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Opened 4 years ago
Closed 4 years ago
#5618 closed defect (can't reproduce)
Changes trigger before pb group restored(?)
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| 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_interfacing_residues_numbers_chainB.cxs
> format session
Log from Tue Nov 16 23:49:20 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_numbers.cxs
> format session
Log from Mon Nov 15 17:39:39 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
Baghdad
Bangla MN
Bangla Sangam MN
Baskerville
Beirut
Big Caslon
Birch Std
Blackoak Std
Bodoni 72
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Bodoni Ornaments
Bradley Hand
Brush Script MT
Brush Script Std
Chalkboard
Chalkboard SE
Chalkduster
Chaparral Pro
Charlemagne Std
Charter
Cochin
Comic Sans MS
Cooper Std
Copperplate
Corsiva Hebrew
Courier
Courier New
DIN Alternate
DIN Condensed
Damascus
DecoType Naskh
Devanagari MT
Devanagari Sangam MN
Didot
Diwan Kufi
Diwan Thuluth
Euphemia UCAS
Farah
Farisi
Futura
GB18030 Bitmap
Geeza Pro
Geneva
Georgia
Giddyup Std
Gill Sans
Gujarati MT
Gujarati Sangam MN
Gurmukhi MN
Gurmukhi MT
Gurmukhi Sangam MN
Heiti SC
Heiti TC
Helvetica
Helvetica Neue
Herculanum
Hiragino Kaku Gothic Pro
Hiragino Kaku Gothic ProN
Hiragino Kaku Gothic Std
Hiragino Kaku Gothic StdN
Hiragino Maru Gothic Pro
Hiragino Maru Gothic ProN
Hiragino Mincho Pro
Hiragino Mincho ProN
Hiragino Sans
Hiragino Sans GB
Hobo Std
Hoefler Text
ITF Devanagari
ITF Devanagari Marathi
Impact
InaiMathi
Iowan Old Style
Kailasa
Kannada MN
Kannada Sangam MN
Kefa
Khmer MN
Khmer Sangam MN
Kohinoor Bangla
Kohinoor Devanagari
Kohinoor Telugu
Kokonor
Kozuka Gothic Pr6N
Kozuka Gothic Pro
Kozuka Mincho Pr6N
Kozuka Mincho Pro
Krungthep
KufiStandardGK
Lao MN
Lao Sangam MN
Letter Gothic Std
Lithos Pro
Lucida Grande
Luminari
Malayalam MN
Malayalam Sangam MN
Marion
Marker Felt
Menlo
Mesquite Std
Microsoft Sans Serif
Minion Pro
Mishafi
Mishafi Gold
Monaco
Mshtakan
Muna
Myanmar MN
Myanmar Sangam MN
Myriad Pro
Nadeem
New Peninim MT
Noteworthy
Noto Nastaliq Urdu
Nueva Std
OCR A Std
Optima
Orator Std
Oriya MN
Oriya Sangam MN
PT Mono
PT Sans
PT Sans Caption
PT Sans Narrow
PT Serif
PT Serif Caption
Palatino
Papyrus
Phosphate
PingFang HK
PingFang SC
PingFang TC
Plantagenet Cherokee
Poplar Std
Prestige Elite Std
Raanana
Rockwell
Rosewood Std
STIXGeneral
STIXIntegralsD
STIXIntegralsSm
STIXIntegralsUp
STIXIntegralsUpD
STIXIntegralsUpSm
STIXNonUnicode
STIXSizeFiveSym
STIXSizeFourSym
STIXSizeOneSym
STIXSizeThreeSym
STIXSizeTwoSym
STIXVariants
STSong
Sana
Sathu
Savoye LET
Seravek
Shree Devanagari 714
SignPainter
Silom
Sinhala MN
Sinhala Sangam MN
Skia
Snell Roundhand
Songti SC
Songti TC
Stencil Std
Sukhumvit Set
Superclarendon
Symbol
Tahoma
Tamil MN
Tamil Sangam MN
Tekton Pro
Telugu MN
Telugu Sangam MN
Thonburi
Times
Times New Roman
Trajan Pro
Trattatello
Trebuchet MS
Verdana
Waseem
Webdings
Wingdings
Wingdings 2
Wingdings 3
Zapf Dingbats
Zapfino
> 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
> ui tool show "Side View"
> save NACP2_Interacting_residues_closeup.png pixelSize 0.05 supersample 24
> transparentBackground false
> select #4/A:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!4 & sel) byhetero
> select clear
> select #4/A:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:786
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:38@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:267@SG
2 atoms, 2 residues, 2 models selected
> distance #4/A:38@OG #4/A:267@SG
Distance between N-ACP2_wDCR-coot-7.pdb #4/A SER 38 OG and CYS 267 SG: 26.874Å
Must select one or more distances in the table
> distance #4/A:38@OG #4/A:267@SG
Distance already exists; modify distance properties with 'distance style'
> select clear
> save NACP2_Interacting_residues_closeup.png pixelSize 0.05 supersample 24
> transparentBackground false
> select clear
> select #4A:30
Expected an objects specifier or a keyword
> select #4A: 30
Expected an objects specifier or a keyword
> select #4/A: 30
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!6 models
> select clear
> select #4/A:38@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:267@SG
2 atoms, 2 residues, 2 models selected
> distance #4/A:38@OG #4/A:267@SG
Distance already exists; modify distance properties with 'distance style'
> show #6.1 models
> hide #6.1 models
> select clear
Must select one or more distances in the table
> ~distance #4/A:358@O #4/A:92@NH2
> ~distance #4/A:384@NH1 #4/A:88@OE2
Must select one or more distances in the table
> ~distance #4/A:98@OD1 #4/A:92@NH1
> ~distance #4/B:975@O #4/A:7@NH2
> ~distance #4/A:92@NE #4/A:389@O
> ~distance #4/B:975@O #4/A:7@NH1
> ~distance #4/A:98@OD1 #4/A:92@NH2
> ~distance #4/A:88@OE2 #4/A:384@NH2
> ~distance #4/A:384@NH2 #4/A:88@OE1
> ~distance #4/A:59@N #4/A:476@O
> ~distance #4/A:388@NZ #4/A:88@OE1
> ~distance #4/A:392@N #4/A:90@O
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_KS_interfacing_residues_numbers.cxs
> includeMaps true
——— End of log from Mon Nov 15 17:39:39 2021 ———
opened ChimeraX session
> select #4/B:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Side View"
> select #4/A:38@OG
1 atom, 1 residue, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select clear
> select #4/B:267@SG
1 atom, 1 residue, 1 model selected
> select add #4/A:38@OG
2 atoms, 2 residues, 2 models selected
> distance #4/B:267@SG #4/A:38@OG
Distance between N-ACP2_wDCR-coot-7.pdb #4/B CYS 267 SG and /A SER 38 OG:
53.962Å
> ~distance #4/B:267@SG #4/A:38@OG
> select clear
> select #4/B:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!4 atoms
> show #!1 models
> hide #!1 models
> select #4/A:4,7,28,76,79-81
57 atoms, 54 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> select #4/B: 699,944,975-977
38 atoms, 35 bonds, 5 residues, 1 model selected
> show sel atoms
> color (#!4 & sel) byhetero
> select #4/A:4,7,28,76,79-81
57 atoms, 54 bonds, 7 residues, 1 model selected
> color (#!4 & sel) byhetero
> select clear
> open /Users/katekim/Desktop/N-ACP2_brokenup_4PISA-coot-0.pdb
Summary of feedback from opening /Users/katekim/Desktop/N-ACP2_brokenup_4PISA-
coot-0.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 5
3
Start residue of secondary structure not found: HELIX 3 3 MET A 31 GLU A 33 5
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 N-ACP2_brokenup_4PISA-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!2 models
> hide #!4 models
> show #!2 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #!2 to #4
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 N-ACP2_wDCR-coot-7.pdb, chain B (#4) with N-ACP2_brokenup_4PISA-
coot-0.pdb, chain B (#2), sequence alignment score = 4707.1
RMSD between 925 pruned atom pairs is 0.000 angstroms; (across all 925 pairs:
0.000)
> select #2:4,7,28,76,79-81
57 atoms, 54 bonds, 7 residues, 1 model selected
> show sel atoms
> select #2:4,7,28,76,79-81
57 atoms, 54 bonds, 7 residues, 1 model selected
> show sel atoms
> hide #!2 models
> show #!2 models
> hide #!4 models
> select #2: 699,944,975-977
76 atoms, 70 bonds, 10 residues, 1 model selected
> show sel atoms
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 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 models
> show #!2 models
> hide #!2 models
> close #2
> open /Users/katekim/Desktop/N-ACP2_brokenup_4PISA-coot-0.pdb
Summary of feedback from opening /Users/katekim/Desktop/N-ACP2_brokenup_4PISA-
coot-0.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 5
3
Start residue of secondary structure not found: HELIX 3 3 MET A 31 GLU A 33 5
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 N-ACP2_brokenup_4PISA-coot-0.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #4
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 N-ACP2_wDCR-coot-7.pdb, chain B (#4) with N-ACP2_brokenup_4PISA-
coot-0.pdb, chain B (#2), sequence alignment score = 4707.1
RMSD between 925 pruned atom pairs is 0.000 angstroms; (across all 925 pairs:
0.000)
> select #2:4,7,28,76,79-81
57 atoms, 54 bonds, 7 residues, 1 model selected
> show sel atoms
> hide sel atoms
[Repeated 2 time(s)]
> close #2
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_interfacing_residues_numbers_chainB.cxs
> includeMaps true
> hide #!6 models
> ui tool show "Side View"
> size #4:1-1074 stickRadius 0.4
Changed 15002 bond radii
> size #4:1-1074 stickRadius 0.3
Changed 15002 bond radii
> save NACP2_chainB_Interacting_residues_closeup_numbers.png pixelSize 0.05
> supersample 24 transparentBackground false
> select #4/A:7@NH2
1 atom, 1 residue, 1 model selected
> select #4/A:975@O
Nothing selected
> select #4:975@O
1 atom, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> 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 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
> distance #4/B:975@O #4/A:7@NH2
Distance already exists; modify distance properties with 'distance style'
> show #!6 models
> show #6.1 models
> 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
> select clear
> ui tool show "Side View"
> select #4:38
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/A:267
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> distance style color #3aeafa
> select clear
[Repeated 1 time(s)]No visible atoms, bonds, or surfaces selected
> select clear
> hide #6.1 models
> save NACP2_chainB_Hbond_Interacting_residues_closeup_numbers.png pixelSize
> 0.05 supersample 24 transparentBackground false
> ~distance #4/B:975@O #4/A:7@NH1
> 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
> ~distance #4/B:975@O #4/A:7@NH2
> 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
> distance style color #3aeafa
> select clear
> show #6.1 models
> ~distance #4/B:975@O #4/A:7@NH2
> 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
> distance style color #3aeafa
> close #6
No distances to delete!
[Repeated 2 time(s)]
> distance style color gold
> distance style dashes 9
> distance style radius 0.1
> 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
> distance #4/B:975@O #4/A:7@NH2
Distance already exists; modify distance properties with 'distance style'
> distance #4/B:975@O #4/A:7@NH2
Distance already exists; modify distance properties with 'distance style'
> distance #4/B:975@O #4/A:7@NH2
Distance already exists; modify distance properties with 'distance style'
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/NACP_interfacing_residues_numbers_chainB.cxs
> includeMaps true
——— End of log from Tue Nov 16 23:49:20 2021 ———
opened ChimeraX session
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dist_monitor/monitor.py", line 104, in _changes_handler
pbg = pb.group
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 100, in get_prop
return astype(v.value)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/ctypes_support.py", line 69, in pseudobond_group
return PseudobondGroupData.c_ptr_to_py_inst(p)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 2211, in <lambda>
class_obj.c_ptr_to_py_inst = lambda ptr, *, fname=func_name: c_function(fname,
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
AttributeError: 'NoneType' object has no attribute 'session'
Error processing trigger "changes":
AttributeError: 'NoneType' object has no attribute 'session'
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/pbgroup.py", line 29, in __init__
session = s.session
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x10b9174c0>
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/67944869-7797-447F-A193-A8A777C56A66/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1183, in __del__
if not self.was_deleted:
AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted'
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: 19 days 10:49
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: 3.0.5
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 (3)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash after session restore |
comment:2 by , 4 years ago
| Status: | accepted → feedback |
|---|---|
| Summary: | Crash after session restore → Changes trigger before pb group restored(?) |
comment:3 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | feedback → closed |
Hi Eric,
Unfortunately I don't have that original .cxs file that kept causing the error.... I overwrote that file name with a different session that I started anew.. will keep an eye on similar >bugs and report if any come up.
Thank you,
Kate
Thanks for getting back to me. Yep, we will just have to keep an eye out for this happening again.
--Eric
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Hi Kate,
--Eric