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Opened 3 years ago
Closed 3 years ago
#8770 closed defect (fixed)
Cartoon style: float division by zero
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/FFF_20230403.cxs"
Log from Mon Apr 3 14:15:51 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/TM3_2R.cxs"
Log from Thu Jan 5 23:58:40 2023UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\12051\Desktop\Experiment data\ADGRE5\color
> pattern_1012\20221209\active mode\active_3.cxs" format session
Log from Sat Dec 24 17:22:32 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\Users\12051\Desktop\Experiment data\ADGRE5\color
> pattern_1012\20221209\active mode\active_2.cxs" format session
Log from Sat Dec 17 00:12:19 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/activation_motif2.cxs"
Log from Mon Dec 12 20:46:52 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Desktop\\\inactive and active CD97.cxs"
Log from Sun Dec 11 22:32:00 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "E:\\\Desktop\\\CD97 apo_G13 alignment.cxs"
Log from Sun Dec 11 21:29:22 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/apo_model.cxs"
Log from Fri Dec 9 22:10:37 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/apo_1_model_renew221205.cxs"
Log from Mon Dec 5 10:35:04 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\12051\Desktop\Experiment
> data\ADGRE5\文章整理202211\final_map_and_model\final_map_and_model\apo_ADGRE5-coot-25_real_space_refined_087.pdb"
> format pdb
Chain information for apo_ADGRE5-coot-25_real_space_refined_087.pdb #1
---
Chain | Description
R | No description available
> set bgColor white
> select #1:258-530
2077 atoms, 2118 bonds, 273 residues, 1 model selected
> color sel dark gray
> select clear
> select add /R:474
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1:531-544
111 atoms, 113 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red
> select #1:545-802
1959 atoms, 2010 bonds, 1 pseudobond, 245 residues, 2 models selected
> ui tool show "Color Actions"
> color sel plum
> select clear
Drag select of 14 atoms, 16 bonds
Drag select of 19 atoms, 18 residues, 18 bonds
Drag select of 12 atoms, 19 residues, 13 bonds
Drag select of 16 atoms, 18 residues, 17 bonds
> color sel dark gray
Drag select of 17 atoms, 25 residues, 18 bonds
Drag select of 45 atoms, 48 residues, 43 bonds
> select clear
Drag select of 43 atoms, 33 residues, 42 bonds
Drag select of 19 atoms, 23 residues, 19 bonds
> color sel dark gray
> color sel byhetero
> select clear
> lighting soft
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 1
> cartoon style width 1 thickness 1
> cartoon style width 3 thickness 1
> cartoon style width 2 thickness 1
> cartoon style width 2 thickness 0.8
> cartoon style width 2.5 thickness 0.8
> cartoon style width 1.8 thickness 0.8
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/apo_1_model_renew221205.cxs"
——— End of log from Mon Dec 5 10:35:04 2022 ———
opened ChimeraX session
> select 258-530
Expected an objects specifier or a keyword
> select #1:258-530
2077 atoms, 2118 bonds, 273 residues, 1 model selected
> color sel #51b7c2ff
> color sel #4fb4bfff
> color sel #4fb3beff
> select clear
Drag select of 4 atoms, 4 residues, 3 bonds
> select clear
Drag select of 5 atoms, 5 bonds
Drag select of 1 atoms, 1 bonds
> select up
10 atoms, 7 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel #4fb4bfff
> color sel #4dafbaff
> color sel #4fb3beff
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> lighting shadows false
> graphics silhouettes false
> lighting soft
> color sel byhetero
> select clear
> hide pseudopond
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudoponds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudoponds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudoponds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudoponds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select 258-530
Expected an objects specifier or a keyword
> select #1:258-530
2077 atoms, 2118 bonds, 273 residues, 1 model selected
> color sel thistle
> color sel light sky blue
> color sel powder blue
> select clear
> select #1:545-802
1959 atoms, 2010 bonds, 1 pseudobond, 245 residues, 2 models selected
> color sel thistle
> select clear
> select #1:531-544
111 atoms, 113 bonds, 14 residues, 1 model selected
> color sel light coral
> select clear
Drag select of 6 atoms, 6 bonds
Drag select of 2 atoms, 5 bonds
Drag select of 6 atoms, 5 bonds
> select up
19 atoms, 16 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> color sel powder blue
> color sel byhetero
> select clear
> lighting flat
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
Drag select of 3 atoms, 5 bonds
Drag select of 4 atoms, 3 bonds
Drag select of 2 atoms, 1 bonds
> select up
12 atoms, 9 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> style sel ball
Changed 42 atom styles
> select clear
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/apo_model.cxs"
——— End of log from Fri Dec 9 22:10:37 2022 ———
opened ChimeraX session
> open "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/final_map_and_model/final_map_and_model/ADGRE5_mG13-coot-7_real_space_refined_128.pdb"
Chain information for ADGRE5_mG13-coot-7_real_space_refined_128.pdb #2
---
Chain | Description
A | No description available
B | No description available
R | No description available
Y | No description available
> hide #!1 models
Drag select of 185 residues
> select up
1890 atoms, 1938 bonds, 237 residues, 1 model selected
> select up
2174 atoms, 2231 bonds, 271 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> select clear
Drag select of 117 residues
> select up
1332 atoms, 1350 bonds, 162 residues, 1 model selected
> select up
1760 atoms, 1788 bonds, 213 residues, 1 model selected
> color sel dark orange
> select clear
Drag select of 37 residues
> select up
671 atoms, 676 bonds, 88 residues, 1 model selected
> select up
2601 atoms, 2648 bonds, 338 residues, 1 model selected
> color sel dark cyan
> select clear
> select #2:530-544
111 atoms, 113 bonds, 14 residues, 1 model selected
> color sel coral
Drag select of 6 residues
> select up
242 atoms, 245 bonds, 32 residues, 1 model selected
> select up
2581 atoms, 2644 bonds, 324 residues, 1 model selected
> select clear
Drag select of 6 residues
> select up
131 atoms, 132 bonds, 18 residues, 1 model selected
> select up
407 atoms, 413 bonds, 53 residues, 1 model selected
> color sel #dfeefaff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #acdeffff
> color sel #577091ff
> color sel #000000ff
> color sel #9ac7ffff
> color sel #e0edf7ff
> color sel #ccccccff
> color sel #ffffffff
> color sel #d8d8d8ff
> color sel #ffffffff
> color sel #000000ff
> color sel #009797ff
> color sel #000000ff
> color sel #6a88b0ff
> color sel #8ab2e6ff
> color sel #90baf0ff
> color sel #8cb4e9ff
> cartoon style width 1.8 thickness 0.8
> select clear
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker apo_ADGRE5-coot-25_real_space_refined_087.pdb, chain R (#1) with
ADGRE5_mG13-coot-7_real_space_refined_128.pdb, chain R (#2), sequence
alignment score = 1257.3
RMSD between 148 pruned atom pairs is 0.867 angstroms; (across all 258 pairs:
8.882)
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/apo_G13.cxs"
——— End of log from Sun Dec 11 21:29:22 2022 ———
opened ChimeraX session
Drag select of 453 residues, 1 pseudobonds
> select up
4183 atoms, 4249 bonds, 1 pseudobond, 532 residues, 2 models selected
> select up
4768 atoms, 4849 bonds, 1 pseudobond, 604 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
Drag select of 15 atoms, 134 residues, 12 bonds
> select up
1024 atoms, 1033 bonds, 137 residues, 1 model selected
> select up
1041 atoms, 1053 bonds, 137 residues, 1 model selected
> select up
1406 atoms, 1431 bonds, 186 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 13 atoms, 18 residues, 11 bonds
> select up
145 atoms, 145 bonds, 19 residues, 1 model selected
> select up
150 atoms, 152 bonds, 19 residues, 1 model selected
> select up
257 atoms, 264 bonds, 31 residues, 1 model selected
> select up
2783 atoms, 2850 bonds, 349 residues, 1 model selected
> select down
257 atoms, 264 bonds, 31 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 11 residues
> select up
153 atoms, 153 bonds, 19 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #1/R:440
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
49 atoms, 48 bonds, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 19 atoms, 26 residues, 1 pseudobonds, 19 bonds
> select add #1/R:510
210 atoms, 25 bonds, 1 pseudobond, 28 residues, 2 models selected
> select add #1/R:511
219 atoms, 33 bonds, 1 pseudobond, 29 residues, 2 models selected
> select add #1/R:512
223 atoms, 36 bonds, 1 pseudobond, 30 residues, 2 models selected
> select add #1/R:513
229 atoms, 41 bonds, 1 pseudobond, 31 residues, 2 models selected
> select add #1/R:528
235 atoms, 46 bonds, 1 pseudobond, 32 residues, 2 models selected
> select add #1/R:529
241 atoms, 51 bonds, 1 pseudobond, 33 residues, 2 models selected
> select add #1/R:530
249 atoms, 58 bonds, 1 pseudobond, 34 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
Drag select of 5 atoms
> delete atoms sel
> delete bonds sel
Drag select of 530 residues
> select clear
> ui tool show "Side View"
> save "E:/Desktop/inactive and active CD97.cxs" includeMaps true
——— End of log from Sun Dec 11 22:32:00 2022 ———
opened ChimeraX session
> cartoon style width 1.5 thickness 0.7
> lighting soft
> lighting flat
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Side View"
> windowsize 800 600
> windowsize 800 800
> windowsize 600 800
> cartoon style width 1.5 thickness 0.5
> cartoon style width 1.0 thickness 0.5
> cartoon style width 1.0 thickness 0.7
> cartoon style width 1.2 thickness 0.7
> cartoon style width 1.2 thickness 0.8
> cartoon style width 1.2 thickness 0.5
> cartoon style width 1.2 thickness 0.7
> cartoon style width 2.0 thickness 0.7
> cartoon style width 1.5 thickness 0.7
> cartoon style width 1.2 thickness 0.7
> select clear
> lighting full
> select clear
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true depthJump 0.01
> graphics silhouettes true depthJump 0.05
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.05
> graphics silhouettes true depthJump 0.03
> graphics silhouettes true depthJump 0.1
> select clear
> graphics silhouettes true depthJump 0.1 width 0.5
> graphics silhouettes true depthJump 0.1 width 0.8
> graphics silhouettes true depthJump 0.1 width 1
> graphics silhouettes true depthJump 0.1 width 5
> graphics silhouettes true depthJump 0.1 width 1
> graphics silhouettes true depthJump 0.1 width 0.5
> graphics silhouettes true depthJump 0.1 width 1
> lighting full
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting soft intensity 5
> lighting soft intensity 2
> lighting soft intensity 1
> lighting soft intensity 0.5
> lighting soft intensity 0.1
> lighting soft intensity 0.01
> lighting soft intensity 0.001
Drag select of 73 residues
> select up
1825 atoms, 1861 bonds, 235 residues, 2 models selected
> transparency sel 80
> transparency sel 10
> transparency sel 10 target c
> transparency sel 80 target c
> transparency sel 20 target c
> transparency sel 30 target c
> select clear
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.15
> graphics silhouettes true depthJump 0.2
> graphics silhouettes true depthJump 0.3
> graphics silhouettes true depthJump 0.5
> graphics silhouettes true depthJump 0.4
> graphics silhouettes true depthJump 0.2
> select clear
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.03
> graphics silhouettes true depthJump 0.01
> graphics silhouettes true depthJump 0.05
> graphics silhouettes true depthJump 0.1
> graphics silhouettes true depthJump 0.06
> graphics silhouettes true depthJump 0.08
> select clear
> graphics silhouettes false
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
Drag select of 94 residues
> select up
1743 atoms, 1779 bonds, 223 residues, 2 models selected
> transparency sel 50 target c
> select clear
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.0 thickness 0.3
> preset cartoons/nucleotides licorice/ovals
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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select clear
> 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
> cartoon style width 1.0 thickness 0.8
> cartoon style width 1.5 thickness 0.8
> select clear
> cartoon style width 1.2 thickness 0.8
> cartoon style width 1.5 thickness 0.8
> cartoon style width 1.2 thickness 0.8
> select clear
> cartoon style width 1.2 thickness 0.6
> select clear
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> save E:/Desktop/alignment_front_1.png width 600 height 800 supersample 4
> transparentBackground true
> save E:/Desktop/alignment_front_2.png width 600 height 800 supersample 4
> save "E:/Desktop/inactive and active CD97_front.cxs"
> turn y 90
> turn y -90
Drag select of 8 residues
> select up
94 atoms, 96 bonds, 12 residues, 1 model selected
> select up
2070 atoms, 2124 bonds, 259 residues, 1 model selected
> select down
94 atoms, 96 bonds, 12 residues, 1 model selected
> select add #1/R:543
103 atoms, 104 bonds, 13 residues, 1 model selected
> select up
142 atoms, 146 bonds, 17 residues, 1 model selected
> cartoon hide sel
Drag select of 3 residues
> select clear
Drag select of 3 residues
> select up
99 atoms, 101 bonds, 12 residues, 1 model selected
Drag select of 1 residues
> select up
111 atoms, 113 bonds, 14 residues, 1 model selected
> cartoon hide sel
Drag select of 499 residues
> transparency sel 0
> transparency sel 0 target c
> select clear
> windowsize 600 600
> save "E:/Desktop/inactive and active CD97_extra.cxs" includeMaps true
> save E:/Desktop/alignment_extra_1.png width 600 height 600 supersample 4
> transparentBackground true
> save E:/Desktop/alignment_extra_2.png width 600 height 600 supersample 4
> save E:/Desktop/alignment_extra_intra_1.png width 600 height 600 supersample
> 4 transparentBackground true
[Repeated 1 time(s)]
> save E:/Desktop/alignment_intra_2.png width 600 height 600 supersample 4
> select clear
> show target ab
> select clear
> cartoon
> select clear
> hide atoms
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show target ab
> select clear
> hide atoms
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1/R:753
28 atoms, 30 bonds, 2 residues, 2 models selected
> show sel target ab
> style sel stick
Changed 28 atom styles
> color sel byhetero
> select clear
> select add #1/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!2 models
> select clear
> select add #1/R:754
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select add #1/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
> show #!2 models
> hide #!1 models
> select add #2/R:537
22 atoms, 22 bonds, 2 residues, 2 models selected
> select up
241 atoms, 245 bonds, 31 residues, 2 models selected
> select up
4244 atoms, 4355 bonds, 530 residues, 2 models selected
> select clear
> select add #2/R:535
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:537
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
99 atoms, 101 bonds, 12 residues, 1 model selected
> show sel target ab
> color sel byhetero
> ui tool show Contacts
> contacts sel restrict cross distanceOnly 4.0 makePseudobonds false showDist
> true reveal true
1110 distances
> contacts sel restrict cross distanceOnly 4.0 makePseudobonds false showDist
> true reveal true
1110 distances
> contacts sel restrict cross distanceOnly 4.0 showDist true reveal true
1110 distances
> contacts sel restrict cross distanceOnly 4.0 makePseudobonds false showDist
> true reveal true
1110 distances
> show #!1 models
> select clear
> hide target a
> hide #!1 models
Drag select of 2 residues
> select add #2/R:753
29 atoms, 15 bonds, 3 residues, 1 model selected
> select clear
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> view clip false
> select add #2/R:623
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:627
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #2/R:630
30 atoms, 29 bonds, 3 residues, 1 model selected
> show sel target ab
> select add #2/R:711
41 atoms, 40 bonds, 4 residues, 1 model selected
> show sel target ab
> select add #2/R:750
45 atoms, 43 bonds, 5 residues, 1 model selected
> select add #2/R:747
56 atoms, 54 bonds, 6 residues, 1 model selected
> show sel target ab
> select add #2/R:775
64 atoms, 61 bonds, 7 residues, 1 model selected
> select add #2/R:778
73 atoms, 69 bonds, 8 residues, 1 model selected
> select add #2/R:779
77 atoms, 72 bonds, 9 residues, 1 model selected
> select add #2/R:781
88 atoms, 83 bonds, 10 residues, 1 model selected
> show sel target ab
> select clear
Drag select of 67 atoms, 271 residues, 65 bonds
> color sel byhetero
> select clear
> show #!1 models
> hide #!2 models
> select add #1/R:775
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:778
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/R:779
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #1/R:781
32 atoms, 29 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select add #1/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #1/R:750
18 atoms, 18 bonds, 2 residues, 1 model selected
> select add #1/R:747
29 atoms, 29 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #1/R:711
40 atoms, 40 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select add #1/R:623
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:627
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #1/R:630
30 atoms, 29 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!2 models
> save E:/Desktop/activation_motif.cxs
Drag select of 9 residues
> select up
510 atoms, 527 bonds, 62 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> save E:/Desktop/activation_motif2.cxs
——— End of log from Mon Dec 12 20:46:52 2022 ———
opened ChimeraX session
> select #1/R:573
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:573
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 5 time(s)]
> hide sel atoms
> select #1/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!2 models
> select add #1/R:757
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #1/R:734
31 atoms, 30 bonds, 3 residues, 1 model selected
> select up
192 atoms, 194 bonds, 25 residues, 1 model selected
> ui tool show "Side View"
> show sel cartoons
Drag select of 59 atoms, 225 residues, 57 bonds
> show sel cartoons
> select #1/R
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> show sel cartoons
> select clear
> select add #1/R:692
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:720
20 atoms, 19 bonds, 2 residues, 1 model selected
> select up
247 atoms, 254 bonds, 30 residues, 1 model selected
> select add #1/R:691
251 atoms, 257 bonds, 31 residues, 1 model selected
> select add #1/R:690
260 atoms, 265 bonds, 32 residues, 1 model selected
> hide sel cartoons
> select add #1/R:735
265 atoms, 269 bonds, 33 residues, 1 model selected
> select add #1/R:757
273 atoms, 276 bonds, 34 residues, 1 model selected
> select clear
> select add #1/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:766
18 atoms, 17 bonds, 2 residues, 1 model selected
> select up
243 atoms, 249 bonds, 29 residues, 1 model selected
> transparency sel 80 cartoons
> transparency sel 60 cartoons
> select clear
> select #1/R:1-735
1517 atoms, 1557 bonds, 1 pseudobond, 192 residues, 2 models selected
> select up
1686 atoms, 1730 bonds, 1 pseudobond, 214 residues, 2 models selected
> select up
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> select up
4244 atoms, 4355 bonds, 1 pseudobond, 530 residues, 3 models selected
> transparency sel 60 cartoons
> select clear
> select add #1/R:757
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:735
13 atoms, 11 bonds, 2 residues, 1 model selected
> select up
174 atoms, 177 bonds, 23 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
[Repeated 1 time(s)]
> select #1/R:627
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/R:623
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/R:630
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:612
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #1/R:642
21 atoms, 18 bonds, 3 residues, 1 model selected
> select up
269 atoms, 276 bonds, 33 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
Drag select of 14 atoms, 54 residues, 12 bonds
> select up
447 atoms, 452 bonds, 54 residues, 1 model selected
> hide sel atoms
> select clear
> hide #!1 models
> show #!2 models
> select add #2/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:749
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #2/R:731
28 atoms, 26 bonds, 3 residues, 1 model selected
> select up
216 atoms, 219 bonds, 27 residues, 1 model selected
> transparency sel 0 cartoons
> select add #2/R:750
220 atoms, 222 bonds, 28 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> select add #2/R:765
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:783
20 atoms, 19 bonds, 2 residues, 1 model selected
> select up
211 atoms, 214 bonds, 26 residues, 1 model selected
> hide sel atoms
> select clear
> select add #2/R:610
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:641
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
262 atoms, 269 bonds, 32 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> show #!1 models
> hide #!1 models
> select add #2/R:531
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/R:534
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #2/R:544
19 atoms, 16 bonds, 3 residues, 1 model selected
> select up
111 atoms, 113 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
[Repeated 2 time(s)]
> hide #!2 models
> show #!1 models
> select add #1/R:532
117 atoms, 118 bonds, 15 residues, 2 models selected
> select add #1/R:544
125 atoms, 125 bonds, 16 residues, 2 models selected
> select up
247 atoms, 253 bonds, 30 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> undo
> select clear
> show #!2 models
> transparency sel 30 cartoons
> transparency 30 cartoons
> transparency 80 cartoons
> select clear
[Repeated 1 time(s)]
> transparency 70 cartoons
Drag select of 3 residues
> select add #2/R:641
27 atoms, 6 bonds, 4 residues, 2 models selected
> select add #1/R:642
34 atoms, 12 bonds, 5 residues, 2 models selected
> select up
593 atoms, 607 bonds, 74 residues, 2 models selected
> transparency sel 0 cartoons
> select clear
[Repeated 1 time(s)]
> select add #1/R:757
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:758
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add #1/R:735
24 atoms, 22 bonds, 3 residues, 2 models selected
> select add #2/R:749
32 atoms, 29 bonds, 4 residues, 2 models selected
> select add #2/R:751
38 atoms, 34 bonds, 5 residues, 2 models selected
> select add #2/R:731
47 atoms, 42 bonds, 6 residues, 2 models selected
> select up
390 atoms, 396 bonds, 50 residues, 2 models selected
> transparency sel 0 cartoons
> select add #2/R:750
394 atoms, 399 bonds, 51 residues, 2 models selected
> transparency sel 0 cartoons
> select clear
[Repeated 1 time(s)]
> select #1
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> show sel cartoons
> select #2
2174 atoms, 2231 bonds, 271 residues, 1 model selected
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> hide #!2 models
> hide #!1 models
> show #!2 models
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.0 resSeparation 5 intraRes true select true
> color #ffa500
187 distances
> select subtract #2/R:537
68 atoms, 19 residues, 2 models selected
> select clear
> select add #2/R:537
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:533
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> select #2/R:559
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:533
19 atoms, 19 bonds, 2 residues, 1 model selected
> select add #2/R:537
27 atoms, 25 bonds, 3 residues, 1 model selected
> color sel byhetero
> select clear
> hide sel
> select clear
> select add #2/R:610
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:641
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
262 atoms, 269 bonds, 32 residues, 1 model selected
> transparency 70 cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> select add #2/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:750
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/R:749
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #2/R:731
32 atoms, 29 bonds, 4 residues, 1 model selected
> select up
220 atoms, 224 bonds, 28 residues, 1 model selected
> transparency sel 0 cartoons
> color sel byhetero
> select clear
> select add #2/R:544
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:531
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #2/R:536
22 atoms, 19 bonds, 3 residues, 1 model selected
> select up
111 atoms, 113 bonds, 14 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!1 models
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel resSeparation 5 intraRes true intraModel false select true
> color #ffa500
127 contacts
> ui tool show Contacts
> show #!1 models
> contacts sel resSeparation 5 intraModel false intraMol false select true
> color #ffa500
412 contacts
> contacts sel resSeparation 5 interModel false intraMol false select true
> color #ffa500
5 contacts
> contacts sel resSeparation 5 intraRes true select true color #ffa500
81 contacts
> select clear
> hide #!1 models
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> show #!1 models
> contacts distanceOnly 4.0 intraModel false intraMol false
23520 distances
> undo
> contacts distanceOnly 4.0 resSeparation 5 intraMol false color #ffa500
23671 distances
> contacts distanceOnly 4.0 resSeparation 5 intraMol false color #ffa500
23671 distances
> contacts distanceOnly 4.0 resSeparation 5 interModel false intraModel false
> color #ffa500
No distances
> contacts distanceOnly 4.0 resSeparation 5 interModel false intraRes true
> intraModel false intraMol false color #ffa500
No distances
> contacts distanceOnly 4.0 interModel false intraRes true intraModel false
> intraMol false color #ffa500
No distances
> contacts distanceOnly 4.0 interModel false intraModel false color #ffa500
No distances
> contacts distanceOnly 4.0 interModel false intraRes true color #ffa500
6198 distances
> undo
[Repeated 5 time(s)]
> close #3
> select clear
> select add #2/R:753@CB
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> contacts distanceOnly 4.0 intraRes true color #ffa500
29718 distances
> undo
[Repeated 1 time(s)]
> close #3
> select clear
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> contacts distanceOnly 4.0 intraRes true select true color #ffa500
29718 distances
> close #3
> select clear
> select add #2/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> contacts distanceOnly 4.0 intraRes true select true color #ffa500
29718 distances
> close #3
> select clear
> select add #2/R:753@CB
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> contacts sel distanceOnly 4.0 intraRes true color #ffa500
204 distances
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> contacts sel distanceOnly 4.0 intraRes true intraModel false color #ffa500
155 distances
> contacts sel distanceOnly 4.0 intraRes true color #ffa500
204 distances
> select add #2/R:755
11 atoms, 11 bonds, 4 pseudobonds, 1 residue, 2 models selected
> select clear
> hide sel pseudobonds
[Repeated 1 time(s)]Drag select of 5 pseudobonds
Drag select of 3 pseudobonds
> hide sel
> select clear
Drag select of 3 residues, 3 pseudobonds
> select clear
Drag select of 3 pseudobonds
> hide sel
[Repeated 1 time(s)]
> select add #2/R:754
7 atoms, 6 bonds, 6 pseudobonds, 1 residue, 2 models selected
> select clear
> hide sel
> select add #2/R:762
8 atoms, 7 bonds, 2 pseudobonds, 1 residue, 2 models selected
> select add #2/R:777
16 atoms, 14 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select add #2/R:779
20 atoms, 17 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select add #2/R:788
28 atoms, 24 bonds, 2 pseudobonds, 4 residues, 2 models selected
> select up
219 atoms, 223 bonds, 2 pseudobonds, 27 residues, 2 models selected
> hide sel cartoons
> select add #2/R:545
233 atoms, 238 bonds, 2 pseudobonds, 28 residues, 2 models selected
> select clear
> select add #2/R:545
14 atoms, 15 bonds, 1 residue, 1 model selected
> select add #2/R:571
22 atoms, 22 bonds, 2 residues, 1 model selected
> select up
215 atoms, 218 bonds, 27 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
Drag select of 1 pseudobonds
[Repeated 1 time(s)]
> color (#!2 & sel) hot pink
> color (#!2 & sel) purple
> select clear
> show #!1 models
Drag select of 2 atoms, 4 residues, 1 bonds, 10 pseudobonds
> hide sel
> select clear
Drag select of 1 atoms, 2 residues, 4 pseudobonds
> select clear
> ui tool show Contacts
> hide #!2 models
> show #!2 models
> hide #!1 models
> close #3
> show #!1 models
> hide #!2 models
> select add #1/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select add #1/R:757
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:735
13 atoms, 11 bonds, 2 residues, 1 model selected
> select up
174 atoms, 177 bonds, 23 residues, 1 model selected
> transparency sel 0 cartoons
> select add #1/R:666
182 atoms, 184 bonds, 24 residues, 1 model selected
> select add #1/R:633
191 atoms, 192 bonds, 25 residues, 1 model selected
> select up
527 atoms, 537 bonds, 69 residues, 1 model selected
> hide sel atoms
> select clear
> undo
[Repeated 2 time(s)]Drag select of 9 residues
> select clear
> select add #1/R:667
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/R:633
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
353 atoms, 360 bonds, 46 residues, 1 model selected
> hide sel atoms
> select clear
> show #!2 models
> hide #!1 models
> show #!1 models
> select add #1/R:765
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #1/R:788
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:766
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
202 atoms, 206 bonds, 25 residues, 1 model selected
> hide sel cartoons
> select add #1/R:548
209 atoms, 212 bonds, 26 residues, 1 model selected
> select add #1/R:572
216 atoms, 218 bonds, 27 residues, 1 model selected
> select up
393 atoms, 398 bonds, 50 residues, 1 model selected
> hide sel cartoons
> select #1
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> show sel cartoons
> select #2
2174 atoms, 2231 bonds, 271 residues, 1 model selected
> show sel cartoons
> select clear
> select add #2/R:545
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #!1 models
> select add #2/R:571
22 atoms, 22 bonds, 2 residues, 1 model selected
> select up
215 atoms, 218 bonds, 27 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> select clear
> show #!1 models
> ui mousemode right distance
> hide #!1 models
> ui mousemode right distance
> select add #2/R:537@CE
1 atom, 1 residue, 1 model selected
> select add #2/R:753@CE3
2 atoms, 2 residues, 1 model selected
> select clear
> select add #2/R:753@CE3
1 atom, 1 residue, 1 model selected
> select add #2/R:537@CE
2 atoms, 2 residues, 1 model selected
> select #2
2174 atoms, 2231 bonds, 271 residues, 1 model selected
> select subtract #2/R:537@CE
1 atom, 1 residue, 1 model selected
> select add #2/R:537@CE
2 atoms, 2 residues, 1 model selected
> select clear
> select add #2/R:753@CE3
1 atom, 1 residue, 1 model selected
> select add #2/R:537@CE
2 atoms, 2 residues, 1 model selected
Drag select of 1 atoms, 3 residues
> select clear
> select add #2/R:537@CE
1 atom, 1 residue, 1 model selected
> select add #2/R:753@CE3
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
> distance #2/R:537@CE #2/R:753@CE3
Distance between ADGRE5_mG13-coot-7_real_space_refined_128.pdb #2/R MET 537 CE
and TRP 753 CE3: 3.404Å
> select clear
> select add #2/R:771
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide #3.1 models
> color #3 orange models transparency 0
> select clear
> select add #2/R:533@CE2
1 atom, 1 residue, 1 model selected
> select add #2/R:753@CH2
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
> distance #2/R:533@CE2 #2/R:753@CH2
Distance between ADGRE5_mG13-coot-7_real_space_refined_128.pdb #2/R PHE 533
CE2 and TRP 753 CH2: 3.759Å
> select clear
> color #3 #ffaa7f models transparency 0
> color #3 orange models transparency 0
> select clear
> show #!1 models
> select add #1/R:691
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #2/R:673
12 atoms, 10 bonds, 2 residues, 2 models selected
> select clear
> select add #1/R:673
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:673
16 atoms, 14 bonds, 2 residues, 2 models selected
> hide #!1 models
> select add #2/R:652
23 atoms, 20 bonds, 3 residues, 2 models selected
> select up
246 atoms, 249 bonds, 35 residues, 2 models selected
> hide sel & #!2 cartoons
> select clear
> show #!1 models
> select add #1/R:672
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select add #1/R:673
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> select add #1/R:652
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
150 atoms, 151 bonds, 21 residues, 1 model selected
> select add #1/R:660
162 atoms, 163 bonds, 22 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!1 models
> select add #2/R:613
173 atoms, 173 bonds, 23 residues, 2 models selected
> select add #2/R:639
184 atoms, 184 bonds, 24 residues, 2 models selected
> select up
424 atoms, 432 bonds, 54 residues, 2 models selected
> hide sel & #!2 cartoons
> select add #2/R:600
428 atoms, 435 bonds, 55 residues, 2 models selected
> select add #2/R:578
434 atoms, 440 bonds, 56 residues, 2 models selected
> select up
598 atoms, 609 bonds, 77 residues, 2 models selected
> hide sel & #!2 cartoons
> select add #2/R:575
606 atoms, 616 bonds, 78 residues, 2 models selected
> select add #2/R:577
610 atoms, 619 bonds, 79 residues, 2 models selected
> select up
637 atoms, 649 bonds, 82 residues, 2 models selected
> hide sel & #!2 cartoons
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select add #1/R:610
645 atoms, 656 bonds, 83 residues, 2 models selected
> select add #1/R:642
652 atoms, 662 bonds, 84 residues, 2 models selected
> select up
906 atoms, 927 bonds, 115 residues, 2 models selected
> hide sel & #!1 cartoons
> select add #1/R:600
910 atoms, 930 bonds, 116 residues, 2 models selected
> select add #1/R:576
919 atoms, 938 bonds, 117 residues, 2 models selected
> select up
1093 atoms, 1117 bonds, 140 residues, 2 models selected
> hide sel & #!1 cartoons
> select add #1/R:651
1099 atoms, 1122 bonds, 141 residues, 2 models selected
> select add #1/R:647
1103 atoms, 1125 bonds, 142 residues, 2 models selected
> select up
1162 atoms, 1188 bonds, 149 residues, 2 models selected
> hide sel & #!1 cartoons
> show #!2 models
> select add #1/R:734
1171 atoms, 1196 bonds, 150 residues, 2 models selected
> transparency sel 0 cartoons
> select clear
> select add #2/R:730
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/R:729
17 atoms, 15 bonds, 2 residues, 1 model selected
> transparency sel 0 cartoons
> select #2/R:704
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> select add #2/R:759
16 atoms, 14 bonds, 2 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> select add #2/R:703
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #2/R:704
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 70 cartoons
> select clear
Drag select of 31 residues
Drag select of 18 residues
> select up
1300 atoms, 1329 bonds, 161 residues, 2 models selected
> transparency sel 80 cartoons
> select clear
> select add #2/R:760
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:763
22 atoms, 21 bonds, 2 residues, 1 model selected
> select up
149 atoms, 151 bonds, 18 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> select add #2/R:759
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons
> select clear
> select add #2/R:760
11 atoms, 11 bonds, 1 residue, 1 model selected
> transparency sel 0 cartoons
> select #2/R:704
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> show sel cartoons
> select clear
> select #2
2174 atoms, 2231 bonds, 2 pseudobonds, 271 residues, 2 models selected
> show sel cartoons
> select clear
Drag select of 12 residues
> select up
879 atoms, 899 bonds, 111 residues, 2 models selected
> select clear
Drag select of 4 residues
> select up
531 atoms, 545 bonds, 65 residues, 2 models selected
> transparency sel 80 cartoons
> select clear
Drag select of 3 residues
> select up
617 atoms, 630 bonds, 79 residues, 2 models selected
> transparency sel 80 cartoons
Drag select of 4 residues
> select up
863 atoms, 879 bonds, 114 residues, 2 models selected
> transparency sel 80 cartoons
Drag select of 4 residues
> select up
4244 atoms, 4355 bonds, 530 residues, 2 models selected
> transparency sel 80 cartoons
> select clear
> undo
[Repeated 1 time(s)]
> select clear
> hide #!1 models
> select add #2/R:755
11 atoms, 11 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select add #2/R:746
27 atoms, 18 bonds, 3 residues, 1 model selected
> select up
216 atoms, 219 bonds, 27 residues, 1 model selected
> transparency sel 0 cartoons
> select add #2/R:750
220 atoms, 222 bonds, 28 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
Drag select of 2 residues
> select up
122 atoms, 123 bonds, 15 residues, 1 model selected
> transparency sel 0 cartoons
> select add #2/R:778
131 atoms, 131 bonds, 16 residues, 1 model selected
> select add #2/R:777
139 atoms, 138 bonds, 17 residues, 1 model selected
> select add #2/R:787
145 atoms, 143 bonds, 18 residues, 1 model selected
> select up
219 atoms, 223 bonds, 27 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
[Repeated 2 time(s)]
> select add #2/R:544
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:531
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #2/R:535
22 atoms, 19 bonds, 3 residues, 1 model selected
> select up
111 atoms, 113 bonds, 14 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> select add #2/R:762
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:788
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
211 atoms, 214 bonds, 26 residues, 1 model selected
> transparency sel 80 cartoons
> select clear
> select add #2/R:777
8 atoms, 7 bonds, 1 residue, 1 model selected
> transparency sel 80 cartoons
> select clear
> select add #2/R:762
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:788
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
211 atoms, 214 bonds, 26 residues, 1 model selected
> select add #2/R:777
219 atoms, 221 bonds, 27 residues, 1 model selected
> hide sel cartoons
> select clear
> select add #2/R:789
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #2/R:759
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:760
19 atoms, 18 bonds, 2 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
[Repeated 2 time(s)]
> select add #2/R:545
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select #2
2174 atoms, 2231 bonds, 2 pseudobonds, 271 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select clear
> select add #2/R:776
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/R:763
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
122 atoms, 123 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 32 atoms, 253 residues, 32 bonds, 2 pseudobonds
> select clear
> select add #2/R:761
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel
[Repeated 3 time(s)]
> hide sel cartoons
> select add #2/R:545
22 atoms, 22 bonds, 2 residues, 1 model selected
> select add #2/R:573
33 atoms, 32 bonds, 3 residues, 1 model selected
> select up
268 atoms, 271 bonds, 33 residues, 1 model selected
> hide sel
> hide sel cartoons
> select add #2/R:777
276 atoms, 278 bonds, 34 residues, 1 model selected
> select add #2/R:572
283 atoms, 284 bonds, 35 residues, 1 model selected
> select add #2/R:789
291 atoms, 291 bonds, 36 residues, 1 model selected
> select up
299 atoms, 301 bonds, 37 residues, 1 model selected
> select add #2/R:788
307 atoms, 308 bonds, 38 residues, 1 model selected
> select up
388 atoms, 394 bonds, 48 residues, 1 model selected
> hide sel
> hide sel cartoons
> select add #2/R:801
394 atoms, 399 bonds, 49 residues, 1 model selected
> select add #2/R:791
403 atoms, 407 bonds, 50 residues, 1 model selected
> select up
494 atoms, 503 bonds, 59 residues, 1 model selected
> hide sel
> hide sel cartoons
Drag select of 110 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 2 residues
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
Drag select of 30 residues
> select add #2/R:697
1697 atoms, 510 bonds, 211 residues, 1 model selected
> select add #2/R:730
1706 atoms, 518 bonds, 212 residues, 1 model selected
> select add #2/R:729
1714 atoms, 525 bonds, 213 residues, 1 model selected
> hide sel
> hide sel cartoons
> select clear
> select add #2/R:700
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> open "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/final_map_and_model/final_map_and_model/ADGRE5_mG13-coot-7_real_space_refined_128.pdb"
Chain information for ADGRE5_mG13-coot-7_real_space_refined_128.pdb #4
---
Chain | Description
A | No description available
B | No description available
R | No description available
Y | No description available
Drag select of 195 residues
> select up
2587 atoms, 2619 bonds, 334 residues, 2 models selected
> select up
6942 atoms, 7080 bonds, 875 residues, 2 models selected
> select down
2587 atoms, 2619 bonds, 334 residues, 2 models selected
> hide #!2 models
> select clear
Drag select of 365 residues, 1 pseudobonds
> select up
3570 atoms, 3630 bonds, 1 pseudobond, 455 residues, 2 models selected
> hide sel cartoons
Drag select of 106 residues
> select up
4482 atoms, 4559 bonds, 1 pseudobond, 568 residues, 2 models selected
> select up
4768 atoms, 4849 bonds, 1 pseudobond, 604 residues, 2 models selected
> hide sel cartoons
Drag select of 258 residues
> ui tool show "Color Actions"
> color sel steel blue
> select clear
Drag select of 236 residues
> color sel steel blue
> select clear
> cartoon style width 1.6 thickness 0.8
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 271 residues
> transparency sel 80 cartoons
> select clear
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!2,4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker apo_ADGRE5-coot-25_real_space_refined_087.pdb, chain R (#1) with
ADGRE5_mG13-coot-7_real_space_refined_128.pdb, chain R (#2), sequence
alignment score = 1278.9
RMSD between 148 pruned atom pairs is 0.867 angstroms; (across all 258 pairs:
8.882)
Matchmaker apo_ADGRE5-coot-25_real_space_refined_087.pdb, chain R (#1) with
ADGRE5_mG13-coot-7_real_space_refined_128.pdb, chain R (#4), sequence
alignment score = 1278.9
RMSD between 148 pruned atom pairs is 0.867 angstroms; (across all 258 pairs:
8.882)
> hide #!2 models
> select add #4/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #4/R:731
20 atoms, 19 bonds, 2 residues, 1 model selected
> select up
216 atoms, 219 bonds, 27 residues, 1 model selected
> select add #4/R:750
220 atoms, 222 bonds, 28 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #4/R:544
228 atoms, 229 bonds, 29 residues, 1 model selected
> select add #4/R:531
234 atoms, 234 bonds, 30 residues, 1 model selected
> select add #4/R:534
239 atoms, 238 bonds, 31 residues, 1 model selected
> select up
331 atoms, 337 bonds, 42 residues, 1 model selected
> hide sel cartoons
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 229 residues
> select up
6942 atoms, 7080 bonds, 875 residues, 1 model selected
> select up
11186 atoms, 11435 bonds, 2 pseudobonds, 1405 residues, 4 models selected
Drag select of 229 residues
[Repeated 1 time(s)]
> transparency sel 90 cartoons
> select clear
> graphics silhouettes false
> transparency sel 80 cartoons
Drag select of 229 residues
> transparency sel 80 cartoons
> select clear
> show #!1 models
> hide #!1 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
> hide #!4 models
> show #!2 models
Drag select of 32 atoms, 42 residues, 32 bonds, 2 pseudobonds
> transparency sel 0 cartoons
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> graphics silhouettes true
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> graphics silhouettes false
> hide #!2 models
> show #!4 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
> graphics silhouettes true
> hide #!2 models
> show #!2 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes #2 true
Expected true or false or a keyword
> graphics silhouettes true #2
Expected a keyword
> graphics silhouettes false
> hide #!2 models
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/active.cxs"
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/文章整理202211/Fig3/active
> mode/background.tif" width 931 height 676 supersample 3
> hide #!4 models
> show #!2 models
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> undo
[Repeated 3 time(s)]
> select clear
> select add #2/R:759
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/R:765
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #2/R:776
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #2/R:800
36 atoms, 34 bonds, 4 residues, 1 model selected
> select up
249 atoms, 253 bonds, 28 residues, 1 model selected
> select add #2/R:781
260 atoms, 264 bonds, 29 residues, 1 model selected
> select up
338 atoms, 344 bonds, 39 residues, 1 model selected
> select add #2/R:790
346 atoms, 351 bonds, 40 residues, 1 model selected
> select up
354 atoms, 361 bonds, 41 residues, 1 model selected
> select add #2/R:801
360 atoms, 366 bonds, 42 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> undo
> hide sel cartoons
> select add #2/R:545
374 atoms, 381 bonds, 43 residues, 1 model selected
> select add #2/R:573
385 atoms, 391 bonds, 44 residues, 1 model selected
> select add #2/R:571
393 atoms, 398 bonds, 45 residues, 1 model selected
> select up
601 atoms, 611 bonds, 72 residues, 1 model selected
> hide sel cartoons
> select add #2/R:777
609 atoms, 618 bonds, 73 residues, 1 model selected
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 99 residues
> hide sel cartoons
Drag select of 14 residues
> select add #2/R:688
1507 atoms, 629 bonds, 188 residues, 1 model selected
> hide sel cartoons
> select add #2/R:697
1515 atoms, 636 bonds, 189 residues, 1 model selected
Drag select of 16 residues
> hide sel cartoons
> select add #2/R:704
1654 atoms, 643 bonds, 206 residues, 1 model selected
> select add #2/R:730
1663 atoms, 651 bonds, 207 residues, 1 model selected
> select up
1843 atoms, 1891 bonds, 229 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/文章整理202211/Fig3/active
> mode/background.tif" width 931 height 676 supersample 3
> show #!2 models
> hide #!4 models
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/文章整理202211/Fig3/active
> mode/G13_TM6.tif" width 931 height 676 supersample 3
> hide sel cartoons
> graphics silhouettes true
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/文章整理202211/Fig3/active
> mode/G13_TM6.tif" width 931 height 676 supersample 3
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/文章整理202211/Fig3/active
> mode/background.cxs"
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6.tif" width 931
> height 676 supersample 3 transparentBackground true
> show #!4 models
> graphics silhouettes false
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> select #1
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> transparency sel 0 cartoons
> select clear
> show #!2 models
> show #!4 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select add #1/R:757
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/R:734
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #1/R:758
28 atoms, 26 bonds, 3 residues, 1 model selected
> select up
263 atoms, 267 bonds, 33 residues, 1 model selected
> select clear
> select add #1/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select add #1/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:766
18 atoms, 17 bonds, 2 residues, 1 model selected
> select up
243 atoms, 249 bonds, 29 residues, 1 model selected
> select clear
> select add #1/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #1/R:766
18 atoms, 17 bonds, 2 residues, 1 model selected
> select up
243 atoms, 249 bonds, 29 residues, 1 model selected
> hide sel cartoons
Drag select of 61 residues
> select up
1154 atoms, 1178 bonds, 143 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 69 residues
> select up
1802 atoms, 1848 bonds, 224 residues, 1 model selected
> hide sel cartoons
> show #!2 models
Drag select of 4 residues
> select up
1890 atoms, 1939 bonds, 235 residues, 1 model selected
> hide sel cartoons
> show #!4 models
> open "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/final_map_and_model/final_map_and_model/apo_ADGRE5-coot-25_real_space_refined_087.pdb"
Chain information for apo_ADGRE5-coot-25_real_space_refined_087.pdb #5
---
Chain | Description
R | No description available
> hide #!1 models
> hide #!2 models
> hide #!3 models
> select #5
4189 atoms, 4288 bonds, 1 pseudobond, 535 residues, 2 models selected
> ui tool show "Color Actions"
> color sel thistle
> cartoon style width 1.6 thickness 0.8
> select clear
> hide #!4 models
Drag select of 260 residues, 1 pseudobonds
> select up
2439 atoms, 2500 bonds, 1 pseudobond, 306 residues, 2 models selected
> transparency sel 80 catoon
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency sel 80 cartoons
> transparency sel 70 cartoons
> select clear
[Repeated 1 time(s)]
> show #!4 models
> show #!1 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> ui mousemode right distance
> select add #2/R:533@CE2
1 atom, 1 residue, 1 model selected
> select add #2/R:753@CH2
2 atoms, 2 residues, 1 model selected
> distance #2/R:753@CH2 #2/R:533@CE2
Distance already exists; modify distance properties with 'distance style'
> select clear
> select add #2/R:753@CH2
1 atom, 1 residue, 1 model selected
> select add #2/R:533@CE2
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
[Repeated 1 time(s)]
> distance #2/R:533@CE2 #2/R:753@CH2
Distance already exists; modify distance properties with 'distance style'
> show #3.1 models
> hide #3.1 models
> select clear
> hide #!1 models
> show #!1 models
> show #!4 models
> show #!5 models
> select add #5/R:649
4 atoms, 3 bonds, 1 residue, 1 model selected
> select subtract #5/R:649
Nothing selected
> hide sel
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select add #5/R:757
8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected
> select add #5/R:736
19 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected
> select add #5/R:735
24 atoms, 21 bonds, 1 pseudobond, 3 residues, 2 models selected
> select up
174 atoms, 177 bonds, 1 pseudobond, 23 residues, 2 models selected
> hide sel cartoons
> show #!2 models
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!2 models
Drag select of 483 residues
> cartoon style sides 30
Invalid "sides" argument: Must be less than or equal to 24
> cartoon style sides 24
> select clear
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/background_2.tif" width
> 931 height 699 supersample 3
> show #!1 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/background_2.tif" width
> 931 height 699 supersample 3
> show #!2 models
> show #!1 models
> hide #!4 models
> hide #!5 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> graphics silhouettes true
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> graphics silhouettes false
> select #5
4189 atoms, 4288 bonds, 1 pseudobond, 535 residues, 2 models selected
> transparency sel 60 cartoons
> transparency sel 40 cartoons
> select clear
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/background_2.tif" width
> 931 height 699 supersample 3
> show #!2 models
> show #!1 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> graphics silhouettes true
> show #!4 models
> show #!5 models
> hide #!1 models
> hide #!2 models
Drag select of 603 residues, 64 atoms, 62 bonds
> transparency sel 60 cartoons
> transparency sel 70 cartoons
> transparency sel 80 cartoons
> select clear
> graphics silhouettes false
> select #5
4189 atoms, 4288 bonds, 1 pseudobond, 535 residues, 2 models selected
> transparency sel 40 cartoons
> select clear
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/background_2.tif" width
> 931 height 699 supersample 3
> hide #!4 models
> hide #!5 models
> show #!2 models
> show #!1 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> graphics silhouettes true
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> lighting fillIntensity 0.1
> lighting fillIntensity 0
> lighting fillIntensity 0.2
> lighting fillIntensity 0.05
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_2.tif" width 931
> height 699 supersample 3 transparentBackground true
> cartoon style width 1.5 thickness 0.6
> cartoon style width 1.2 thickness 0.6
[Repeated 1 time(s)]
> cartoon style width 1.2 thickness 0.9
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_3.tif" width 931
> height 699 supersample 3
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_3.tif" width 931
> height 699 supersample 3 transparentBackground true
> hide #!1 models
> hide #!2 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> cartoon style width 1.5 thickness 0.9
> undo
[Repeated 2 time(s)]
> show #!4 models
> show #!5 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> select #4
6942 atoms, 7080 bonds, 1 pseudobond, 875 residues, 2 models selected
> select #5
4189 atoms, 4288 bonds, 1 pseudobond, 535 residues, 2 models selected
> cartoon style width 1.5 thickness 0.9
> select #4
6942 atoms, 7080 bonds, 1 pseudobond, 875 residues, 2 models selected
> cartoon style width 1.5 thickness 0.9
> select clear
[Repeated 1 time(s)]Drag select of 495 residues, 19 atoms, 19 bonds
> select up
3999 atoms, 2206 bonds, 496 residues, 2 models selected
> select up
4284 atoms, 2499 bonds, 534 residues, 2 models selected
> select up
6363 atoms, 6519 bonds, 806 residues, 2 models selected
> cartoon style width 1.8 thickness 0.8
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> transparency sel 70 cartoons
> transparency sel 90 cartoons
> transparency sel 80 cartoons
> select clear
> graphics silhouettes false
> select #5
4189 atoms, 4288 bonds, 1 pseudobond, 535 residues, 2 models selected
> transparency sel 60 cartoons
> transparency sel 40 cartoons
> transparency sel 50 cartoons
> transparency sel 60 cartoons
> transparency sel 50 cartoons
> select clear
[Repeated 2 time(s)]
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> select #4
6942 atoms, 7080 bonds, 1 pseudobond, 875 residues, 2 models selected
> transparency sel 850 cartoons
> transparency sel 80 cartoons
> transparency sel 85 cartoons
> select clear
> transparency sel 09 cartoons
> select #4
6942 atoms, 7080 bonds, 1 pseudobond, 875 residues, 2 models selected
> transparency sel 90 cartoons
> select clear
> transparency sel 85 cartoons
> select clear
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/background_3.tif" width
> 931 height 699 supersample 3
> show #!1 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> graphics silhouettes true
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_3.tif" width 931
> height 699 supersample 3 transparentBackground true
> cartoon style width 1.5 thickness 0.9
> cartoon style width 1.3 thickness 0.9
> cartoon style width 1.2 thickness 0.9
> cartoon style width 1. thickness 0.9
> cartoon style width 1. thickness 1.2
> cartoon style width 1. thickness 1
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/active mode/G13_TM6_3.tif" width 931
> height 699 supersample 3 transparentBackground true
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/active_2.cxs"
——— End of log from Sat Dec 17 00:12:19 2022 ———
opened ChimeraX session
> show #!5 models
> hide #!5 models
> show #!5 models
> ui tool show "Side View"
> hide #!5 models
> open "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/final_map_and_model/final_map_and_model/apo_ADGRE5-735down.pdb"
Chain information for apo_ADGRE5-735down.pdb #6
---
Chain | Description
R | No description available
Drag select of 17 residues
> select up
325 atoms, 334 bonds, 42 residues, 1 model selected
> select up
4189 atoms, 4288 bonds, 535 residues, 1 model selected
> ui tool show "Color Actions"
> color sel thistle
> cartoon style sel width 1.6 thickness 0.8
> cartoon style sel width 1.6 thickness 0.6
> cartoon style sel width 1.2 thickness 0.6
> cartoon style sel width 1.2 thickness 0.8
> hide pesudobonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide pseudobonds
> select clear
[Repeated 1 time(s)]Drag select of 61 residues
> select up
747 atoms, 766 bonds, 94 residues, 1 model selected
> select clear
Drag select of 68 residues
> select up
904 atoms, 932 bonds, 112 residues, 1 model selected
> hide sel cartoons
Drag select of 29 residues
> select up
1428 atoms, 1465 bonds, 176 residues, 1 model selected
Drag select of 2 residues
> select up
4189 atoms, 4288 bonds, 535 residues, 1 model selected
> select down
1441 atoms, 1465 bonds, 178 residues, 1 model selected
> select up
4189 atoms, 4288 bonds, 535 residues, 1 model selected
> select down
1441 atoms, 1465 bonds, 178 residues, 1 model selected
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 14 residues
> select up
1621 atoms, 1662 bonds, 202 residues, 1 model selected
> select down
1561 atoms, 1465 bonds, 193 residues, 1 model selected
> select up
1621 atoms, 1662 bonds, 202 residues, 1 model selected
> select up
4189 atoms, 4288 bonds, 535 residues, 1 model selected
> select down
1621 atoms, 1662 bonds, 202 residues, 1 model selected
> hide sel cartoons
Drag select of 13 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 286 residues, 69 atoms, 66 bonds
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]Drag select of 27 atoms, 21 bonds
> select up
45 atoms, 39 bonds, 6 residues, 1 model selected
> hide sel
> select #6/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
Drag select of 16 atoms, 19 residues, 16 bonds
> select up
164 atoms, 116 bonds, 20 residues, 3 models selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> select #6/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #2/R:537
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select add #2/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
[Repeated 2 time(s)]
> select #2/R:756
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/R:759
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> transparency sel 0 cartoons
> select clear
> hide #!1 models
> select add #6/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
174 atoms, 177 bonds, 23 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> transparency sel 0100 cartoons
> show #!1 models
> select clear
> hide #!1 models
> select add #6/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select add #6/R:753
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
174 atoms, 177 bonds, 23 residues, 1 model selected
> cartoon style width 1.1 thickness 0.8
> cartoon style sel width 1.1 thickness 0.8
> cartoon style sel width 1.1 thickness 0.2
> cartoon style sel width 0.2 thickness 0.2
> select clear
> graphics silhouettes false
> graphics silhouettes true
Drag select of 3 residues
> select up
174 atoms, 177 bonds, 23 residues, 1 model selected
> graphics silhouettes sel false
Expected true or false or a keyword
> select clear
Drag select of 3 residues
> select clear
> show #!1 models
> select add #6/R:765
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
71 atoms, 72 bonds, 8 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6/R:764
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #2/R:759
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/R:760
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #2/R:761
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> select add #2/R:760
19 atoms, 18 bonds, 2 residues, 1 model selected
> transparency sel 0 cartoons
> select clear
> select add #2/R:533
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:534
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #2/R:536
24 atoms, 22 bonds, 3 residues, 1 model selected
> select subtract #2/R:536
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add #2/R:535
24 atoms, 22 bonds, 3 residues, 1 model selected
> select add #2/R:536
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #2/R:537
40 atoms, 36 bonds, 5 residues, 1 model selected
> select add #2/R:538
45 atoms, 40 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select add #2/R:534
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/1221 align/2-3-total align_tether.tif"
> width 857 height 644 supersample 3
[Repeated 1 time(s)]
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/1221 align/2-3-total align_tether.tif"
> width 976 height 644 supersample 3
> select add #2/R:536
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/R:758
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:537
19 atoms, 18 bonds, 2 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select add #2/R:537
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> undo
> hide sel atoms
> select clear
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/1221 align/2-3-total align_tether.tif"
> width 976 height 644 supersample 3
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/active_3.cxs"
——— End of log from Sat Dec 24 17:22:32 2022 ———
opened ChimeraX session
Drag select of 2 atoms, 2 residues, 2 bonds
> select clear
Drag select of 5 atoms, 5 residues, 4 bonds
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> select up
111 atoms, 113 bonds, 14 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> ui tool show "Side View"
> hide #!3 models
> select #1:610-641
262 atoms, 269 bonds, 32 residues, 1 model selected
> show sel cartoons
> select #2:610-641
262 atoms, 269 bonds, 32 residues, 1 model selected
> show sel cartoons
> transparency sel 0 cartoons
> select clear
> select #2:775
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #2:630
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1:630
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1:623
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2]:623
Expected an objects specifier or a keyword
> select #2:623
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2:627
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1:627
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "C:/Users/12051/Desktop/Experiment
> data/ADGRE5/文章整理202211/202212109/Fig4/1221 TM3_7/4_inactive_TM3_7.tif" width
> 789 height 646 supersample 3
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/TM3_2R.cxs"
——— End of log from Thu Jan 5 23:58:40 2023 ———
opened ChimeraX session
> show #!1-2,6 cartoons
> ui tool show "Side View"
Drag select of 75 atoms, 480 residues, 76 bonds
> select up
3801 atoms, 3885 bonds, 480 residues, 3 models selected
> select up
5143 atoms, 5260 bonds, 647 residues, 3 models selected
> select up
8433 atoms, 8643 bonds, 1065 residues, 3 models selected
> select up
19564 atoms, 20011 bonds, 2 pseudobonds, 2475 residues, 6 models selected
> select up
19564 atoms, 20011 bonds, 2 pseudobonds, 2475 residues, 6 models selected
> select up
19564 atoms, 20011 bonds, 2 pseudobonds, 2475 residues, 6 models selected
> select up
19564 atoms, 20011 bonds, 2 pseudobonds, 2475 residues, 6 models selected
> select up
19564 atoms, 20011 bonds, 2 pseudobonds, 2475 residues, 6 models selected
> transparency sel 0 cartoons
> select clear
Drag select of 14 residues
> select up
569 atoms, 579 bonds, 72 residues, 2 models selected
> select up
6259 atoms, 6412 bonds, 794 residues, 2 models selected
> select down
569 atoms, 579 bonds, 72 residues, 2 models selected
> select clear
Drag select of 298 residues
> select add #1/R:544
2282 atoms, 7 bonds, 299 residues, 2 models selected
> select add #6/R:431
2291 atoms, 15 bonds, 300 residues, 2 models selected
> hide sel cartoons
Drag select of 75 atoms, 762 residues, 76 bonds
> select up
8391 atoms, 8598 bonds, 1062 residues, 3 models selected
> select up
8433 atoms, 8643 bonds, 1065 residues, 3 models selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> hide #!6 models
> select #1/R/785
2070 atoms, 2124 bonds, 1 pseudobond, 259 residues, 2 models selected
> select #1/R:785
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> show sel atoms
> color sel byhetero
> select #2/R:785
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #2/R:747
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/R:747
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/R:743
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/R:743
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/R:711
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/R:711
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #1/R:711
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/R:711
22 atoms, 22 bonds, 2 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
> select add #1/R:743
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select add #2/R:712
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/R:711
18 atoms, 17 bonds, 2 residues, 2 models selected
> select up
510 atoms, 527 bonds, 62 residues, 2 models selected
> hide sel cartoons
> select #1/R:781
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/R:781
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/R:777
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/R:777
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/R:774
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/R:774
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1/R:743
16 atoms, 14 bonds, 2 residues, 2 models selected
> hide sel atoms
> select clear
> select add #1/R:774
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/R:774
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #2/R:634
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #1/R:634
16 atoms, 13 bonds, 3 residues, 2 models selected
Drag select of 2 residues
> select up
881 atoms, 900 bonds, 110 residues, 2 models selected
> select clear
> select add #2/R:634
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/R:634
8 atoms, 6 bonds, 2 residues, 2 models selected
> select add #2/R:651
14 atoms, 11 bonds, 3 residues, 2 models selected
> select add #1/R:651
20 atoms, 16 bonds, 4 residues, 2 models selected
> select up
676 atoms, 692 bonds, 84 residues, 2 models selected
> hide sel cartoons
> select add #1/R:652
683 atoms, 698 bonds, 85 residues, 2 models selected
> select add #2/R:652
690 atoms, 704 bonds, 86 residues, 2 models selected
> select up
904 atoms, 926 bonds, 114 residues, 2 models selected
> hide sel cartoons
> select add #1/R:660
916 atoms, 938 bonds, 115 residues, 2 models selected
> select up
4244 atoms, 4355 bonds, 530 residues, 2 models selected
> select clear
> select add #1/R:660
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
2070 atoms, 2124 bonds, 259 residues, 1 model selected
> select clear
> select add #1/R:663
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
84 atoms, 84 bonds, 13 residues, 1 model selected
> hide sel cartoons
> select add #1/R:660
96 atoms, 96 bonds, 14 residues, 1 model selected
> hide sel cartoons
Drag select of 42 residues
> select up
843 atoms, 854 bonds, 111 residues, 2 models selected
> hide sel cartoons
> select add #1/R:720
852 atoms, 862 bonds, 112 residues, 2 models selected
Drag select of 33 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
Drag select of 35 residues
> select up
1677 atoms, 1707 bonds, 210 residues, 2 models selected
> select add #2/R:544
1685 atoms, 1714 bonds, 211 residues, 2 models selected
> select up
1744 atoms, 1776 bonds, 218 residues, 2 models selected
> select add #2/R:533
1755 atoms, 1787 bonds, 219 residues, 2 models selected
> select up
1776 atoms, 1810 bonds, 222 residues, 2 models selected
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
Drag select of 27 atoms, 24 residues, 25 bonds
> select up
2001 atoms, 2036 bonds, 251 residues, 2 models selected
> select up
2007 atoms, 2043 bonds, 251 residues, 2 models selected
> select up
2390 atoms, 2436 bonds, 300 residues, 2 models selected
> select up
4244 atoms, 4355 bonds, 530 residues, 2 models selected
> cartoon style sel width 0.8 thickness 0.8
> cartoon style sel width 1.0 thickness 0.6
> cartoon style sel width 1.0 thickness 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting shadows false
> select clear
Drag select of 35 atoms, 27 residues, 32 bonds
> select up
211 atoms, 211 bonds, 28 residues, 2 models selected
> select up
218 atoms, 218 bonds, 28 residues, 2 models selected
> select up
717 atoms, 728 bonds, 91 residues, 2 models selected
> select up
4244 atoms, 4355 bonds, 530 residues, 2 models selected
> select up
19564 atoms, 20011 bonds, 2 pseudobonds, 2475 residues, 6 models selected
> cartoon style sel width 0.9 thickness 0.5
> cartoon style sel width 0.9 thickness 0.4
> cartoon style sel width 0.9 thickness 0.5
> cartoon style sel width 0.7 thickness 0.5
> select clear
Drag select of 35 atoms, 39 residues, 33 bonds
> select up
298 atoms, 301 bonds, 39 residues, 2 models selected
> select up
613 atoms, 622 bonds, 78 residues, 2 models selected
> cartoon style sel width 0.7 thickness 0.4
> cartoon style sel width 0.7 thickness 0.3
> cartoon style sel width 0.6 thickness 0.3
> cartoon style sel width 0.6 thickness 0.4
> cartoon style sel width 0. thickness 0.4
> cartoon style sel width 0.7 thickness 0.4
Traceback (most recent call last):
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
297, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
ZeroDivisionError: float division by zero
ZeroDivisionError: float division by zero
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
See log for complete Python traceback.
> cartoon style sel width 0.7 thickness 0.4
Traceback (most recent call last):
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
297, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
ZeroDivisionError: float division by zero
ZeroDivisionError: float division by zero
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
See log for complete Python traceback.
> select clear
Drag select of 67 atoms, 72 residues, 60 bonds
> select up
573 atoms, 586 bonds, 72 residues, 2 models selected
> select up
815 atoms, 830 bonds, 103 residues, 2 models selected
> select up
4244 atoms, 4355 bonds, 530 residues, 2 models selected
> cartoon style sel width 0.7 thickness 0.4
Traceback (most recent call last):
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
297, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
ZeroDivisionError: float division by zero
ZeroDivisionError: float division by zero
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
See log for complete Python traceback.
> cartoon style sel width 0.8 thickness 0.4
Traceback (most recent call last):
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
297, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
ZeroDivisionError: float division by zero
ZeroDivisionError: float division by zero
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
See log for complete Python traceback.
> save "C:/Users/12051/Desktop/Experiment data/ADGRE5/color
> pattern_1012/20221209/active mode/FFF_20230403.cxs"
——— End of log from Mon Apr 3 14:15:51 2023 ———
opened ChimeraX session
> cartoon style sel width 0.8 thickness 0.4
Traceback (most recent call last):
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
297, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
ZeroDivisionError: float division by zero
ZeroDivisionError: float division by zero
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
See log for complete Python traceback.
> select clear
Drag select of 66 atoms, 58 residues, 60 bonds
> select up
449 atoms, 455 bonds, 58 residues, 2 models selected
> select up
785 atoms, 800 bonds, 99 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> cartoon style sel width 1.0 thickness 0.4
Traceback (most recent call last):
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
297, in execute
cmd.run(cmd_text)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run
result = ci.function(session, **kw_args)
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
ZeroDivisionError: float division by zero
ZeroDivisionError: float division by zero
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\cartoon.py",
line 298, in cartoon_style
old_arrow_scale = aw / w
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.8682
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Pro
OS: Microsoft Windows 10 家庭版 (Build 19044)
Memory: 8,502,935,552
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7300U CPU @ 2.60GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
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: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
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-DistUI: 1.0
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: 1.1.4
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: 1.2.6
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: 1.7
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: 1.0.1
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: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 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: 1.13.7
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
comtypes: 1.1.10
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: 3.6.0
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: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
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: 2.2.0
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
tables: 3.6.1
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
WMI: 1.5.1
Change History (3)
comment:1 by , 3 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cartoon style: float division by zero |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed in 1.6 and daily build.
Made cartoon style width, thickness, bar_scale and radius require positive values.
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User set cartoon width to 0 accidentally and that produced no error
cartoon style sel width 0. thickness 0.4
Then subsequently the tried t change the width to greater than 0 and the code divided by the old width producing division by zero.