Opened 4 years ago

Closed 4 years ago

#5722 closed defect (duplicate)

Show Distances tool: wrapped C/C++ object of type QTabWidget has been deleted

Reported by: kimsk@… Owned by: pett
Priority: moderate 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-10.14.5-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202111111002 (2021-11-11 10:02:38 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4.dev202111111002 (2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.

open
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs

Log from Wed Dec 1 23:32:50 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.

open
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs

Log from Mon Nov 15 15:23:49 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.

open
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
format session

Log from Mon Nov 15 15:07:58 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.

open
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
format session

Log from Mon Nov 15 14:47:15 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.

open
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
format session

Log from Mon Nov 15 14:16:35 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 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 Fri Nov 12 15:09:46 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 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 Fri Nov 12 14:34:37 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 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 16:26:07 2021UCSF ChimeraX version: 1.4.dev202111111002
(2021-11-11)
© 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 15:51:45 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/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

——— End of log from Thu Nov 11 15:51:45 2021 ———

opened ChimeraX session

ui tool show Distances

hide hbonds

select #4/A:92@NH2

1 atom, 1 residue, 1 model selected

select add #4/A:282@NH2

2 atoms, 2 residues, 1 model selected

distance #4/A:92@NH2 #4/A:282@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 92 NH2 and ARG 282 NH2:
3.607Å

select #4/A:89@OD1

1 atom, 1 residue, 1 model selected

select add #4/A:388@NZ

2 atoms, 2 residues, 1 model selected

distance #4/A:89@OD1 #4/A:388@NZ

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 89 OD1 and LYS 388 NZ: 5.933Å

select #4/A:88@OE2

1 atom, 1 residue, 1 model selected

select add #4/A:384@NH1

2 atoms, 2 residues, 1 model selected

distance #4/A:88@OE2 #4/A:384@NH1

Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 88 OE2 and ARG 384 NH1:
3.308Å

select #4/A:88@OE1

1 atom, 1 residue, 1 model selected

select add #4/A:384@NH2

2 atoms, 2 residues, 1 model selected

distance #4/A:88@OE1 #4/A:384@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 88 OE1 and ARG 384 NH2:
3.642Å

~distance #4/A:89@OD1 #4/A:388@NZ

ui tool show "Side View"

select clear

select #4/A:87@OD2

1 atom, 1 residue, 1 model selected

select add #4/A:395@NH2

2 atoms, 2 residues, 1 model selected

distance #4/A:87@OD2 #4/A:395@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 87 OD2 and ARG 395 NH2:
7.086Å

~distance #4/A:87@OD2 #4/A:395@NH2

select #4/A:85@OD2

1 atom, 1 residue, 1 model selected

select add #4/A:395@NH2

2 atoms, 2 residues, 1 model selected

distance #4/A:85@OD2 #4/A:395@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 85 OD2 and ARG 395 NH2:
5.736Å

~distance #4/A:85@OD2 #4/A:395@NH2

select #4/A:82@OE2

1 atom, 1 residue, 1 model selected

select add #4/A:424@NZ

2 atoms, 2 residues, 1 model selected

distance #4/A:82@OE2 #4/A:424@NZ

Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 82 OE2 and LYS 424 NZ: 5.776Å

~distance #4/A:82@OE2 #4/A:424@NZ

select #4/A:85@OD1

1 atom, 1 residue, 1 model selected

select add #4/A:384@NH1

2 atoms, 2 residues, 1 model selected

distance #4/A:85@OD1 #4/A:384@NH1

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 85 OD1 and ARG 384 NH1:
8.590Å

~distance #4/A:85@OD1 #4/A:384@NH1

select #4/A:85@OD2

1 atom, 1 residue, 1 model selected

select add #4/A:395@NH2

2 atoms, 2 residues, 1 model selected

distance #4/A:85@OD2 #4/A:395@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 85 OD2 and ARG 395 NH2:
5.736Å

~distance #4/A:85@OD2 #4/A:395@NH2

select #4/A:82@OE2

1 atom, 1 residue, 1 model selected

select add #4/A:424@NZ

2 atoms, 2 residues, 1 model selected

distance #4/A:82@OE2 #4/A:424@NZ

Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 82 OE2 and LYS 424 NZ: 5.776Å

~distance #4/A:82@OE2 #4/A:424@NZ

select #4/A:78@OE2

1 atom, 1 residue, 1 model selected

select add #4/A:482@NZ

2 atoms, 2 residues, 1 model selected

distance #4/A:78@OE2 #4/A:482@NZ

Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 78 OE2 and LYS 482 NZ: 6.075Å

~distance #4/A:78@OE2 #4/A:482@NZ

select clear

surface #4-6

transparency #4-6 90

ui tool show "Surface Color"

No map chosen for coloring

hide #!4 surfaces

show #!4 surfaces

coulombic #!4

Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for N-ACP2_wDCR-coot-7.pdb_A SES surface #4.2: minimum,
-26.54, mean -4.52, maximum 12.20
Coulombic values for N-ACP2_wDCR-coot-7.pdb_B SES surface #4.3: minimum,
-19.09, mean -4.05, maximum 13.50
To also show corresponding color key, enter the above coulombic command and
add key true

transparency #4-6 80

hide #!4 surfaces

select #4/A:93-552

3232 atoms, 3291 bonds, 34 pseudobonds, 433 residues, 3 models selected

hide sel atoms

select #4/A:420,482,424,484,384,388,426,395,430,500,496

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

show sel atoms

select #4/A:500,496,426,430,484

51 atoms, 46 bonds, 5 residues, 1 model selected

hide sel atoms

select #4/A:282

11 atoms, 10 bonds, 1 residue, 1 model selected

show sel atoms

select clear

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 16:26:07 2021 ———

opened ChimeraX session

ui tool show Distances

select #4/A:476@O

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

select #4/A:59@N

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

size #4/A:1-552 stickRadius 0.4

Changed 4015 bond radii

select clear

select #4/A:59@N

1 atom, 1 residue, 1 model selected

select add #4/A:476@O

2 atoms, 2 residues, 2 models selected

distance #4/A:59@N #4/A:476@O

Distance between N-ACP2_wDCR-coot-7.pdb #4/A THR 59 N and PRO 476 O: 3.791Å

~distance #4/A:88@OE2 #4/A:384@NH1

~distance #4/A:88@OE1 #4/A:384@NH2

~distance #4/A:92@NH2 #4/A:282@NH2

distance style radius 0.4

distance style radius 0.3

select #6.1

1 model selected

~select #6.1

Nothing selected

distance style radius 0.25

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

label listfonts

270 fonts available:
.Al Bayan PUA
.Al Nile PUA
.Al Tarikh PUA
.Apple Color Emoji UI
.Apple SD Gothic NeoI
.Apple Symbols Fallback
.Aqua Kana
.Arabic UI Display
.Arabic UI Text
.Arial Hebrew Desk Interface
.Baghdad PUA
.Beirut PUA
.Damascus PUA
.DecoType Naskh PUA
.Diwan Kufi PUA
.Farah PUA
.Geeza Pro Interface
.Geeza Pro PUA
.Helvetica Neue DeskInterface
.Hiragino Kaku Gothic Interface
.Hiragino Sans GB Interface
.Keyboard
.KufiStandardGK PUA
.LastResort
.Lucida Grande UI
.Muna PUA
.Nadeem PUA
.Noto Nastaliq Urdu UI
.Noto Sans Universal
.PingFang HK
.PingFang SC
.PingFang TC
.SF Compact Display
.SF Compact Rounded
.SF Compact Text
.SF NS Display
.SF NS Display Condensed
.SF NS Rounded
.SF NS Symbols
.SF NS Text
.SF NS Text Condensed
.Sana PUA
.Savoye LET CC.
Adobe Arabic
Adobe Caslon Pro
Adobe Fan Heiti Std
Adobe Fangsong Std
Adobe Garamond Pro
Adobe Gothic Std
Adobe Hebrew
Adobe Heiti Std
Adobe Kaiti Std
Adobe Ming Std
Adobe Myungjo Std
Adobe Song Std
Al Bayan
Al Nile
Al Tarikh
American Typewriter
Andale Mono
Apple Braille
Apple Chancery
Apple Color Emoji
Apple SD Gothic Neo
Apple Symbols
AppleGothic
AppleMyungjo
Arial
Arial Black
Arial Hebrew
Arial Hebrew Scholar
Arial Narrow
Arial Rounded MT Bold
Arial Unicode MS
Athelas
Avenir
Avenir Next
Avenir Next Condensed
Ayuthaya
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help help:user/tools/modelpanel.html

distance style color #3aeafa

distance style color gold

distance style radius 0.1

distance style color #25faea

[Repeated 1 time(s)]

distance style radius 0.2

hide #6.1 models

show #6.1 models

label #6.1 height

Missing "height" keyword's argument

label #6.1 size 24

label #6.1 size 48

hide #6.1 models

show #6.1 models

label #6.1 size 90

label #6.1 height 1

label #6.1 height 3

select #6.1

1 model selected

hide #!6 models

show #!6 models

label #6 height 3

label #6 height 2

label #6 height 1

label #6 height 1.5

select #6

1 pseudobond, 2 models selected

~select #6

Nothing selected

select #6.1

1 model selected
No visible atoms, bonds, or surfaces selected

color #6.1 |default

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

color #6.1 | default

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

color #6.1 default

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

color #6.1 black

color #6 black

color #6.1 black

No visible atoms, bonds, or surfaces selected

distance style color #6df5e7

[Repeated 1 time(s)]

distance style color #6cf5e7

distance style color #353ef5

distance style color #363ff5

distance style color #2b87f5

distance style color #2dc1f5

[Repeated 1 time(s)]

distance style color #25f5f3

distance style color #25f5f2

distance style color #67f5ee

distance style color #05f5e9

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

——— End of log from Fri Nov 12 14:34:37 2021 ———

opened ChimeraX session

select #4/A:92@NE

1 atom, 1 residue, 1 model selected

select #4/A:389@O

1 atom, 1 residue, 1 model selected

show (#!4 & sel-residues & sidechain) target ab

color (#!4 & sel) byhetero

select #4/A:389@O

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

select #4/A:389@O

1 atom, 1 residue, 1 model selected

select #4/A:389@O

1 atom, 1 residue, 1 model selected
Drag select of 2 residues

select clear

select #4/A:389@O

1 atom, 1 residue, 1 model selected

select clear

select #4/A:389@O

1 atom, 1 residue, 1 model selected

select add #4/A:92@NE

2 atoms, 2 residues, 2 models selected

ui tool show Distances

[Repeated 1 time(s)]

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

——— End of log from Fri Nov 12 15:09:46 2021 ———

opened ChimeraX session

ui tool show Distances

distance #4/A:92@NE #4/A:389@O

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 92 NE and ASP 389 O: 3.245Å

select #4/A:92@NH2

1 atom, 1 residue, 1 model selected

select #4/A:98@OD1

1 atom, 1 residue, 1 model selected

show (#!4 & sel-residues & sidechain) target ab

select add #4/A:92@NH2

2 atoms, 2 residues, 2 models selected

distance #4/A:98@OD1 #4/A:92@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 98 OD1 and ARG 92 NH2: 2.421Å

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

select #4/A:92@NH2

1 atom, 1 residue, 1 model selected

select #4/A:358@O

1 atom, 1 residue, 1 model selected

hide (sel-residues & (protein|nucleic)) target a

cartoon hide sel-residues

show (sel-residues & backbone) target ab

show (sel-residues & sidechain) target ab

select add #4/A:92@NH2

2 atoms, 2 residues, 1 model selected

distance #4/A:358@O #4/A:92@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ALA 358 O and ARG 92 NH2: 2.951Å

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

select #4/A:88@OE1

1 atom, 1 residue, 1 model selected

ui tool show "Side View"

select #4/A:88@OE1,384@NH2

1 atom, 1 residue, 1 model selected

select #4/A:384@NH2

1 atom, 1 residue, 1 model selected

select add #4/A:88@OE1

2 atoms, 2 residues, 2 models selected

distance #4/A:384@NH2 #4/A:88@OE1

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 384 NH2 and GLU 88 OE1:
3.642Å

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

select #4/A:388@NZ

1 atom, 1 residue, 1 model selected

select add #4/A:88@OE1

2 atoms, 2 residues, 2 models selected

distance #4/A:388@NZ #4/A:88@OE1

Distance between N-ACP2_wDCR-coot-7.pdb #4/A LYS 388 NZ and GLU 88 OE1: 2.780Å

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

select #4/A:384@NH1

1 atom, 1 residue, 1 model selected

select add #4/A:88@OE2

2 atoms, 2 residues, 2 models selected

distance #4/A:384@NH1 #4/A:88@OE2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ARG 384 NH1 and GLU 88 OE2:
3.308Å

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

select clear

select #4/A:88@OE2

1 atom, 1 residue, 1 model selected

select clear

select #4/A:88@OE2

1 atom, 1 residue, 1 model selected

select add #4/A:384@NH2

2 atoms, 2 residues, 2 models selected

distance #4/A:88@OE2 #4/A:384@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/A GLU 88 OE2 and ARG 384 NH2:
3.683Å

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

select #4/A:90@O

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

select #4/A:392@N

1 atom, 1 residue, 1 model selected

hide (sel-residues & (protein|nucleic)) target a

cartoon hide sel-residues

show (sel-residues & backbone) target ab

show (sel-residues & sidechain) target ab

select #4/A:392

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

color (#!4 & sel) byhetero

select #4/A:392@N

1 atom, 1 residue, 1 model selected

select add #4/A:90@O

2 atoms, 2 residues, 1 model selected

distance #4/A:392@N #4/A:90@O

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ILE 392 N and TRP 90 O: 3.567Å

select #4/A:91@O

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

select #4/A:93@N

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

color (#!4 & sel) byhetero

select #4/A:93

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

color (#!4 & sel) byhetero

select #4/A:93@N

1 atom, 1 residue, 1 model selected

select #4/A:91@O

1 atom, 1 residue, 1 model selected

select add #4/A:93@N

2 atoms, 2 residues, 2 models selected

distance #4/A:91@O #4/A:93@N

Distance between N-ACP2_wDCR-coot-7.pdb #4/A SER 91 O and THR 93 N: 3.505Å

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

hide #!5 models

show #!5 models

hide #5.1 models

show #5.1 models

close #5

hide #!6 models

show #!6 models

color #6 cyan

distance style radius 0.25

distance style dashes 8

distance style dashes 7

distance style dashes 6

[Repeated 2 time(s)]

distance style dashes 7

distance style dashes 8

distance style radius 0.2

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

select #4/A:92@NH1

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

select #4/A:92@NH1

1 atom, 1 residue, 1 model selected

select #4/A:98@OD1

1 atom, 1 residue, 1 model selected

select add #4/A:92@NH1

2 atoms, 2 residues, 2 models selected

distance #4/A:98@OD1 #4/A:92@NH1

Distance between N-ACP2_wDCR-coot-7.pdb #4/A ASP 98 OD1 and ARG 92 NH1: 3.488Å

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

select #4/A:92@O

1 atom, 1 residue, 1 model selected

select #4/A:93@N

1 atom, 1 residue, 1 model selected

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

ui tool show "Side View"

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

distance style color #3aeafa

select #4/A:7@NH2

1 atom, 1 residue, 1 model selected

show (#!4 & sel-residues & sidechain) target ab

select #4/A:975@O

1 atom, 1 residue, 1 model selected

select #4/A:975@O

1 atom, 1 residue, 1 model selected

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

select #4/A:975@O

1 atom, 1 residue, 1 model selected

select #4/A:975@O

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

delete atoms (#!4 & sel)

delete bonds (#!4 & sel)

select #4/B:975@O

1 atom, 1 residue, 1 model selected

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

color (#!4 & sel) byhetero

select #4/B:975

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

color (#!4 & sel) byhetero

size #4:1-1074 stickRadius 0.4

Changed 15002 bond radii

select clear

select #4/B:975@O

1 atom, 1 residue, 1 model selected

select add #4/A:7@NH2

2 atoms, 2 residues, 2 models selected

distance #4/B:975@O #4/A:7@NH2

Distance between N-ACP2_wDCR-coot-7.pdb #4/B ASP 975 O and /A ARG 7 NH2:
3.834Å

select clear

select #4/B:975@O

1 atom, 1 residue, 1 model selected

select add #4/A:7@NH1

2 atoms, 2 residues, 2 models selected

distance #4/B:975@O #4/A:7@NH1

Distance between N-ACP2_wDCR-coot-7.pdb #4/B ASP 975 O and /A ARG 7 NH1:
3.482Å

distance style color #3aeafa

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

show #3 models

hide #3 models

hide #!4 models

show #3 models

hide #3 models

show #!2 models

hide #!2 models

show #1 models

hide #1 models

close #1

show #3 models

hide #3 models

close #3

show #!2 models

hide #!2 models

show #!4 models

hide #!4 models

open "/Users/katekim/Dropbox/PKS13/MAPS and
MODELS_UPDATED/NACP1_noHETATM_real_space_refined.pdb"

Chain information for NACP1_noHETATM_real_space_refined.pdb #1
---
Chain | Description
A | No description available
B | No description available

show #!4 models

hide #!1 models

hide #!4 models

show #!1 models

show #!2 models

hide #!2 models

open /Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined-
coot-0_brokenup4PISA_edited.pdb

Summary of feedback from opening
/Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined-
coot-0_brokenup4PISA_edited.pdb
---
warning | Cannot find LINK/SSBOND residue SER (38 )

Chain information for NACP1-KSAT_wHET_real_space_refined-
coot-0_brokenup4PISA_edited.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available

hide #!1 models

hide #!3 models

show #!3 models

show #!1 models

hide #!1 models

close #1

close #3

show #!2 models

hide #!2 models

open
/Users/katekim/Box/Kate_Oren_figs/N_ACP1_conformer/RealSpaceRefine_5/N-ACP1_wPNSnDCR_real_space_refined-
coot-2_real_space_refined.pdb

Chain information for N-ACP1_wPNSnDCR_real_space_refined-
coot-2_real_space_refined.pdb #1
---
Chain | Description
A | No description available
B | No description available

close #1

open /Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined-
coot-0_brokenup4PISA_edited.pdb

Summary of feedback from opening
/Users/katekim/Desktop/NACP1-KSAT_wHET_real_space_refined-
coot-0_brokenup4PISA_edited.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 3
THR A 18 1 16
Start residue of secondary structure not found: HELIX 2 2 ALA A 22 ALA A 24 1
3
Start residue of secondary structure not found: HELIX 3 3 MET A 31 GLU A 33 1
3
Start residue of secondary structure not found: HELIX 4 4 SER A 38 THR A 52 1
15
Start residue of secondary structure not found: HELIX 5 5 ALA A 58 ARG A 63 1
6
1 messages similar to the above omitted

Chain information for NACP1-KSAT_wHET_real_space_refined-
coot-0_brokenup4PISA_edited.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available

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

[Repeated 1 time(s)]

show #!4 models

hide #!1 models

select #4/A:39,42,45,46,49,55,56,57,58,59,61,62,63,78,80,81,83-85,88-92

199 atoms, 195 bonds, 24 residues, 1 model selected

select
#4/A:39,42,45,46,49,55,56,57,58,59,61,62,63,78,80,81,83-85,88-92,93,94,96-98,282,358,384,387-396,421,430,460,461,463,496-499,521-524,527,528,645,646,1047-1053

517 atoms, 502 bonds, 10 pseudobonds, 66 residues, 2 models selected

select clear

select
#4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483

411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected

save
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
includeMaps true

——— End of log from Mon Nov 15 14:16:35 2021 ———

opened ChimeraX session

select clear

hide #!4 atoms

cartoon #4,​6

ui tool show "Side View"

hide #!6 models

select
#4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483

411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected

show sel atoms

cartoon style (#!4 & sel) modeHelix tube sides 20

select clear

size #4:1-1074 stickRadius 0.2

Changed 15002 bond radii

select
#4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483

411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected

style sel sphere

Changed 411 atom styles

select clear

save
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
includeMaps true

style #!4 stick

Changed 14748 atom styles

style #!4 ball

Changed 14748 atom styles

style #!4 stick

Changed 14748 atom styles

select
#4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483

411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected

surface (#!4 & sel)

hide sel surfaces

coulombic sel

Coulombic values for N-ACP2_wDCR-coot-7.pdb_A SES surface #4.2: minimum,
-26.53, mean -4.46, maximum 12.24
To also show corresponding color key, enter the above coulombic command and
add key true

hide sel surfaces

interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier

select clear

cartoon style #4 xsection oval modeHelix default

cartoon style #4 xsection rectangle modeHelix default

cartoon style (#4 & coil) xsection oval

cartoon style #4 xsection barbell modeHelix default

cartoon style #4 modeHelix tube sides 20

cartoon style (#4 & coil) xsection oval

cartoon style #4 xsection barbell modeHelix default

select
#4/A:30,33,38,58,59,62,63,82-92,93,94,96-98,282,358,369,384,387-395,409,412,413,416,421,424,425,476-479,482,483

411 atoms, 403 bonds, 11 pseudobonds, 49 residues, 2 models selected

color (#!4 & sel) byhetero

select clear

hide #!4 models

show #!4 models

show #!1 models

hide #!1 models

hide #!4 models

show #!4 models

show #!2 models

hide #!2 models

show #!2 models

close #2

save
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
includeMaps true

——— End of log from Mon Nov 15 14:47:15 2021 ———

opened ChimeraX session

ui tool show "Side View"

ui tool show Distances

[Repeated 1 time(s)]

save
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
includeMaps true

——— End of log from Mon Nov 15 15:07:58 2021 ———

opened ChimeraX session

show #!6 models

ui tool show Distances

distance style dashes 6

distance style radius 0.12

hide #6.1 models

~distance #4/A:91@O #4/A:93@N

save
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
includeMaps true

——— End of log from Mon Nov 15 15:23:49 2021 ———

opened ChimeraX session

show #!1 models

hide #!1 models

hide #!4 models

show #!4 models

ui tool show "Side View"

hide #!4 atoms

hide #!6 models

show #!1 models

hide #!1 models

transparency #4 0 target cr

lighting simple

lighting soft

lighting full

lighting soft

save
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues.cxs
includeMaps true

——— End of log from Wed Dec 1 23:32:50 2021 ———

opened ChimeraX session

save NACP2_KSAT_Interacting_residues_closeup_numbers.png pixelSize 0.05
supersample 24 transparentBackground false

select #4/C:30,33,58,59,62,63

Nothing selected

select #4/A:30,33,58,59,62,63,369,409,412,413,416,476-479,482,483

142 atoms, 137 bonds, 1 pseudobond, 17 residues, 2 models selected

show sel atoms

color (#!4 & sel) byhetero

select clear

cartoon style (#4 & coil) xsection oval

cartoon style #4 xsection barbell modeHelix default

cartoon style #4 modeHelix tube sides 20

select #4/A:59

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

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

select clear

select #4/A:476

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

hide (#!4 & sel-residues & (protein|nucleic)) target a

cartoon hide (#!4 & sel-residues)

show (#!4 & sel-residues & backbone) target ab

show (#!4 & sel-residues & sidechain) target ab

select clear

cartoon style (#4 & coil) xsection oval

cartoon style #4 xsection barbell modeHelix default

cartoon style #4 xsection rectangle modeHelix default

cartoon style #4 xsection oval modeHelix default

select #4/A:476@O

1 atom, 1 residue, 1 model selected

select clear

select #4/A:476@O

1 atom, 1 residue, 1 model selected

select #4/A:476@O

1 atom, 1 residue, 1 model selected

select add #4/A:59@N

2 atoms, 2 residues, 2 models selected

ui tool show Distances

Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/init.py", line 1264, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1672, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2875, in run
result = ci.function(session, kw_args)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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/C8AD8CCD-
FEC5-47EE-A919-E30D4C9AA4B4/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: 8 days 8:05

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: 4.1.7
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.dev202111111002
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: 2.0.4
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: 1.3.2
ChimeraX-ModelPanel: 1.2.1
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: 2.0.1
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: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
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: 1.3.0
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: 3.0.22
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: 3.0.6
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

Change History (1)

comment:1 by pett, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Hi Kate,

Thanks for reporting this problem. It was fixed about 4 days after the release you have, so if you upgrade to the latest version you won't run into this again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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