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Opened 4 years ago
Closed 4 years ago
#5587 closed defect (fixed)
Cannot reshow Distances tool
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.14.5-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202110301952 (2021-10-30 19:52:32 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4.dev202110301952 (2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> format session
Log from Thu Nov 11 12:44:42 2021UCSF ChimeraX version: 1.4.dev202110301952
(2021-10-30)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs
Log from Wed Oct 27 22:15:56 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
Log from Wed Dec 23 20:51:39 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
Log from Wed Dec 23 20:29:05 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> format session
Log from Wed Dec 23 19:41:28 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
Log from Mon Dec 21 23:31:32 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
Log from Thu Dec 17 16:57:46 2020UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/katekim/Downloads/electrostatics.cxs
Log from Mon Nov 9 14:23:02 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /home/sasha/Desktop/pks/sasha_figs/figure1/NACPs.cxs
Log from Mon Nov 2 15:10:34 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /home/sasha/Desktop/pks/figure_1.cxs
Log from Mon Nov 2 14:59:47 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open CACP_KS_AT_conformer-coot-3.pdb
Chain information for CACP_KS_AT_conformer-coot-3.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open NACP_KS_AT_conformer_4.pdb
Chain information for NACP_KS_AT_conformer_4.pdb #2
---
Chain | Description
A | No description available
B | No description available
> lighting gentle
> select #1/A:1-98
753 atoms, 765 bonds, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> set bgColor white
> select #1:99-1074
14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected
> hide sel cartoons
> select #1/B:1-99
58 atoms, 57 bonds, 1 model selected
> hide sel cartoons
> select #2/B:1-99
768 atoms, 781 bonds, 1 model selected
> color sel tomato
> graphics silhouettes true
> hide pbonds
> select #2/A:99-521
3126 atoms, 3185 bonds, 2 pseudobonds, 2 models selected
> select clear
> select #2/B:99
8 atoms, 7 bonds, 1 model selected
> color sel cyan
> color sel deep sky blue
> color sel deep sky blue
> color sel dark turquoise
> color sel medium spring green
> color sel dodger blue
> color sel turquoise
> color sel light sea green
> color sel cornflower blue
> color sel cornflower blue
> color sel dark cyan
> color sel medium aquamarine
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel sky blue
> color sel light sky blue
> color sel sky blue
> select clear
> select #2/B:99
8 atoms, 7 bonds, 1 model selected
> select clear
> select #2:99-1074
14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #2/A:97
9 atoms, 8 bonds, 1 model selected
> select up
50 atoms, 49 bonds, 2 models selected
> hide sel cartoons
> select #2:99-1074
14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected
> show sel surfaces
> select #2/A:867@OH
1 atom, 1 model selected
> select up
12 atoms, 12 bonds, 2 models selected
> select up
29 atoms, 29 bonds, 2 models selected
> select up
6964 atoms, 7102 bonds, 2 models selected
> select down
29 atoms, 29 bonds, 2 models selected
> select clear
> select #2/A
6964 atoms, 7102 bonds, 6 pseudobonds, 2 models selected
> color sel gold target s
> color sel yellow target s
> color sel yellow target s
> color sel chartreuse target s
> color sel green target s
> color sel pale green target s
> color sel light green target s
> color sel burly wood target s
> color sel aquamarine target s
> color sel light coral target s
> color sel sky blue target s
> color sel light sky blue target s
> color sel light blue target s
> color sel light steel blue target s
> color sel pale turquoise target s
> color sel pale turquoise target s
> color sel light steel blue target s
> color sel powder blue target s
> color sel sky blue target s
> color sel white smoke target s
> color sel wheat target s
> color sel azure target s
> color sel beige target s
> color sel wheat target s
> color sel khaki target s
> color sel pale goldenrod target s
> select #2/B
7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected
> color sel floral white target s
> color sel lemon chiffon target s
> color sel lemon chiffon target s
> color sel seashell target s
> color sel lavender blush target s
> color sel light yellow target s
> color sel snow target s
> color sel misty rose target s
> select clear
> transparency #2 70 target s
> select #2/A
6964 atoms, 7102 bonds, 6 pseudobonds, 2 models selected
> color sel lemon chiffon target cs
> transparency #2/A 70 target s
> select #2/B
7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected
> color sel lemon chiffon target cs
> color sel papaya whip target cs
> color sel lavender blush target cs
> transparency #2/B 70 target s
> select #2/B:1098
Nothing selected
> select #2/B:1-98
760 atoms, 773 bonds, 1 model selected
> color sel tomato target cs
> select #2/B
7674 atoms, 7826 bonds, 6 pseudobonds, 2 models selected
> select #2/B:99-1074
6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected
> color sel medium purple target cs
> color sel dark orchid target cs
> color sel medium purple target cs
> color sel medium purple target cs
> color sel medium purple target cs
> color sel wheat target cs
> color sel khaki target cs
> color sel pale goldenrod target cs
> color sel violet target cs
> color sel violet target cs
> color sel lavender target cs
> color sel plum target cs
> color sel cornsilk target cs
> color sel powder blue target cs
> select clear
> select #2:99-1074
14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> undo
> undo
> undo
> select #2:99-1074
14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected
> show sel surfaces
> select clear
> lighting flat
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting gentle
> ui tool show "Side View"
> select #2/A:99-1074
6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected
> color sel medium slate blue target cs
> color sel medium orchid target cs
> color sel medium violet red target cs
> color sel light sky blue target cs
> color sel aquamarine target cs
> color sel light coral target cs
> color sel rosy brown target cs
> color sel light coral target cs
> select #2/B:99-1074
6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected
> color sel peach puff target cs
> color sel navajo white target cs
> color sel navajo white target cs
> color sel peach puff target cs
> color sel navajo white target cs
> color sel moccasin target cs
> color sel navajo white target cs
> color sel peach puff target cs
> color sel navajo white target cs
> color sel bisque target cs
> color sel lemon chiffon target cs
> color sel cornsilk target cs
> color sel seashell target cs
> color sel lavender blush target cs
> color sel papaya whip target cs
> color sel blanched almond target cs
> color sel misty rose target cs
> color sel bisque target cs
> color sel pale turquoise target cs
> select #2/B:1-98 #1/A:1-98
1513 atoms, 1538 bonds, 2 models selected
> color sel light goldenrod yellow target cs
> color sel yellow target cs
> color sel orange target cs
> color sel gold target cs
> color sel orange target cs
> color sel dark orange target cs
> color sel fire brick target cs
> color sel tomato target cs
> color sel light salmon target cs
> color sel blue target cs
> color sel dark magenta target cs
> select clear
> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 quality 100 transparentBackground true
Expected a keyword
> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 transparentBackground true
> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 quality 100 transparentBackground true
Expected a keyword
> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 quality 100 transparentBackground true
Expected a keyword
Unknown data format: 'png'
> save /home/sasha/Desktop/pks/sasha_figs/NACPs.png pixelSize 0.1 supersample
> 24 transparentBackground true
> lighting flat
> lighting soft
> lighting simple
> lighting shadows true
> lighting flat
> graphics silhouettes false
> lighting gentle
> graphics silhouettes true
> select :76-86
182 atoms, 178 bonds, 2 models selected
> show sel atoms
> size stickRadius 0.4
Changed 29848 bond radii
> select #2/B:1-98 #1/A:1-98
1513 atoms, 1538 bonds, 2 models selected
> color sel gold target acs
> color sel yellow target acs
> color sel gold target acs
> color sel byhetero
> select #2:99-521
6525 atoms, 6370 bonds, 4 pseudobonds, 2 models selected
> color sel fire brick target acs
> select #2:522-1074
7576 atoms, 7732 bonds, 8 pseudobonds, 2 models selected
> color sel royal blue target acs
> color sel indigo target acs
> color sel navy target acs
> color sel dark blue target acs
> color sel blue target acs
> color sel dodger blue target acs
> select clear
> select :HOH
573 atoms, 2 models selected
> hide sel atoms
> select clear
> select #2:420,500
40 atoms, 36 bonds, 1 model selected
> select #2:420,482,484,424,388,384,426,87-92,395,430,500,496
285 atoms, 257 bonds, 1 model selected
> show sel atoms
> color sel byhetero
> color sel byhetero
> color sel fire brick target acs
> select #2:420,482,484,424,388,384,426,395,430,500,496
223 atoms, 200 bonds, 1 model selected
> color sel byhetero
> select #2:99-521
6525 atoms, 6370 bonds, 4 pseudobonds, 2 models selected
> color sel fire brick target s
> select #2/B:1-98
760 atoms, 773 bonds, 1 model selected
> color sel gold target s
> color sel gold target acs
> color sel byhetero
> select clear
> select :HOH
573 atoms, 2 models selected
> hide sel atoms
> select #1/A:1-72
541 atoms, 548 bonds, 1 model selected
> show sel atoms
> hide sel atoms
> save /home/sasha/Desktop/pks/figure_1.cxs
opened ChimeraX session
> open /home/sasha/Desktop/pks/sasha_figs/NACP1_ppant.pdb
Chain information for NACP1_ppant.pdb #3
---
Chain | Description
A | No description available
B | No description available
> select #3/A:99-1074
6914 atoms, 7052 bonds, 6 pseudobonds, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #3:99-1074
14101 atoms, 14104 bonds, 12 pseudobonds, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #3/A:76-86
83 atoms, 85 bonds, 1 model selected
> show sel atoms
> select #1/A:1-98
753 atoms, 765 bonds, 1 model selected
> hide sel atoms
> hide sel cartoons
> size stickRadius 0.4
Changed 44789 bond radii
> select #3/A:1-98
753 atoms, 765 bonds, 1 model selected
> color sel gold target acs
> color sel byhetero
> select clear
> select #3/A:1101@C43
1 atom, 1 model selected
> select up
21 atoms, 20 bonds, 1 model selected
> select up
7688 atoms, 7839 bonds, 1 model selected
> select down
21 atoms, 20 bonds, 1 model selected
> color sel gold target acs
> color sel byhetero
> select clear
> lighting gentle
> save /home/sasha/Desktop/pks/sasha_figs/figure1/NACPs.cxs
opened ChimeraX session
> coloumbic #2:99-521 range -10,10
Unknown command: coloumbic #2:99-521 range -10,10
> coulombic #2:99-521 range -10,10
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: NACP_KS_AT_conformer_4.pdb #2/A PHE 1074 OXT and
NACP_KS_AT_conformer_4.pdb #2/B PHE 1074 OXT
> open "/home/sasha/Desktop/pks/FINAL FINAL maps&pdb.zip"
Unrecognized file suffix '.zip'
> open "/home/sasha/Desktop/pks/FINAL FINAL
> maps&pdb/NACP_KS_AT_conformer_4.pdb"
Chain information for NACP_KS_AT_conformer_4.pdb #4
---
Chain | Description
A | No description available
B | No description available
> select #4:1-98
831 atoms, 822 bonds, 125 residues, 1 model selected
> delete sel
> select #4:553-1074
7464 atoms, 7622 bonds, 4 pseudobonds, 968 residues, 2 models selected
> delete sel
> select #2
14932 atoms, 14928 bonds, 12 pseudobonds, 2220 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> select #4
6637 atoms, 6482 bonds, 4 pseudobonds, 1127 residues, 2 models selected
> coulombic #4 range -10,10
> hide #4.3 models
> show #4.3 models
> hide #4.2 models
> show #4.2 models
> hide #4.1 models
> hide #4.2 models
> show #4.2 models
> select #4
6637 atoms, 6482 bonds, 4 pseudobonds, 1127 residues, 2 models selected
> cartoon hide (#!4 & sel)
> select clear
> transparency #4 60
> select clear
> ui tool show "Side View"
> save /home/sasha/Desktop/pks/sasha_figs/figure1/electrostatics.cxs
opened ChimeraX session
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> hide #!4.3 models
> show #!4.3 models
> select #1, 2, 3, 4:93-521
26418 atoms, 25780 bonds, 16 pseudobonds, 4498 residues, 8 models selected
> color (#!1-4 & sel) red
> select clear
> select #1, 2, 3, 4:93-529
26866 atoms, 26228 bonds, 16 pseudobonds, 4562 residues, 8 models selected
> color (#!1-4 & sel) red
> select clear
> ui tool show "Side View"
> hide #4.2 models
> hide #4.3 models
> select ::name="PNS"
21 atoms, 20 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel navy
> color sel byhetero
> color sel blue
> color sel dark slate blue
> color sel dark slate gray
> color sel byhetero
> select clear
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> hide #!1 models
> show #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> show #2.3 models
> close #2.2
> close #2.1
> close #1.1
> close #2.3
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #2 models
> hide #2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> close #1
> hide #!4 models
> show #!4 models
> show #4.1 models
> hide #4.1 models
> show #4.2 models
> hide #4.2 models
> show #4.3 models
> hide #4.3 models
> close #4.2
> close #4.3
> close #4.1
> show #2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> close #3.1
> hide #4 models
> show #4 models
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
opened ChimeraX session
> close #4
> color #2/A:1-552 #f79292
> color #2/A:553-1074 #9eddff
> lighting soft
> lighting full
> lighting simple
> lighting soft
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> turn
> turn
> turn
> turn
> turn y
> turn y
> turn y
> turn y
> turn x
> turn x
> turn x
> lighting soft
> select #2/A:1-552
3232 atoms, 3291 bonds, 433 residues, 1 model selected
> hide sel atoms
> select clear
> select #2/B: 420, 482,424,484,384,388,426,395,430,500,496
111 atoms, 100 bonds, 11 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> select #2/B:93-552
3232 atoms, 3291 bonds, 433 residues, 1 model selected
> show sel surfaces
> color (#!2 & sel) black
> transparency #32.1 80
> transparency #2.1 80
> select up
3399 atoms, 3463 bonds, 453 residues, 2 models selected
> select up
7674 atoms, 7826 bonds, 1009 residues, 2 models selected
> select up
14932 atoms, 14928 bonds, 2220 residues, 2 models selected
> select up
14932 atoms, 14928 bonds, 2220 residues, 2 models selected
> select #2/B:93-552
3232 atoms, 3291 bonds, 433 residues, 1 model selected
> color #2/B:93-552 #ff1616
> color #2/B:2.1 white
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #2.1 white
> transparency #2.1 80
> select clear
> lighting soft
> lighting soft
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> select #2/B: 420, 482,424,484,384,388,426,395,430,500,496
111 atoms, 100 bonds, 11 residues, 1 model selected
> select #2.1: 420, 482,424,484,384,388,426,395,430,500,496
Nothing selected
> select #2/B: 420, 482,424,484,384,388,426,395,430,500,496
111 atoms, 100 bonds, 11 residues, 1 model selected
> color (#!2 & sel) byhetero
> select clear
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #3/B
Alignment identifier is 1
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/NACP1_ppant_edited.pdb models
> #3 relModel #3
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> swapaa #3/A:84 tyrosine
Using Dunbrack library
NACP1_ppant.pdb #3/A ALA 84: phi -116.3, psi 124.7 trans
Dunbrack rotamer library does not support TYROSINE
> open /Users/katekim/Box/Pks13_ChimeraX_stuff/NACP1_ppant_edited.pdb
Chain information for NACP1_ppant_edited.pdb #1
---
Chain | Description
A | No description available
B | No description available
> delete #1: 93-1074
> hide #3 models
> sel#1
Unknown command: sel#1
> select #1
731 atoms, 744 bonds, 93 residues, 1 model selected
> color sel yellow
> select clear
> select #1
731 atoms, 744 bonds, 93 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> color sel gold
> select clear
> select ::name="PNS"
42 atoms, 40 bonds, 2 residues, 2 models selected
> color (#1 & sel) light gray
> ui tool show "Color Actions"
> color sel dark slate gray
> color sel byhetero
> hide #1 models
> show #1 models
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> size #1 atomRadius 2
Changed 731 atom radii
> size #1 atomRadius 1
Changed 731 atom radii
> size #1 stickRadius 1
Changed 744 bond radii
> size #1 stickRadius 0.4
Changed 744 bond radii
> select clear
> select #1: 76-92
146 atoms, 151 bonds, 17 residues, 1 model selected
> show sel cartoons
> show sel atoms
> color sel byhetero
> select clear
> select #2/B: 76-92
146 atoms, 151 bonds, 17 residues, 1 model selected
> show sel atoms
> show sel atoms
> select clear
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
> select clear
> turn center cofr
> turn
> turn
> turn
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
opened ChimeraX session
> save Fig1_D.png pixelSize 0.05 supersample 24 transparentBackground false
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #3 models
> hide #3 models
> hide #1 models
> hide #!2 models
> show #3 models
> hide #3 models
> show #1 models
> hide #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> close #3
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
opened ChimeraX session
> open /Users/katekim/Box/Pks13_ChimeraX_stuff/composite_4ACPs.pdb
Chain information for composite_4ACPs.pdb #3
---
Chain | Description
A | No description available
B | No description available
C D | No description available
> ui tool show Matchmaker
> matchmaker #!3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NACP_KS_AT_conformer_4.pdb, chain B (#2) with composite_4ACPs.pdb,
chain A (#3), sequence alignment score = 4887.4
RMSD between 900 pruned atom pairs is 0.412 angstroms; (across all 1009 pairs:
19.178)
> matchmaker #!3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NACP_KS_AT_conformer_4.pdb, chain B (#2) with composite_4ACPs.pdb,
chain A (#3), sequence alignment score = 4887.4
RMSD between 900 pruned atom pairs is 0.412 angstroms; (across all 1009 pairs:
19.178)
> close #3.1
> hide #!2 models
> hide #1 models
> delete #3/A,D
> delete #3:93-1074
> show #!2 models
> show #1 models
> save /Users/katekim/Box/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
opened ChimeraX session
> ui tool show "Model Panel"
> select #3
1413 atoms, 1438 bonds, 184 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light goldenrod yellow
> color sel lemon chiffon
> color sel lemon chiffon
> color sel lemon chiffon
> select clear
> turn center cofr
> turn
> turn
> turn
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk.cxs
——— End of log from Wed Dec 23 20:51:39 2020 ———
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> select #2/B:588-694
821 atoms, 831 bonds, 107 residues, 1 model selected
> ui tool show "Color Actions"
> color sel navy
> select #2/A:588-694
821 atoms, 831 bonds, 107 residues, 1 model selected
> color sel royal blue
> select clear
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs
> includeMaps true
> ui tool show "Volume Viewer"
> lighting soft
> lighting soft
> lighting soft
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Fig2_electrostatics_kk_3.cxs
> includeMaps true
——— End of log from Wed Oct 27 22:15:56 2021 ———
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide surfaces
> ui tool show "Side View"
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true
——— End of log from Thu Nov 11 12:44:42 2021 ———
opened ChimeraX session
> open /Users/katekim/Desktop/N-ACP2_wDCR-coot-7.pdb
Chain information for N-ACP2_wDCR-coot-7.pdb #4
---
Chain | Description
A | No description available
B | No description available
> hide #1 models
> hide #!2 models
> hide #3 models
> hide #!4 atoms
> hide pbonds
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select #4/A:76-92
146 atoms, 151 bonds, 17 residues, 1 model selected
> show sel atoms
> view matrix models
> #4,0.95994,-0.18223,0.21284,2.2549,0.2145,0.96667,-0.13976,-7.2093,-0.18028,0.17982,0.96704,5.3272
> ui mousemode right zoom
> select #4/A:93-552
3232 atoms, 3291 bonds, 1 pseudobond, 433 residues, 2 models selected
> select ::name="ARG"
2706 atoms, 2472 bonds, 246 residues, 4 models selected
> show sel & #!4 atoms
> select ::name="LYS"
1332 atoms, 1192 bonds, 148 residues, 2 models selected
> show sel & #!4 atoms
> ui tool show "Side View"
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true
> select #4/A:1-92
710 atoms, 723 bonds, 92 residues, 1 model selected
> color sel #FFF200
> color sel byhetero
> select #4/A:93-552
3232 atoms, 3291 bonds, 1 pseudobond, 433 residues, 2 models selected
> color sel ##ff1616
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel #ff1616
> color (#!4 & sel) byhetero
> select #4/A:553-694
821 atoms, 831 bonds, 107 residues, 1 model selected
> ui tool show "Color Actions"
> color sel navy
> select #4/A:695-1074
2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected
> select up
7693 atoms, 7844 bonds, 1 pseudobond, 1010 residues, 2 models selected
> select down
2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected
> color sel #23a7ff
> hide sel atoms
> select #4/A:553-694
821 atoms, 831 bonds, 107 residues, 1 model selected
> hide sel atoms
> select #4/B:553-694
821 atoms, 831 bonds, 107 residues, 1 model selected
> ui tool show "Color Actions"
> color sel royal blue
> select #4/B:695-1074
2911 atoms, 2979 bonds, 1 pseudobond, 377 residues, 2 models selected
> color sel #9eddff
> select #4/B:1-552
3305 atoms, 3366 bonds, 1 pseudobond, 441 residues, 2 models selected
> color sel #f79292
> select clear
> select #4/B:1-1074
7037 atoms, 7177 bonds, 3 pseudobonds, 925 residues, 2 models selected
> hide sel atoms
> select clear
> select #4/B:1-75
Nothing selected
> select #4/A:1-75
564 atoms, 571 bonds, 75 residues, 1 model selected
> hide sel atoms
> select clear
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true
> style #!4 stick
Changed 14749 atom styles
> style #!4 ball
Changed 14749 atom styles
> style #!4 stick
Changed 14749 atom styles
> size #4/A:78 atomRadius 1
Changed 9 atom radii
> size #4/A:78 atomRadius 2
Changed 9 atom radii
> size #4/A:78 stickRadius 2
Changed 8 bond radii
> size #4/A:78 stickRadius 1
Changed 8 bond radii
> size #4/A:78 stickRadius 0.5
Changed 8 bond radii
> size #4/A:76-92 stickRadius 0.5
Changed 151 bond radii
> size #4/A:76-92 stickRadius 0.4
Changed 151 bond radii
> size #4/A:93-552 stickRadius 0.4
Changed 3291 bond radii
> transparency #4 80 target cr
> transparency #4 70 target cr
> transparency #4 90 target cr
> transparency #4 80 target cr
> ui tool show Contacts
> ui tool show H-Bonds
> hbonds showDist true twoColors true saltOnly true intraRes false select true
269 hydrogen bonds found
97 strict hydrogen bonds found
> hbonds showDist true distSlop 0.5 twoColors true saltOnly true intraRes
> false select true
299 hydrogen bonds found
97 strict hydrogen bonds found
> select clear
> ui tool show Distances
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1263, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/__init__.py", line 45, in start_tool
return get_tool(session, tool_name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 19, in get_tool
_tool.show_tab(tool_name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 56, in show_tab
self.tab_widget.setCurrentIndex(index)
RuntimeError: wrapped C/C++ object of type QTabWidget has been deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1671, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show
bi.start_tool(session, name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:
wrapped C/C++ object of type QTabWidget has been deleted
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:
wrapped C/C++ object of type QTabWidget has been deleted
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool
raise ToolshedError(
See log for complete Python traceback.
> save
> /Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/DElinker_KS_pairwise_interaction.cxs
> includeMaps true
> ui tool show Distances
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool
ti = api._api_caller.start_tool(api, session, self, tool_info)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1263, in start_tool
return cls._get_func(api, "start_tool")(session, ti.name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/__init__.py", line 45, in start_tool
return get_tool(session, tool_name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 19, in get_tool
_tool.show_tab(tool_name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 56, in show_tab
self.tab_widget.setCurrentIndex(index)
RuntimeError: wrapped C/C++ object of type QTabWidget has been deleted
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1671, in <lambda>
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show
bi.start_tool(session, name)
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:
wrapped C/C++ object of type QTabWidget has been deleted
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Distances
in bundle ChimeraX-StructMeasure:
wrapped C/C++ object of type QTabWidget has been deleted
File
"/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/8BD80293-7898-4A7F-8D15-E3D8FD33D478/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool
raise ToolshedError(
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,2
Processor Name: Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 194.0.0.0.0
SMC Version (system): 2.44f1
Software:
System Software Overview:
System Version: macOS 10.14.5 (18F132)
Kernel Version: Darwin 18.6.0
Time since boot: 14 days 2:46
Graphics/Displays:
Intel Iris Plus Graphics 650:
Chipset Model: Intel Iris Plus Graphics 650
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5927
Revision ID: 0x0006
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.1.6
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202110301952
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.3
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.3.1
ChimeraX-ModelPanel: 1.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.14
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.21
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.4
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Cannot reshow Distances tool |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Hi Kate,
Thanks for reporting this problem. I have fixed it now and the fix will be in tomorrow's daily build.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
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Reported by Kate Kim