Cannot reshow Distances tool

[kimsk@…]

The following bug report has been submitted:
Platform:        macOS-10.14.5-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202110301952 (2021-10-30 19:52:32 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4.dev202110301952 (2021-10-30)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> format session

Log from Thu Nov 11 12:44:42 2021UCSF ChimeraX version: 1.4.dev202110301952
(2021-10-30)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs

Log from Wed Oct 27 22:15:56 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

Log from Wed Dec 23 20:51:39 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

Log from Wed Dec 23 20:29:05 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> format session

Log from Wed Dec 23 19:41:28 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

Log from Mon Dec 21 23:31:32 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

Log from Thu Dec 17 16:57:46 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /Users/katekim/Downloads/electrostatics.cxs

Log from Mon Nov 9 14:23:02 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home/sasha/Desktop/pks/sasha_figs/figure1/NACPs.cxs

Log from Mon Nov 2 15:10:34 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home/sasha/Desktop/pks/figure_1.cxs

Log from Mon Nov 2 14:59:47 2020UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open CACP_KS_AT_conformer-coot-3.pdb

Chain information for CACP_KS_AT_conformer-coot-3.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open NACP_KS_AT_conformer_4.pdb

Chain information for NACP_KS_AT_conformer_4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> lighting gentle

> select #1/A:1-98

753 atoms, 765 bonds, 1 model selected  

> ui tool show "Color Actions"

> color sel tomato

> set bgColor white

> select #1:99-1074

14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected  

> hide sel cartoons

> select #1/B:1-99

58 atoms, 57 bonds, 1 model selected  

> hide sel cartoons

> select #2/B:1-99

768 atoms, 781 bonds, 1 model selected  

> color sel tomato

> graphics silhouettes true

> hide pbonds

> select #2/A:99-521

3126 atoms, 3185 bonds, 2 pseudobonds, 2 models selected  

> select clear

> select #2/B:99

8 atoms, 7 bonds, 1 model selected  

> color sel cyan

> color sel deep sky blue

> color sel deep sky blue

> color sel dark turquoise

> color sel medium spring green

> color sel dodger blue

> color sel turquoise

> color sel light sea green

> color sel cornflower blue

> color sel cornflower blue

> color sel dark cyan

> color sel medium aquamarine

> color sel teal

> color sel steel blue

> color sel cadet blue

> color sel sky blue

> color sel light sky blue

> color sel sky blue

> select clear

> select #2/B:99

8 atoms, 7 bonds, 1 model selected  

> select clear

> select #2:99-1074

14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select #2/A:97

9 atoms, 8 bonds, 1 model selected  

> select up

50 atoms, 49 bonds, 2 models selected  

> hide sel cartoons

> select #2:99-1074

14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected  

> show sel surfaces

> select #2/A:867@OH

1 atom, 1 model selected  

> select up

12 atoms, 12 bonds, 2 models selected  

> select up

29 atoms, 29 bonds, 2 models selected  

> select up

6964 atoms, 7102 bonds, 2 models selected  

> select down

29 atoms, 29 bonds, 2 models selected  

> select clear

> select #2/A

6964 atoms, 7102 bonds, 6 pseudobonds, 2 models selected  

> color sel gold target s

> color sel yellow target s

> color sel yellow target s

> color sel chartreuse target s

> color sel green target s

> color sel pale green target s

> color sel light green target s

> color sel burly wood target s

> color sel aquamarine target s

> color sel light coral target s

> color sel sky blue target s

> color sel light sky blue target s

> color sel light blue target s

> color sel light steel blue target s

> color sel pale turquoise target s

> color sel pale turquoise target s

> color sel light steel blue target s

> color sel powder blue target s

> color sel sky blue target s

> color sel white smoke target s

> color sel wheat target s

> color sel azure target s

> color sel beige target s

> color sel wheat target s

> color sel khaki target s

> color sel pale goldenrod target s

> select #2/B

7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected  

> color sel floral white target s

> color sel lemon chiffon target s

> color sel lemon chiffon target s

> color sel seashell target s

> color sel lavender blush target s

> color sel light yellow target s

> color sel snow target s

> color sel misty rose target s

> select clear

> transparency #2 70 target s

> select #2/A

6964 atoms, 7102 bonds, 6 pseudobonds, 2 models selected  

> color sel lemon chiffon target cs

> transparency #2/A 70 target s

> select #2/B

7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected  

> color sel lemon chiffon target cs

> color sel papaya whip target cs

> color sel lavender blush target cs

> transparency #2/B 70 target s

> select #2/B:1098

Nothing selected  

> select #2/B:1-98

760 atoms, 773 bonds, 1 model selected  

> color sel tomato target cs

> select #2/B

7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected  

> select #2/B:99-1074

6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected  

> color sel medium purple target cs

> color sel dark orchid target cs

> color sel medium purple target cs

> color sel medium purple target cs

> color sel medium purple target cs

> color sel wheat target cs

> color sel khaki target cs

> color sel pale goldenrod target cs

> color sel violet target cs

> color sel violet target cs

> color sel lavender target cs

> color sel plum target cs

> color sel cornsilk target cs

> color sel powder blue target cs

> select clear

> select #2:99-1074

14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> undo

> undo

> undo

> select #2:99-1074

14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected  

> show sel surfaces

> select clear

> lighting flat

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting shadows true

> lighting gentle

> ui tool show "Side View"

> select #2/A:99-1074

6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected  

> color sel medium slate blue target cs

> color sel medium orchid target cs

> color sel medium violet red target cs

> color sel light sky blue target cs

> color sel aquamarine target cs

> color sel light coral target cs

> color sel rosy brown target cs

> color sel light coral target cs

> select #2/B:99-1074

6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected  

> color sel peach puff target cs

> color sel navajo white target cs

> color sel navajo white target cs

> color sel peach puff target cs

> color sel navajo white target cs

> color sel moccasin target cs

> color sel navajo white target cs

> color sel peach puff target cs

> color sel navajo white target cs

> color sel bisque target cs

> color sel lemon chiffon target cs

> color sel cornsilk target cs

> color sel seashell target cs

> color sel lavender blush target cs

> color sel papaya whip target cs

> color sel blanched almond target cs

> color sel misty rose target cs

> color sel bisque target cs

> color sel pale turquoise target cs

> select #2/B:1-98 #1/A:1-98

1513 atoms, 1538 bonds, 2 models selected  

> color sel light goldenrod yellow target cs

> color sel yellow target cs

> color sel orange target cs

> color sel gold target cs

> color sel orange target cs

> color sel dark orange target cs

> color sel fire brick target cs

> color sel tomato target cs

> color sel light salmon target cs

> color sel blue target cs

> color sel dark magenta target cs

> select clear

> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 quality 100 transparentBackground true

Expected a keyword  

> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 transparentBackground true

> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 quality 100 transparentBackground true

Expected a keyword  

> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 quality 100 transparentBackground true

Expected a keyword  
Unknown data format: 'png'  

> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 transparentBackground true

> lighting flat

> lighting soft

> lighting simple

> lighting shadows true

> lighting flat

> graphics silhouettes false

> lighting gentle

> graphics silhouettes true

> select :76-86

182 atoms, 178 bonds, 2 models selected  

> show sel atoms

> size stickRadius 0.4

Changed 29848 bond radii  

> select #2/B:1-98 #1/A:1-98

1513 atoms, 1538 bonds, 2 models selected  

> color sel gold target acs

> color sel yellow target acs

> color sel gold target acs

> color sel byhetero

> select #2:99-521

6525 atoms, 6370 bonds, 4 pseudobonds, 2 models selected  

> color sel fire brick target acs

> select #2:522-1074

7576 atoms, 7732 bonds, 8 pseudobonds, 2 models selected  

> color sel royal blue target acs

> color sel indigo target acs

> color sel navy target acs

> color sel dark blue target acs

> color sel blue target acs

> color sel dodger blue target acs

> select clear

> select :HOH

573 atoms, 2 models selected  

> hide sel atoms

> select clear

> select #2:420,500

40 atoms, 36 bonds, 1 model selected  

> select #2:420,482,484,424,388,384,426,87-92,395,430,500,496

285 atoms, 257 bonds, 1 model selected  

> show sel atoms

> color sel byhetero

> color sel byhetero

> color sel fire brick target acs

> select #2:420,482,484,424,388,384,426,395,430,500,496

223 atoms, 200 bonds, 1 model selected  

> color sel byhetero

> select #2:99-521

6525 atoms, 6370 bonds, 4 pseudobonds, 2 models selected  

> color sel fire brick target s

> select #2/B:1-98

760 atoms, 773 bonds, 1 model selected  

> color sel gold target s

> color sel gold target acs

> color sel byhetero

> select clear

> select :HOH

573 atoms, 2 models selected  

> hide sel atoms

> select #1/A:1-72

541 atoms, 548 bonds, 1 model selected  

> show sel atoms

> hide sel atoms

> save /home/sasha/Desktop/pks/figure_1.cxs

opened ChimeraX session  

> open /home/sasha/Desktop/pks/sasha_figs/NACP1_ppant.pdb

Chain information for NACP1_ppant.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #3/A:99-1074

6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #3:99-1074

14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #3/A:76-86

83 atoms, 85 bonds, 1 model selected  

> show sel atoms

> select #1/A:1-98

753 atoms, 765 bonds, 1 model selected  

> hide sel atoms

> hide sel cartoons

> size stickRadius 0.4

Changed 44789 bond radii  

> select #3/A:1-98

753 atoms, 765 bonds, 1 model selected  

> color sel gold target acs

> color sel byhetero

> select clear

> select #3/A:1101@C43

1 atom, 1 model selected  

> select up

21 atoms, 20 bonds, 1 model selected  

> select up

7688 atoms, 7839 bonds, 1 model selected  

> select down

21 atoms, 20 bonds, 1 model selected  

> color sel gold target acs

> color sel byhetero

> select clear

> lighting gentle

> save /home/sasha/Desktop/pks/sasha_figs/figure1/NACPs.cxs

opened ChimeraX session  

> coloumbic #2:99-521 range -10,10

Unknown command: coloumbic #2:99-521 range -10,10  

> coulombic #2:99-521 range -10,10

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: NACP_KS_AT_conformer_4.pdb #2/A PHE 1074 OXT and
NACP_KS_AT_conformer_4.pdb #2/B PHE 1074 OXT  

> open "/home/sasha/Desktop/pks/FINAL FINAL maps&pdb.zip"

Unrecognized file suffix '.zip'  

> open "/home/sasha/Desktop/pks/FINAL FINAL
> maps&pdb/NACP_KS_AT_conformer_4.pdb"

Chain information for NACP_KS_AT_conformer_4.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #4:1-98

831 atoms, 822 bonds, 125 residues, 1 model selected  

> delete sel

> select #4:553-1074

7464 atoms, 7622 bonds, 4 pseudobonds, 968 residues, 2 models selected  

> delete sel

> select #2

14932 atoms, 14928 bonds, 12 pseudobonds, 2220 residues, 2 models selected  

> surface hidePatches (#!2 & sel)

> select #4

6637 atoms, 6482 bonds, 4 pseudobonds, 1127 residues, 2 models selected  

> coulombic #4 range -10,10

> hide #4.3 models

> show #4.3 models

> hide #4.2 models

> show #4.2 models

> hide #4.1 models

> hide #4.2 models

> show #4.2 models

> select #4

6637 atoms, 6482 bonds, 4 pseudobonds, 1127 residues, 2 models selected  

> cartoon hide (#!4 & sel)

> select clear

> transparency #4 60

> select clear

> ui tool show "Side View"

> save /home/sasha/Desktop/pks/sasha_figs/figure1/electrostatics.cxs

opened ChimeraX session  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.1 models

> show #2.1 models

> hide #2.2 models

> show #2.2 models

> hide #2.2 models

> show #2.2 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #2.3 models

> show #2.3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.2 models

> show #!4.2 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> hide #!4.3 models

> show #!4.3 models

> select #1, 2, 3, 4:93-521

26418 atoms, 25780 bonds, 16 pseudobonds, 4498 residues, 8 models selected  

> color (#!1-4 & sel) red

> select clear

> select #1, 2, 3, 4:93-529

26866 atoms, 26228 bonds, 16 pseudobonds, 4562 residues, 8 models selected  

> color (#!1-4 & sel) red

> select clear

> ui tool show "Side View"

> hide #4.2 models

> hide #4.3 models

> select ::name="PNS"

21 atoms, 20 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel navy

> color sel byhetero

> color sel blue

> color sel dark slate blue

> color sel dark slate gray

> color sel byhetero

> select clear

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> hide #2.2 models

> show #2.2 models

> hide #2.3 models

> show #2.3 models

> close #2.2

> close #2.1

> close #1.1

> close #2.3

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #2 models

> hide #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> close #1

> hide #!4 models

> show #!4 models

> show #4.1 models

> hide #4.1 models

> show #4.2 models

> hide #4.2 models

> show #4.3 models

> hide #4.3 models

> close #4.2

> close #4.3

> close #4.1

> show #2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> close #3.1

> hide #4 models

> show #4 models

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

opened ChimeraX session  

> close #4

> color #2/A:1-552 #f79292

> color #2/A:553-1074 #9eddff

> lighting soft

> lighting full

> lighting simple

> lighting soft

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> turn

> turn

> turn

> turn

> turn y

> turn y

> turn y

> turn y

> turn x

> turn x

> turn x

> lighting soft

> select #2/A:1-552

3232 atoms, 3291 bonds, 433 residues, 1 model selected  

> hide sel atoms

> select clear

> select #2/B: 420, 482,424,484,384,388,426,395,430,500,496

111 atoms, 100 bonds, 11 residues, 1 model selected  

> color sel byhetero

> select clear

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> select #2/B:93-552

3232 atoms, 3291 bonds, 433 residues, 1 model selected  

> show sel surfaces

> color (#!2 & sel) black

> transparency #32.1 80

> transparency #2.1 80

> select up

3399 atoms, 3463 bonds, 453 residues, 2 models selected  

> select up

7674 atoms, 7826 bonds, 1009 residues, 2 models selected  

> select up

14932 atoms, 14928 bonds, 2220 residues, 2 models selected  

> select up

14932 atoms, 14928 bonds, 2220 residues, 2 models selected  

> select #2/B:93-552

3232 atoms, 3291 bonds, 433 residues, 1 model selected  

> color #2/B:93-552 #ff1616

> color #2/B:2.1 white

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

> color #2.1 white

> transparency #2.1 80

> select clear

> lighting soft

> lighting soft

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> select #2/B: 420, 482,424,484,384,388,426,395,430,500,496

111 atoms, 100 bonds, 11 residues, 1 model selected  

> select #2.1: 420, 482,424,484,384,388,426,395,430,500,496

Nothing selected  

> select #2/B: 420, 482,424,484,384,388,426,395,430,500,496

111 atoms, 100 bonds, 11 residues, 1 model selected  

> color (#!2 & sel) byhetero

> select clear

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> hide #!2 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #3/B

Alignment identifier is 1  

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show "Show Sequence Viewer"

> sequence chain #2/B

Alignment identifier is 2/B  

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/NACP1_ppant_edited.pdb models
> #3 relModel #3

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> swapaa #3/A:84 tyrosine

Using Dunbrack library  
NACP1_ppant.pdb #3/A ALA 84: phi -116.3, psi 124.7 trans  
Dunbrack rotamer library does not support TYROSINE  

> open /Users/katekim/Box/Pks13_ChimeraX_stuff/NACP1_ppant_edited.pdb

Chain information for NACP1_ppant_edited.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> delete #1: 93-1074

> hide #3 models

> sel#1

Unknown command: sel#1  

> select #1

731 atoms, 744 bonds, 93 residues, 1 model selected  

> color sel yellow

> select clear

> select #1

731 atoms, 744 bonds, 93 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> color sel gold

> select clear

> select ::name="PNS"

42 atoms, 40 bonds, 2 residues, 2 models selected  

> color (#1 & sel) light gray

> ui tool show "Color Actions"

> color sel dark slate gray

> color sel byhetero

> hide #1 models

> show #1 models

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> size #1 atomRadius 2

Changed 731 atom radii  

> size #1 atomRadius 1

Changed 731 atom radii  

> size #1 stickRadius 1

Changed 744 bond radii  

> size #1 stickRadius 0.4

Changed 744 bond radii  

> select clear

> select #1: 76-92

146 atoms, 151 bonds, 17 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> color sel byhetero

> select clear

> select #2/B: 76-92

146 atoms, 151 bonds, 17 residues, 1 model selected  

> show sel atoms

> show sel atoms

> select clear

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

> select clear

> turn center cofr

> turn

> turn

> turn

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

opened ChimeraX session  

> save Fig1_D.png pixelSize 0.05 supersample 24 transparentBackground false

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #3 models

> hide #3 models

> hide #1 models

> hide #!2 models

> show #3 models

> hide #3 models

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> close #3

> show #1 models

> show #!2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

opened ChimeraX session  

> open /Users/katekim/Box/Pks13_ChimeraX_stuff/composite_4ACPs.pdb

Chain information for composite_4ACPs.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
  

> ui tool show Matchmaker

> matchmaker #!3 to #2

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 NACP_KS_AT_conformer_4.pdb, chain B (#2) with composite_4ACPs.pdb,
chain A (#3), sequence alignment score = 4887.4  
RMSD between 900 pruned atom pairs is 0.412 angstroms; (across all 1009 pairs:
19.178)  
  

> matchmaker #!3 to #2

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 NACP_KS_AT_conformer_4.pdb, chain B (#2) with composite_4ACPs.pdb,
chain A (#3), sequence alignment score = 4887.4  
RMSD between 900 pruned atom pairs is 0.412 angstroms; (across all 1009 pairs:
19.178)  
  

> close #3.1

> hide #!2 models

> hide #1 models

> delete #3/A,D

> delete #3:93-1074

> show #!2 models

> show #1 models

> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

opened ChimeraX session  

> ui tool show "Model Panel"

> select #3

1413 atoms, 1438 bonds, 184 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light goldenrod yellow

> color sel lemon chiffon

> color sel lemon chiffon

> color sel lemon chiffon

> select clear

> turn center cofr

> turn

> turn

> turn

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs

——— End of log from Wed Dec 23 20:51:39 2020 ———

opened ChimeraX session  

> hide #1 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #3 models

> show #3 models

> select #2/B:588-694

821 atoms, 831 bonds, 107 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel navy

> select #2/A:588-694

821 atoms, 831 bonds, 107 residues, 1 model selected  

> color sel royal blue

> select clear

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs
> includeMaps true

> ui tool show "Volume Viewer"

> lighting soft

> lighting soft

> lighting soft

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs
> includeMaps true

——— End of log from Wed Oct 27 22:15:56 2021 ———

opened ChimeraX session  

> hide #1 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide surfaces

> ui tool show "Side View"

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true

——— End of log from Thu Nov 11 12:44:42 2021 ———

opened ChimeraX session  

> open /Users/katekim/Desktop/N-ACP2_wDCR-coot-7.pdb

Chain information for N-ACP2_wDCR-coot-7.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #1 models

> hide #!2 models

> hide #3 models

> hide #!4 atoms

> hide pbonds

> lighting simple

> lighting soft

> lighting full

> lighting soft

> select #4/A:76-92

146 atoms, 151 bonds, 17 residues, 1 model selected  

> show sel atoms

> view matrix models
> #4,0.95994,-0.18223,0.21284,2.2549,0.2145,0.96667,-0.13976,-7.2093,-0.18028,0.17982,0.96704,5.3272

> ui mousemode right zoom

> select #4/A:93-552

3232 atoms, 3291 bonds, 1 pseudobond, 433 residues, 2 models selected  

> select ::name="ARG"

2706 atoms, 2472 bonds, 246 residues, 4 models selected  

> show sel & #!4 atoms

> select ::name="LYS"

1332 atoms, 1192 bonds, 148 residues, 2 models selected  

> show sel & #!4 atoms

> ui tool show "Side View"

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true

> select #4/A:1-92

710 atoms, 723 bonds, 92 residues, 1 model selected  

> color sel #FFF200

> color sel byhetero

> select #4/A:93-552

3232 atoms, 3291 bonds, 1 pseudobond, 433 residues, 2 models selected  

> color sel ##ff1616

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

> color sel #ff1616

> color (#!4 & sel) byhetero

> select #4/A:553-694

821 atoms, 831 bonds, 107 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel navy

> select #4/A:695-1074

2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected  

> select up

7693 atoms, 7844 bonds, 1 pseudobond, 1010 residues, 2 models selected  

> select down

2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected  

> color sel #23a7ff

> hide sel atoms

> select #4/A:553-694

821 atoms, 831 bonds, 107 residues, 1 model selected  

> hide sel atoms

> select #4/B:553-694

821 atoms, 831 bonds, 107 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel royal blue

> select #4/B:695-1074

2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected  

> color sel #9eddff

> select #4/B:1-552

3305 atoms, 3366 bonds, 1 pseudobond, 441 residues, 2 models selected  

> color sel #f79292

> select clear

> select #4/B:1-1074

7037 atoms, 7177 bonds, 3 pseudobonds, 925 residues, 2 models selected  

> hide sel atoms

> select clear

> select #4/B:1-75

Nothing selected  

> select #4/A:1-75

564 atoms, 571 bonds, 75 residues, 1 model selected  

> hide sel atoms

> select clear

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true

> style #!4 stick

Changed 14749 atom styles  

> style #!4 ball

Changed 14749 atom styles  

> style #!4 stick

Changed 14749 atom styles  

> size #4/A:78 atomRadius 1

Changed 9 atom radii  

> size #4/A:78 atomRadius 2

Changed 9 atom radii  

> size #4/A:78 stickRadius 2

Changed 8 bond radii  

> size #4/A:78 stickRadius 1

Changed 8 bond radii  

> size #4/A:78 stickRadius 0.5

Changed 8 bond radii  

> size #4/A:76-92 stickRadius 0.5

Changed 151 bond radii  

> size #4/A:76-92 stickRadius 0.4

Changed 151 bond radii  

> size #4/A:93-552 stickRadius 0.4

Changed 3291 bond radii  

> transparency #4 80 target cr

> transparency #4 70 target cr

> transparency #4 90 target cr

> transparency #4 80 target cr

> ui tool show Contacts

> ui tool show H-Bonds

> hbonds showDist true twoColors true saltOnly true intraRes false select true

269 hydrogen bonds found  
97 strict hydrogen bonds found  

> hbonds showDist true distSlop 0.5 twoColors true saltOnly true intraRes
> false select true

299 hydrogen bonds found  
97 strict hydrogen bonds found  

> select clear

> ui tool show Distances

Traceback (most recent call last):  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1263, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/__init__.py", line 45, in start_tool  
return get_tool(session, tool_name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 19, in get_tool  
_tool.show_tab(tool_name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 56, in show_tab  
self.tab_widget.setCurrentIndex(index)  
RuntimeError: wrapped C/C++ object of type QTabWidget has been deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1671, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:  
wrapped C/C++ object of type QTabWidget has been deleted  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:  
wrapped C/C++ object of type QTabWidget has been deleted  
  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true

> ui tool show Distances

Traceback (most recent call last):  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1263, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/__init__.py", line 45, in start_tool  
return get_tool(session, tool_name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 19, in get_tool  
_tool.show_tab(tool_name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 56, in show_tab  
self.tab_widget.setCurrentIndex(index)  
RuntimeError: wrapped C/C++ object of type QTabWidget has been deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1671, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:  
wrapped C/C++ object of type QTabWidget has been deleted  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:  
wrapped C/C++ object of type QTabWidget has been deleted  
  
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,2
      Processor Name: Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 194.0.0.0.0
      SMC Version (system): 2.44f1

Software:

    System Software Overview:

      System Version: macOS 10.14.5 (18F132)
      Kernel Version: Darwin 18.6.0
      Time since boot: 14 days 2:46

Graphics/Displays:

    Intel Iris Plus Graphics 650:

      Chipset Model: Intel Iris Plus Graphics 650
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5927
      Revision ID: 0x0006
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.5
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.1.6
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202110301952
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.3
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.3.1
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.14
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.4
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[pett]

Reported by Kate Kim

[pett]

Hi Kate,

Thanks for reporting this problem. I have fixed it now and the fix will be in tomorrow's daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab