 10 bonds  

> select clear

> addh

Summary of feedback from adding hydrogens to custom built #1  
---  
notes | No usable SEQRES records for custom built (#1) chain bèta; guessing
termini instead  
Chain-initial residues that are actual N termini: /bèta LYS 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /bèta ALA 16  
Chain-final residues that are not actual C termini:  
1 hydrogen bonds  
139 hydrogens added  
  

> save /Users/paulienpenne/Desktop/image19.png supersample 3

> save "/Users/paulienpenne/Desktop/bèta streng.cxs"

——— End of log from Sat Oct 29 18:56:22 2022 ———

opened ChimeraX session  

> save /Users/paulienpenne/Desktop/bèta.pdb relModel #1

Chain IDs longer than 2 characters; truncating  

> close session

> open /Users/paulienpenne/Desktop/bèta.pdb format pdb

Traceback (most recent call last):  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 335, in interceptRequest  
self._callback(info)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 368, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 470, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 399, in thread_safe  
func(*args, **kw)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 461, in defer  
cxcmd(session, topic)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 479, in cxcmd  
run(session, cmd)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/__init__.py", line 34, in open  
return pdb.open_pdb(session, data, file_name, **kw)  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/pdb/pdb.py", line 77, in open_pdb  
pointers = _pdbio.read_pdb_file(stream, session.logger, not coordsets, atomic,
segid_chains,  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc3 in position 11:
invalid continuation byte  
  
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc3 in position 11:
invalid continuation byte  
  
File
"/Users/paulienpenne/Desktop/ChimeraX-1.4.app/Contents/MacOS/../Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/codecs.py",
line 322, in decode  
(result, consumed) = self._buffer_decode(data, self.errors, final)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.11
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir8,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1,6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.6.6 (20G624)
      Kernel Version: Darwin 20.6.0
      Time since boot: 8 days 2:19

Graphics/Displays:

    Intel UHD Graphics 617:

      Chipset Model: Intel UHD Graphics 617
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x87c0
      Revision ID: 0x0002
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0