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#15857 closed defect (fixed)

Index out of range updating header sequence

Reported by:	jdietrich3@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
lighting simple; 
open 2wva; 
hide atoms; 
show cartoons; 
color /z green; 
show :113,114 atoms; 
style :113,114 stick; 
color :113,114 magenta; 
sel ligand; 
show sel atoms; 
color sel byhet; 
hide #1/v,x,y,z cartoons; 
delete #1/v,x,y,z,a,b; 
sel :PYR; 
alphafold fetch A0A3D8TPB7; 
color #2 cyan; 
alphafold fetch A0A3D8TPB7; 
color #3 pink; 
matchmaker #2 to #1/E show true; 
matchmaker #3 to #1/F show true; 
color #2-3:112,113 magenta; 
color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green; 
color #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539 byhetero; 
show #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539 atoms; 
style #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539 stick; 
sel :pyr; 
view sel clip false; 
hide #1 cartoons; 
hide #1:113,114;
swapaa #2:285 LEU; 

Log:
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 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> lighting simple

> open "C:/Users/Joshua_Dietrich/OneDrive - UW-Madison/JD - Josh
> Dietrich/Machine_Learning/KDC_specificity/KDC_structures/2023_0726_Ll-
> Lk_dimer.pse"

Unrecognized file suffix '.pse'  

> alphafold fetch A0A3D8TPB7

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold A0A3D8TPB7 from
https://alphafold.ebi.ac.uk/files/AF-A0A3D8TPB7-F1-model_v4.cif  
Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> help cpy

No help found for 'cpy'  

> help copy

No help found for 'copy'  

> help duplicate

No help found for 'duplicate'  

> help sym

[Repeated 1 time(s)]

> sym sel

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> undo

> sym sel

2wva mmCIF Assemblies  
---  
1| software_defined_assembly| 1 copy of chain  
2| software_defined_assembly| 1 copy of chains E,F  
  

> select #1

9221 atoms, 8775 bonds, 12 pseudobonds, 1764 residues, 2 models selected  

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> select #3

Nothing selected  

> hide #1

> hide #1 cartoons

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> sym sel symmetry #1

No symmetry for "#1"  

> sym sel axis

Missing "axis" keyword's argument  

> sym sel axis z

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> select #3

Nothing selected  

> help assembly

No help found for 'assembly'  

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> sym sel assembly 1

Assembly "1" not found, have  

> select assembly 1

Expected an objects specifier or a keyword  
Drag select of 5 residues  

> select #@

Expected an objects specifier or a keyword  

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  
Drag select of 1 residues  

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> sym #2

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> select assembly 1

Expected an objects specifier or a keyword  

> select sym sym-type #1

Expected an objects specifier or a keyword  

> sym sym-type #1

Missing or invalid "structures" argument: invalid atomic structures specifier  

> sym sel sym-type #1

Expected a keyword  

> sym sel sym-type symmetry #1

Repeated keyword argument "symmetry"  

> sym sel sym-type #1

Expected a keyword  

> sym sel sym-type d7

Expected a keyword  

> sym sel sym-type axis z

Unknown symmetry group "sym-type"  

> sym sel #1

No symmetry for "#1"  

> show #1 cartoons

> hide #1 cartoons

> sym sel axis

Missing "axis" keyword's argument  

> sym sel axis z

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> sym sel axis x

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> sym sel d7

Made 14 graphical clones for AlphaFold A0A3D8TPB7 symmetry d7  

> undo

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> hide #2 cartoons

> undo

> hide #1 cartoons

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> sym d2

Missing or invalid "structures" argument: invalid atomic structures specifier  

> sym sel d2

Made 4 copies for AlphaFold A0A3D8TPB7 symmetry d2  

> delete #2

> delete #3

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> delete #3

[Repeated 1 time(s)]

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> sym sel d1

Made 2 copies for AlphaFold A0A3D8TPB7 symmetry d1  

> color #2 teal

> color #2 cartoons teal

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

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> select #3

1 model selected  

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> hide #1 cartoons

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> color #2 cyan

> lighting simple

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> show #1 cartoons

> volume showOutlineBox true

No volumes specified  

> volume planes z style image imageMode "full region"

No volumes specified  

> select #2

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> sym sel axis z

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> view #2 clip false

> show #2 target m

> sym #1

2wva mmCIF Assemblies  
---  
1| software_defined_assembly| 1 copy of chain  
2| software_defined_assembly| 1 copy of chains E,F  
  

> define axis

Axis 'root #/axis' centered at [ -1.32325225 -19.97732841 7.34184023] with
direction [ 0.64133308 -0.30709673 -0.70312408], radius 17.6102, and length
109.664  

> undo

[Repeated 5 time(s)]

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> zalign #1

Unknown command: zalign #1  

> sym #2 axis y

AlphaFold A0A3D8TPB7 mmCIF Assemblies  
---  
  

> lighting simple

> sym #!

Missing or invalid "structures" argument: invalid atomic structures specifier  

> sym #1

2wva mmCIF Assemblies  
---  
1| software_defined_assembly| 1 copy of chain  
2| software_defined_assembly| 1 copy of chains E,F  
  

> log metadata #2

The model has no metadata

> log chains #2

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  

> sym #1

2wva mmCIF Assemblies  
---  
1| software_defined_assembly| 1 copy of chain  
2| software_defined_assembly| 1 copy of chains E,F  
  

> log metadata #1

Metadata for 2wva #1  
---  
Title | Structural insights into the pre-reaction state of pyruvate decarboxylase from Zymomonas mobilis  
Citation | Pei, X.Y., Erixon, K., Luisi, B.F., Leeper, F.J. (2010). Structural Insights Into the Pre-Reaction State of Pyruvate Decarboxylase from Zymomonas Mobilis. Biochemistry, 49, 1727. PMID: 20099870. DOI: 10.1021/BI901864J  
Non-standard residues | MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
Gene source | Zymomonas mobilis  
Experimental method | X-ray diffraction  
Resolution | 2.200Å  
  
> log chains #1

Chain information for 2wva #1  
---  
Chain | Description | UniProt  
E F | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  

> show #!1 target m

> view orient

> hide #2 models

> yalign :257

Unknown command: yalign :257  

> show #2 models

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 blue

> undo

[Repeated 2 time(s)]

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 blue

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> select #3

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> orient

Unknown command: orient  

> view orient

> lighting simple

> view orient

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select down

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select down

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select down

4231 atoms, 4321 bonds, 548 residues, 1 model selected  

> matchmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1204.6  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> color #1 bychain

> matchmaker #3 to #1/F

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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> matchmaker #2 to #1/E

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 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> hide #1/v,x,y,z cartoons

> hide #1 cartoons

Drag select of 9 residues  

> select ligand

58 atoms, 59 bonds, 3 residues, 1 model selected  

> color sel byhetero

> select up

9221 atoms, 8775 bonds, 1764 residues, 1 model selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> matchmaker #3 to #1/F 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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
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: 2wva #1/F, AlphaFold
A0A3D8TPB7 #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> select
> #1/F:3-22,24-35,39-105,108,110-133,144-168,171-172,174-179,210-212,215,221,240-263,265-266,269-274,282-290,293-294,300-301,304,306,352,362-367,370-371,374-375,378-396,400-477,481-496,506,510-522,532-555,557-558
> #3/A:2-21,23-34,38-104,107,109-132,142-166,169-170,172-177,205-207,210,216,235-258,260-261,264-269,277-285,288-289,295-296,299,301,342,352-357,360-361,364-365,368-386,390-467,473-488,494,498-510,520-543,545-546

5734 atoms, 5809 bonds, 746 residues, 2 models selected  

> select up

6942 atoms, 7082 bonds, 911 residues, 2 models selected  

> select up

8497 atoms, 8679 bonds, 1113 residues, 2 models selected  

> show 2-3:112,113 atoms

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

> show 2,3:112,113 atoms

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

> show 2:112,113 atoms

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

> show 2-3/112,113 atoms

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

> show 2/112,113 atoms

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

> help show

> show #2/:/112,113 atoms

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

> show #2/:/112-113 atoms

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

> show #2/A/112-113 atoms

> undo

> show #2/A/112,113 atoms

> show #2/A/112 atoms

> show :112 atoms

> help show

> help sel

> show #2-3/A:112-113 atoms

> style #2-3/A:112-113 stick

Changed 40 atom styles  

> select up

8864 atoms, 8711 bonds, 1450 residues, 2 models selected  

> select up

13452 atoms, 13096 bonds, 2312 residues, 2 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select down

13452 atoms, 13096 bonds, 2312 residues, 2 models selected  

> select down

8864 atoms, 8711 bonds, 1450 residues, 2 models selected  

> hide :112 atoms

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #1 atoms

> hide #1/E-F:HIS

> select up

13452 atoms, 13096 bonds, 2312 residues, 2 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select down

13452 atoms, 13096 bonds, 2312 residues, 2 models selected  

> show #2-3/A:112-113 atoms

> color #2-3/A:112-113 byhetero

> color #3 #ff55ffff

> color #2-3/A:112-113 byhetero

> color #2-3/A:112-113 green

> color #2-3/A:112-113 byhetero

> select PYR

Expected an objects specifier or a keyword  

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> orient sel

Unknown command: orient sel  

> view sel

> lighting simple

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> view orient

Drag select of 6 residues  

> help help:user

> select PYR

Expected an objects specifier or a keyword  

> select /PYR

Nothing selected  

> select /PYR

Nothing selected  

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel

> view orient

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1:pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select ~sel & ##selected

9215 atoms, 8770 bonds, 12 pseudobonds, 1763 residues, 2 models selected  

> delete sel

> select #2-3

8462 atoms, 8642 bonds, 1096 residues, 2 models selected  

> help dockprep

> dockprep sel

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Termini for AlphaFold A0A3D8TPB7 (#2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: AlphaFold A0A3D8TPB7 #2/A
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold A0A3D8TPB7 #2/A SER
548  
Chain-final residues that are not actual C termini:  
541 hydrogen bonds  
Termini for AlphaFold A0A3D8TPB7 (#3) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: AlphaFold A0A3D8TPB7 #3/A
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold A0A3D8TPB7 #3/A SER
548  
Chain-final residues that are not actual C termini:  
541 hydrogen bonds  
8382 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 byhetero

> show #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 atoms

> show #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 stick;

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

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 blue

> matchmaker #2 to #1/E 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 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
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: 2wva #1/E, AlphaFold
A0A3D8TPB7 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> matchmaker #3 to #1/F 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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 2wva #1/F, AlphaFold
A0A3D8TPB7 #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 byhetero

> show #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 atoms

> show #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 stick;

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

> style #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 stick

Changed 208 atom styles  

> color #3 #ffaaffff

> lighting simple

> color #3 pink

> hide #!1 models

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #1 cartoons

> select up

4633 atoms, 4390 bonds, 902 residues, 1 model selected  

> select up

9221 atoms, 8775 bonds, 1764 residues, 1 model selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select up

17683 atoms, 17417 bonds, 2860 residues, 3 models selected  

> select down

9221 atoms, 8775 bonds, 1764 residues, 1 model selected  

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 byhetero

> surface sel

> hide #1 surfaces

> show #2-3 surfaces

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel

> view orient

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip=false

Expected an integer >= 1 or a keyword  

> help clip

> help view

> view sel clip false

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> color #2-3:112,113 magenta

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> byhetero

> show #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 atoms

> style #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 stick

Changed 208 atom styles  

> hide #!2 models

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #1:113,114

> select pyr

Expected an objects specifier or a keyword  

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view pyr clip false

Expected an objects specifier or a view name or a keyword  

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip false

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 blue

> matchmaker #2 to #1/E 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 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
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: 2wva #1/E, AlphaFold
A0A3D8TPB7 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> matchmaker #3 to #1/F 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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 2wva #1/F, AlphaFold
A0A3D8TPB7 #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> color #2-3:112,113 magenta

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> byhetero

> show #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 atoms

> style #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 stick

Changed 208 atom styles  

> color #3 pink

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> set bgColor black

> set bgColor transparent

> lighting simple

> hide #!1 models

> show #!1 models

> hide #1 cartoons

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip false

> hide #1:113,114

> show #2-3:112,113 atoms

> show sel surfaces

[Repeated 1 time(s)]

> undo

[Repeated 2 time(s)]

> redo

> close session

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 pink

> matchmaker #2 to #1/E 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 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
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: 2wva #1/E, AlphaFold
A0A3D8TPB7 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> matchmaker #3 to #1/F 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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 2wva #1/F, AlphaFold
A0A3D8TPB7 #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> color #2-3:112,113 magenta

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> byhetero

> show #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> atoms

> style #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> stick

Changed 248 atom styles  

> hide #!1 models

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clips false

Expected an integer >= 1 or a keyword  

> view sel clip false

> show #!1 models

> lighting simple

> hide #1 cartoons

> hide #1:113,114

> select #2-3:285

12 atoms, 10 bonds, 2 residues, 2 models selected  

> view sel clip false

> select up

242 atoms, 244 bonds, 34 residues, 2 models selected  

> select up

8462 atoms, 8642 bonds, 1096 residues, 2 models selected  

> select down

242 atoms, 244 bonds, 34 residues, 2 models selected  

> select #2:285

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip false

> select #3:285

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip false

> swapaa #2:285 LEU

Using Dunbrack library  
AlphaFold A0A3D8TPB7 #2/A SER 285: phi -65.4, psi -28.2 trans  
Applying LEU rotamer (chi angles: -67.8 174.1) to AlphaFold A0A3D8TPB7 #2/A
LEU 285  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show Rotamers

> swapaa interactive sel THR rotLib Dunbrack

AlphaFold A0A3D8TPB7 #3/A SER 285: phi -65.4, psi -28.2 trans  
Changed 12 bond radii  

> swapaa #!3/A:285 THR criteria 1 rotLib Dunbrack

Using Dunbrack library  
AlphaFold A0A3D8TPB7 #!3/A SER 285: phi -65.4, psi -28.2 trans  
Applying THR rotamer (chi angles: 59.6) to AlphaFold A0A3D8TPB7 #!3/A THR 285  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  

> close session

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #1  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> swapaa #1:285 LEU

Using Dunbrack library  
/A SER 285: phi -65.4, psi -28.2 trans  
Applying LEU rotamer (chi angles: -67.8 174.1) to /A LEU 285  

> select :285

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

> show sel atoms

> swapaa #1:285 ser

Using Dunbrack library  
/A LEU 285: phi -65.4, psi -28.2 trans  
Applying SER rotamer (chi angles: 65.8) to /A SER 285  

> close session

> lighting simple

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 pink

> matchmaker #2 to #1/E 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 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
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: 2wva #1/E, AlphaFold
A0A3D8TPB7 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> matchmaker #3 to #1/F 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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 2wva #1/F, AlphaFold
A0A3D8TPB7 #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> color #2-3:112,113 magenta

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> byhetero

> show #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> atoms

> style #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> stick

Changed 248 atom styles  

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip false

> hide #1 cartoons

> hide #1:113,114

> swapaa #1:285 LEU

Using Dunbrack library  
2wva #1/E PRO 285: phi -87.5, psi 156.7 trans  
2wva #1/F PRO 285: phi -84.1, psi 157.4 trans  
Applying LEU rotamer (chi angles: -59.9 176.3) to 2wva #1/E LEU 285  
Applying LEU rotamer (chi angles: -61.5 176.1) to 2wva #1/F LEU 285  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 252, in _actually_resize  
self._reformat()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat  
self.lead_block = SeqBlock(label_scene, self.main_scene,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[Previous line repeated 33 more times]  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1646, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line  
item = self.make_item(line, self.seq_offset + i, xs[i],  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2402, in make_item  
info = line[offset]  
~~~~^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 252, in _actually_resize  
self._reformat()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat  
self.lead_block = SeqBlock(label_scene, self.main_scene,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[Previous line repeated 33 more times]  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1646, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line  
item = self.make_item(line, self.seq_offset + i, xs[i],  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2402, in make_item  
info = line[offset]  
~~~~^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  

> lighting simple

> close session

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #1  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> swapaa :545 LYS

Using Dunbrack library  
/A LYS 545: phi -72.1, psi -33.7 trans  
Applying LYS rotamer (chi angles: -70.4 -177.2 175.0 65.8) to /A LYS 545  

> close session

> lighting simple

> open 2wva

2wva title:  
Structural insights into the pre-reaction state of pyruvate decarboxylase from
Zymomonas mobilis [more info...]  
  
Chain information for 2wva #1  
---  
Chain | Description | UniProt  
A B E F V X Y Z | PYRUVATE DECARBOXYLASE | PDC_ZYMMO 1-568  
  
Non-standard residues in 2wva #1  
---  
MG — magnesium ion  
PYR — pyruvic acid  
TPU —
2-{1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-methyl-1H-1,2,3-triazol-4-yl}ethyl
trihydrogen diphosphate  
  
2wva mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
  
20 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> color /z green

> show :113,114 atoms

> style :113,114 stick

Changed 160 atom styles  

> color :113,114 magenta

> select ligand

226 atoms, 231 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> hide #1/v,x,y,z cartoons

> delete #1/v,x,y,z,a,b

> select :PYR

6 atoms, 5 bonds, 1 residue, 1 model selected  

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #2  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #2 cyan

> alphafold fetch A0A3D8TPB7

Chain information for AlphaFold A0A3D8TPB7 #3  
---  
Chain | Description | UniProt  
A | Indole-3-pyruvate decarboxylase | A0A3D8TPB7_9LIST 1-548  
  
Color AlphaFold A0A3D8TPB7 by residue attribute pLDDT_score  

> color #3 pink

> matchmaker #2 to #1/E 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 2wva, chain E (#1) with AlphaFold A0A3D8TPB7, chain A (#2),
sequence alignment score = 1204.6  
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: 2wva #1/E, AlphaFold
A0A3D8TPB7 #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 374 pruned atom pairs is 1.002 angstroms; (across all 545 pairs:
2.556)  
  

> matchmaker #3 to #1/F 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 2wva, chain F (#1) with AlphaFold A0A3D8TPB7, chain A (#3),
sequence alignment score = 1199.5  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: 2wva #1/F, AlphaFold
A0A3D8TPB7 #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 373 pruned atom pairs is 1.001 angstroms; (across all 545 pairs:
2.566)  
  

> color #2-3:112,113 magenta

> color #2-3/A:105,285,319,323,382,398,405,421,445,462,477,509,539 green

> color #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> byhetero

> show #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> atoms

> style #2-3/A:105,112,113,285,319,323,382,398,405,421,445,462,477,509,539
> stick

Changed 248 atom styles  

> select :pyr

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view sel clip false

> hide #1 cartoons

> hide #1:113,114

> swapaa #2:285 LEU

Using Dunbrack library  
AlphaFold A0A3D8TPB7 #2/A SER 285: phi -65.4, psi -28.2 trans  
Applying LEU rotamer (chi angles: -67.8 174.1) to AlphaFold A0A3D8TPB7 #2/A
LEU 285  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 894, in
_seq_characters_changed_cb  
self._notify_observers(self.NOTE_SEQ_CONTENTS, seq)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 124, in
alignment_notification  
self.reevaluate()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 196, in reevaluate  
return super().reevaluate(pos1, pos2, evaluation_func=evaluation_func)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\header_sequence.py", line 220, in
reevaluate  
evaluation_func(pos1, pos2)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\conservation.py", line 295, in
_reeval_al2co  
temp_alignment.save(temp_stream, format_name="aln")  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 707, in save  
mod.save(self.session, self, stream)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\io\saveALN.py", line 60, in save  
if seq[pos].upper() != first:  
~~~^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
Error processing trigger "characters changed":  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 252, in _actually_resize  
self._reformat()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat  
self.lead_block = SeqBlock(label_scene, self.main_scene,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[Previous line repeated 33 more times]  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1646, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line  
item = self.make_item(line, self.seq_offset + i, xs[i],  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2402, in make_item  
info = line[offset]  
~~~~^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 252, in _actually_resize  
self._reformat()  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat  
self.lead_block = SeqBlock(label_scene, self.main_scene,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__  
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[Previous line repeated 33 more times]  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1646, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line  
item = self.make_item(line, self.seq_offset + i, xs[i],  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2402, in make_item  
info = line[offset]  
~~~~^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
IndexError: string index out of range  
  
IndexError: string index out of range  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 926, in __getitem__  
return self.characters[key]  
~~~~~~~~~~~~~~~^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 527.56
OpenGL renderer: NVIDIA GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Book 2
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 8,502,915,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    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: 2024.6.2
    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
    comtypes: 1.4.1
    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: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    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
    pywin32: 306
    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
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 14 months ago

Component:	Unassigned → Sequence
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Index out of range updating header sequence

comment:2 by Eric Pettersen, 14 months ago

Resolution:	→ fixed
Status:	accepted → closed

Fix in tomorrow's daily build.

Fix: https://github.com/RBVI/ChimeraX/commit/e72bb89ab992c03de21b05850556c8d4349c81ed

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