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#14961 closed defect (duplicate)

Angle tool allows decimal places to go to -1

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

Description

The following bug report has been submitted:
Platform:        macOS-13.6.6-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
This field shouldn't be able to take negative numbers.

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7vz4 format mmcif fromDatabase pdb

7vz4 title:  
Cryo-EM structure of human nucleosome core particle composed of the Widom 601L
DNA sequence [more info...]  
  
Chain information for 7vz4 #1  
---  
Chain | Description | UniProt  
A E | Histone H3.1 | H31_HUMAN 1-135  
B F | Histone H4 | H4_HUMAN 1-102  
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 1-129  
D H | Histone H2B type 1-J | H2B1J_HUMAN 1-125  
I | DNA (145-MER) |  
J | DNA (145-MER) |  
  

> open 32220 fromDatabase emdb

Opened emdb 32220 as #2, grid size 320,320,320, pixel 0.65, shown at level
5.2, step 2, values float32, fit PDB 7vz4  

> set bgColor white

> select protein

5904 atoms, 5982 bonds, 746 residues, 1 model selected  

> color sel cyan

> show sel cartoons

> style sel stick

Changed 5904 atom styles  

> show sel cartoons

> hide sel atoms

> hide #!2 models

> select nucleic-acid

5939 atoms, 6662 bonds, 372 pseudobonds, 290 residues, 2 models selected  

> style sel stick

Changed 5939 atom styles  

> color (#!1 & sel) byhetero

> show #!2 models

> color #2 #79bfbbff models

> color #2 #79bfbb5b models

> select add #2

5939 atoms, 6662 bonds, 372 pseudobonds, 290 residues, 4 models selected  

> select add #1

11843 atoms, 12644 bonds, 372 pseudobonds, 1036 residues, 4 models selected  

> volume #2 level 3

> select subtract #2

11843 atoms, 12644 bonds, 372 pseudobonds, 1036 residues, 2 models selected  

> select protein

5904 atoms, 5982 bonds, 746 residues, 1 model selected  

> color sel red

> ui tool show "Show Sequence Viewer"

> sequence chain /A /E

Alignment identifier is 1  

> sequence chain /B /F

Alignment identifier is 2  

> sequence chain /C /G

Alignment identifier is 3  

> sequence chain /D /H

Alignment identifier is 4  

> select /D,H:36

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select /D,H:32-36

82 atoms, 80 bonds, 10 residues, 1 model selected  

> color sel blue

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel atoms

> hide sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> show sel cartoons

> lighting soft

> select /C,G:77

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select /C,G:74-77

72 atoms, 70 bonds, 8 residues, 1 model selected  

> select /C,G:41

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select /C,G:37-41

78 atoms, 78 bonds, 10 residues, 1 model selected  

> select /D,H:51-66

226 atoms, 226 bonds, 32 residues, 1 model selected  

> select /D,H:51-66

226 atoms, 226 bonds, 32 residues, 1 model selected  

> select clear

[Repeated 3 time(s)]

> select /A,E:43-44

22 atoms, 22 bonds, 4 residues, 1 model selected  

> select /A,E:39-44

110 atoms, 114 bonds, 12 residues, 1 model selected  

> color sel blue

> select /A,E:60

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A,E:60-67

140 atoms, 142 bonds, 16 residues, 1 model selected  

> select /A,E:94-95

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select /A,E:89-95

102 atoms, 100 bonds, 14 residues, 1 model selected  

> color sel blue

> ui tool show H-Bonds

> hbonds sel color #fad81a showDist true restrict both interModel false
> intraModel false reveal true

0 hydrogen bonds found  

> hide #!2 models

> select clear

> ui tool show H-Bonds

> hbonds sel color #fad81a showDist true restrict both interModel false
> intraModel false reveal true

Atom specifier selects no atoms  

> ui tool show H-Bonds

> hbonds sel color #fad81a showDist true reveal true

Atom specifier selects no atoms  

> select protein

5904 atoms, 5982 bonds, 746 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #fad81a showDist true reveal true

904 hydrogen bonds found  

> undo

[Repeated 1 time(s)]

> select clear

> ui tool show H-Bonds

> hbonds sel color #fad81a showDist true intraModel false distSlop 0.5
> intraMol false intraRes false reveal true

Atom specifier selects no atoms  

> select protein

5904 atoms, 5982 bonds, 786 pseudobonds, 746 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #fad81a showDist true intraModel false distSlop 0.5
> intraMol false intraRes false reveal true

0 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel color #000000 dashes 5 showDist true intraMol false intraRes
> false reveal true

222 hydrogen bonds found  

> select clear

> view

> open 8jlb

Summary of feedback from opening 8jlb fetched from pdb  
---  
note | Fetching compressed mmCIF 8jlb from
http://files.rcsb.org/download/8jlb.cif  
  
8jlb title:  
Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant
[more info...]  
  
Chain information for 8jlb #3  
---  
Chain | Description | UniProt  
A E | Histone H3.2 | H32_HUMAN 1-135  
B F | Histone H4 | H4_HUMAN 0-102  
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 0-129  
D H | Histone H2B type 1-J | H2B1J_HUMAN 0-125  
I | DNA (145-MER) |  
J | DNA (145-MER) |  
  

> hide #!3 models

> show #!3 models

> style stick

Changed 23687 atom styles  

> select clear

> color #3 #000eb2ff

> ui tool show Matchmaker

> 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 7vz4, chain C (#1) with 8jlb, chain C (#3), sequence alignment
score = 626.6  
RMSD between 107 pruned atom pairs is 0.202 angstroms; (across all 107 pairs:
0.202)  
  

> select protein

11806 atoms, 11962 bonds, 104 pseudobonds, 1492 residues, 3 models selected  

> color (#!1,3 & sel) lime

> select add #1

17745 atoms, 18624 bonds, 222 pseudobonds, 1782 residues, 4 models selected  

> select subtract #1

5902 atoms, 5980 bonds, 746 residues, 1 model selected  

> select add #3

11844 atoms, 12645 bonds, 369 pseudobonds, 1036 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select protein

11806 atoms, 11962 bonds, 104 pseudobonds, 1492 residues, 3 models selected  

> color (#!1,3 & sel) red

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A #3/E

Alignment identifier is 1  

> select #3/A,E:44-57,63-77,85-114,120-132

1150 atoms, 1156 bonds, 144 residues, 1 model selected  

> select #3/A,E:114

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select #3/A,E:110-114

66 atoms, 66 bonds, 10 residues, 1 model selected  

> view sel

> select clear

> ui mousemode right select

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> select #3/A:109@C

1 atom, 1 residue, 1 model selected  

> label sel attribute name

> label sel text "{0.name} {0.number}{0.insertion_code}"

[Repeated 1 time(s)]

> select up

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

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select add #3

11844 atoms, 12645 bonds, 369 pseudobonds, 1036 residues, 3 models selected  

> select subtract #3

Nothing selected  

> select protein

11806 atoms, 11962 bonds, 104 pseudobonds, 1492 residues, 3 models selected  

> color (#!1,3 & sel) blue

> select add #1

17745 atoms, 18624 bonds, 222 pseudobonds, 1782 residues, 4 models selected  

> select subtract #1

5902 atoms, 5980 bonds, 746 residues, 1 model selected  

> hide #!1 models

> select protein

11806 atoms, 11962 bonds, 104 pseudobonds, 1492 residues, 3 models selected  

> show sel & #!3 cartoons

> hide #!3 models

> show #!1 models

> select protein

11806 atoms, 11962 bonds, 104 pseudobonds, 1492 residues, 3 models selected  

> select add #3

17748 atoms, 18627 bonds, 473 pseudobonds, 1782 residues, 5 models selected  

> select subtract #3

5904 atoms, 5982 bonds, 104 pseudobonds, 746 residues, 2 models selected  

> color (#!1 & sel) red

> show #!3 models

> select add #1

11843 atoms, 12644 bonds, 222 pseudobonds, 1036 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select #3/A,E:112

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #3/A,E:110-112

36 atoms, 34 bonds, 6 residues, 1 model selected  

> view sel

> ui tool show "Side View"

> ui mousemode right select

> select #3/A:114

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

> select #1/A:110

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

> color sel byhetero

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> save "/Users/mini1/Desktop/Workshop/Workshop 2.cxs"

> select clear

> ui tool show Distances

> select #1/A:110@SG

1 atom, 1 residue, 1 model selected  

> hide #!3 models

> show #!3 models

> select clear

> select #1/G:112@OE1

1 atom, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select clear

Exactly two atoms must be selected!  

> ui mousemode right select

> select add #3/G:114@CG1

1 atom, 1 bond, 1 residue, 2 models selected  

> select down

1 atom, 1 bond, 1 residue, 2 models selected  
Exactly two atoms must be selected!  

> select #1/A:110@SG

1 atom, 1 residue, 1 model selected  

> select #1/A:110@SG

1 atom, 1 residue, 1 model selected  

> select down

1 bond, 1 model selected  

> select #1/A:110@SG

1 atom, 1 residue, 1 model selected  

> select #3/A:109@CD1

1 atom, 1 residue, 1 model selected  

> select #3/A:109@CD1

1 atom, 1 residue, 1 model selected  

> select #3/A:109@CD2

1 atom, 1 residue, 1 model selected  

> select clear

> select down

1 bond, 1 model selected  
Exactly two atoms must be selected!  

> select down

2 bonds, 2 models selected  
Exactly two atoms must be selected!  

> hide #!1 models

> select #3/A:110@CB

1 atom, 1 residue, 1 model selected  

> select add #3/E:126@CD2

2 atoms, 2 residues, 1 model selected  

> distance #3/A:110@CB #3/E:126@CD2

Distance between 8jlb #3/A ALA 110 CB and /E LEU 126 CD2: 5.183Å  

> select #3/A:112@CD1

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select add #3/G:115@CD1

1 atom, 1 bond, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  

> select subtract #3/G:115@CD1

1 bond, 1 model selected  
Exactly two atoms must be selected!  

> select add #3/A:112@CD1

1 atom, 1 bond, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select #3/A:113@CD2

1 atom, 1 residue, 1 model selected  

> select #3/A:113@CD2

1 atom, 1 residue, 1 model selected  

> select add #3/E:116@NH2

2 atoms, 2 residues, 1 model selected  

> distance #3/A:113@CD2 #3/E:116@NH2

Distance between 8jlb #3/A HIS 113 CD2 and /E ARG 116 NH2: 4.789Å  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #4.1 models

> show #4.1 models

> distance style symbol false

[Repeated 2 time(s)]

> distance style symbol true

[Repeated 2 time(s)]

> distance style decimalPlaces 2

[Repeated 2 time(s)]

> distance style decimalPlaces 1

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 9

[Repeated 2 time(s)]

> distance style dashes 10

[Repeated 2 time(s)]

> distance style dashes 11

[Repeated 2 time(s)]

> distance style dashes 12

[Repeated 2 time(s)]

> distance style dashes 11

[Repeated 2 time(s)]

> distance style dashes 10

[Repeated 2 time(s)]

> distance style dashes 9

[Repeated 2 time(s)]

> distance style color #faade0

[Repeated 2 time(s)]

> distance style color #faacdf

[Repeated 2 time(s)]

> distance style color #faaadb

[Repeated 2 time(s)]

> distance style color #faa9d8

[Repeated 2 time(s)]

> distance style color #fa402e

[Repeated 2 time(s)]

> distance style color #fa402d

[Repeated 2 time(s)]

> distance style color #fa402c

[Repeated 2 time(s)]

> distance style color #fa4615

[Repeated 2 time(s)]

> distance style color #fa4614

[Repeated 2 time(s)]

> distance style color #fa4410

[Repeated 2 time(s)]

> distance style color #fa4510

[Repeated 2 time(s)]

> distance style color #fa4410

[Repeated 2 time(s)]

> distance style color #fa4310

[Repeated 2 time(s)]

> distance style color #fa4112

[Repeated 2 time(s)]

> distance style color #fa381c

[Repeated 2 time(s)]

> distance style color #fa351f

[Repeated 2 time(s)]

> distance style color #fa3123

[Repeated 2 time(s)]

> distance style color #fa53e3

[Repeated 2 time(s)]

> distance style color #fa50e6

[Repeated 2 time(s)]

> distance style color #fa4ce8

[Repeated 2 time(s)]

> distance style color #fa48ea

[Repeated 2 time(s)]

> distance style color #fa43eb

[Repeated 2 time(s)]

> distance style color #fa3deb

[Repeated 2 time(s)]

> distance style color #fa37ea

[Repeated 2 time(s)]

> distance style color #fa28e7

[Repeated 2 time(s)]

> distance style color #fa00c2

[Repeated 2 time(s)]

> distance style color #fa00c1

[Repeated 2 time(s)]

> distance style color #fa00bc

[Repeated 2 time(s)]

> distance style color #fa0cba

[Repeated 2 time(s)]

> distance style color #fa2bbd

[Repeated 2 time(s)]

> distance style color #fa3bbe

[Repeated 2 time(s)]

> distance style color #c7fab4

[Repeated 2 time(s)]

> distance style color #c6faaf

[Repeated 2 time(s)]

> distance style color #c4faa6

[Repeated 2 time(s)]

> distance style color #edfa48

[Repeated 2 time(s)]

> distance style color #edfa46

[Repeated 2 time(s)]

> distance style color #eefa43

[Repeated 2 time(s)]

> distance style color #effa41

[Repeated 2 time(s)]

> distance style color #f0fa3d

[Repeated 2 time(s)]

> distance style color #f0fa3a

[Repeated 2 time(s)]

> distance style color #f3fa1e

[Repeated 2 time(s)]

> distance style color #f3fa1d

[Repeated 2 time(s)]

> distance style color #f5fa00

[Repeated 2 time(s)]

> distance style color #f6fa00

[Repeated 2 time(s)]

> distance style color #f5fa00

[Repeated 2 time(s)]

> distance style color #7a7c00

[Repeated 2 time(s)]

> distance style color #6d6f00

[Repeated 2 time(s)]

> distance style color #6c6f00

[Repeated 2 time(s)]

> distance style color #676900

[Repeated 2 time(s)]

> distance style color #686a00

[Repeated 2 time(s)]

> distance style color #575900

[Repeated 2 time(s)]

> distance style color #4d4f00

[Repeated 2 time(s)]

> distance style color #474800

[Repeated 2 time(s)]

> distance style color #0d0d00

[Repeated 2 time(s)]

> distance style color #070700

[Repeated 2 time(s)]

> distance style color #040400

[Repeated 2 time(s)]

> distance style color #010100

[Repeated 2 time(s)]

> distance style color black

[Repeated 2 time(s)]

> distance style color #020200

[Repeated 2 time(s)]

> distance style color #1a1a00

[Repeated 2 time(s)]

> distance style color #4b4c00

[Repeated 2 time(s)]

> distance style color #585a00

[Repeated 2 time(s)]

> distance style color #595b00

[Repeated 2 time(s)]

> distance style color #5a5b00

[Repeated 2 time(s)]

> distance style color #686a00

[Repeated 2 time(s)]

> distance style color #6b6d00

[Repeated 2 time(s)]

> distance style color #6c6e00

[Repeated 2 time(s)]

> distance style color #6d6f00

[Repeated 2 time(s)]

> distance style color #6e7000

[Repeated 2 time(s)]

> distance style color #7d8000

[Repeated 2 time(s)]

> distance style color #878a00

[Repeated 2 time(s)]

> distance style color #888a00

[Repeated 2 time(s)]

> distance style color #888b00

[Repeated 2 time(s)]

> distance style color #8c8f00

[Repeated 2 time(s)]

> distance style color #8d9000

[Repeated 2 time(s)]

> distance style color #9c9f00

[Repeated 2 time(s)]

> distance style color #9da000

[Repeated 2 time(s)]

> distance style color #9ea100

[Repeated 2 time(s)]

> distance style color #9fa200

[Repeated 2 time(s)]

> distance style color #a0a300

[Repeated 2 time(s)]

> distance style color #a2a500

[Repeated 2 time(s)]

> distance style color #a4a700

[Repeated 2 time(s)]

> distance style color #a6aa00

[Repeated 2 time(s)]

> distance style color #a9ad00

[Repeated 2 time(s)]

> distance style color #abaf00

[Repeated 2 time(s)]

> distance style color #aeb100

[Repeated 2 time(s)]

> distance style color #b0b300

[Repeated 2 time(s)]

> distance style color #b2b500

[Repeated 2 time(s)]

> distance style color #b4b800

[Repeated 2 time(s)]

> distance style color #b7bb00

[Repeated 2 time(s)]

> distance style color #bbbf00

[Repeated 2 time(s)]

> distance style color #bcc000

[Repeated 2 time(s)]

> distance style color #bec100

[Repeated 2 time(s)]

> distance style color #bec200

[Repeated 2 time(s)]

> distance style color #bfc300

[Repeated 2 time(s)]

> distance style color #c5c900

[Repeated 2 time(s)]

> distance style color #c9cd00

[Repeated 2 time(s)]

> distance style color #cace00

[Repeated 2 time(s)]

> distance style color #cbcf00

[Repeated 2 time(s)]

> distance style color #cdd100

[Repeated 2 time(s)]

> distance style color #cdd200

[Repeated 2 time(s)]

> distance style color #d25c3a

[Repeated 2 time(s)]

> distance style color #d25b39

[Repeated 2 time(s)]

> distance style color #d25b38

[Repeated 2 time(s)]

> distance style color #d25a37

[Repeated 2 time(s)]

> distance style color #d25e00

[Repeated 2 time(s)]

> distance style color #d26100

[Repeated 2 time(s)]

> distance style color #d26300

[Repeated 2 time(s)]

> distance style color #d26900

[Repeated 2 time(s)]

> distance style color #d26b00

[Repeated 2 time(s)]

> distance style color #d27200

[Repeated 2 time(s)]

> distance style color #d27b00

[Repeated 2 time(s)]

> distance style color #d28004

[Repeated 2 time(s)]

> distance style color #d2b528

[Repeated 2 time(s)]

> distance style color #d2bc1e

[Repeated 2 time(s)]

> distance style color #d2bc1d

[Repeated 2 time(s)]

> distance style color #d2b619

[Repeated 2 time(s)]

> distance style color #d2b519

[Repeated 2 time(s)]

> distance style color #d2b518

[Repeated 2 time(s)]

> distance style color #d2b010

[Repeated 2 time(s)]

> distance style color #d2b110

[Repeated 2 time(s)]

> distance style color #d2b20f

[Repeated 2 time(s)]

> distance style color #d2bc0f

[Repeated 2 time(s)]

> distance style color #d2c710

[Repeated 2 time(s)]

> distance style color #d2cf0f

[Repeated 2 time(s)]

> distance style color #d2d00f

[Repeated 2 time(s)]

> distance style color #d2d10f

[Repeated 2 time(s)]

> distance style color #ccd20e

[Repeated 2 time(s)]

> distance style color #cbd20d

[Repeated 2 time(s)]

> distance style color #cbd20e

[Repeated 2 time(s)]

> distance style color #cad20e

[Repeated 2 time(s)]

> distance style color #cbd20e

[Repeated 2 time(s)]

> distance style color #ced20a

[Repeated 2 time(s)]

> distance style color #cfd20a

[Repeated 2 time(s)]

> distance style color #cfd209

[Repeated 2 time(s)]

> distance style color #d0d209

[Repeated 2 time(s)]

> distance style color #d2cf08

[Repeated 2 time(s)]

> select #3/E:124@CG2

1 atom, 1 residue, 1 model selected  

> select down

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #3/B:31@NZ

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

> select down

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

> distance #3/E:124@CG2 #3/B:31@NZ

Distance between 8jlb #3/E ILE 124 CG2 and /B LYS 31 NZ: 35.2Å  

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 5

[Repeated 2 time(s)]

> distance style dashes 4

[Repeated 2 time(s)]

> distance style dashes 3

[Repeated 2 time(s)]

> distance style dashes 2

[Repeated 2 time(s)]

> distance style dashes 1

[Repeated 2 time(s)]

> distance style dashes 0

[Repeated 2 time(s)]

> distance style dashes 1

[Repeated 2 time(s)]

> distance style dashes 2

[Repeated 2 time(s)]

> distance style dashes 3

[Repeated 2 time(s)]

> distance style dashes 4

[Repeated 2 time(s)]

> distance style dashes 5

[Repeated 2 time(s)]

> distance style dashes 6

[Repeated 2 time(s)]

> distance style dashes 7

[Repeated 2 time(s)]

> distance style dashes 8

[Repeated 2 time(s)]

> distance style dashes 9

[Repeated 2 time(s)]

> distance style dashes 10

[Repeated 2 time(s)]

> distance style dashes 11

[Repeated 2 time(s)]

> distance style dashes 12

[Repeated 2 time(s)]

> distance style dashes 13

[Repeated 2 time(s)]

> distance style dashes 14

[Repeated 2 time(s)]

> distance style dashes 15

[Repeated 2 time(s)]

> distance style dashes 16

[Repeated 2 time(s)]

> distance style dashes 17

[Repeated 2 time(s)]

> distance style dashes 18

[Repeated 2 time(s)]

> distance style dashes 19

[Repeated 2 time(s)]

> select #3/A:106@OD2

1 atom, 1 residue, 1 model selected  

> select add #3/A:128@NH1

2 atoms, 2 residues, 1 model selected  

> select add #3/A:133@OE1

3 atoms, 3 residues, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/options/options.py", line 58, in proxy_handler  
pself._callback(pself)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 332, in <lambda>  
lambda opt, settings=settings:
self._set_angle_decimal_places(settings.decimal_places),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 599, in
_set_angle_decimal_places  
self._update_angles()  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 642, in _update_angles  
self.angle_table.item(i, 4).setText(self._angle_text(atoms))  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 94, in _angle_text  
return self._angle_fmt % func(*[a.scene_coord for a in atoms])  
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  
ValueError: unsupported format character '-' (0x2d) at index 2  
  
Error processing trigger "setting changed":  
ValueError: unsupported format character '-' (0x2d) at index 2  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/tool.py", line 94, in _angle_text  
return self._angle_fmt % func(*[a.scene_coord for a in atoms])  
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Mac14,3
      Model Number: MMFJ3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.6 (22G630)
      Kernel Version: Darwin 22.6.0
      Time since boot: 23 hours, 13 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        SH272U:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 100.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Component:	Unassigned → Structure Analysis
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Angle tool allows decimal places to go to -1

comment:2 by Eric Pettersen, 19 months ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Jason,

Thanks for reporting this problem. It was reported a few days ago but I haven't had time to fix it yet. I will add you to the recipient list for the ticket that we already have open for this.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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