![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7325 closed defect (fixed)
Update surface selection: index is out of bounds for axis
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Windows-10-10.0.19043
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\\\jvarg\\\Documents\\\huji\\\fusolisin\\\fusolisin_figure_surface.cxs
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Sun Jul 24 00:35:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cxs format
> session
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Sat Jul 23 20:33:38 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cxs format
> session
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Tue Jul 12 00:05:22 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open V:\\\projects\\\fusolisin\\\figures\\\fusolisin_figure_v2.cxs
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Mon Jun 13 21:11:39 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open V:/projects/fusolisin/fusolisin_figure_v2.cxs
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Tue Jun 7 11:23:29 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open fusolisin_figure.cxs
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Mon Jun 6 17:29:07 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open fusolisin_figure.cxs
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Mon Jun 6 16:08:31 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\jvarg\Documents\huji\fusolisin_figure.cxs format session
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Sat Jun 4 20:15:09 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open C:\Users\jvarg\Documents\huji\fusolisin_figure.cxs format session
registering illegal selector name "interface_res"
registering illegal selector name "int_res"
Log from Thu Jun 2 10:16:36 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/jvarg/Documents/huji/fusolisin.pse
Unrecognized file suffix '.pse'
> open
> C:/Users/jvarg/Documents/huji/relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb
> C:/Users/jvarg/Documents/huji/relax_short_fusolisin_SQAS_0001_0064_top1.pdb
Chain information for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb #1
---
Chain | Description
D | No description available
P | No description available
Chain information for relax_short_fusolisin_SQAS_0001_0064_top1.pdb #2
---
Chain | Description
D | No description available
P | No description available
> hide cartoons
> show cartoons
> color #1 white transparency 0
> select #1/D:77-414
2597 atoms, 2649 bonds, 338 residues, 1 model selected
> select #1/P:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> style sel stick
Changed 41 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> color sel bychain
> select #2/D:77-414
2597 atoms, 2649 bonds, 338 residues, 1 model selected
> color sel white
> select #2/P:76-79
27 atoms, 26 bonds, 4 residues, 1 model selected
> color sel cornflower blue
> color sel medium blue
> color sel byelement
> select #1/P:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel byhetero
> select clear
> color byhetero
> lighting flat
> lighting full
> lighting soft
> set bgColor white
Drag select of 2 atoms, 9 residues, 1 bonds
> lighting simple
> lighting full
> select clear
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
[Repeated 1 time(s)]
> lighting full
No Surface models open
> volume planes z style image imageMode "full region"
No volumes specified
> transparency 50
> volume style surface
No volumes specified
> select #1/D:77-414
2597 atoms, 2649 bonds, 338 residues, 1 model selected
> volume style surface
No volumes specified
> volume hide
No volumes specified
> open
> C:/Users/jvarg/Documents/huji/relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb
Chain information for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb #3
---
Chain | Description
D | No description available
P | No description available
> hide #3 models
> select #2/P:76-79
27 atoms, 26 bonds, 4 residues, 1 model selected
> color sel light sea green
> color sel forest green
> color sel light sea green
> ui tool show "Color Actions"
> color sel teal
> color sel byhetero
> color sel steel blue
> color sel byhetero
Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 0 maps.
> volume step 1
No volumes specified
> volume planes z style image imageMode "full region"
No volumes specified
> ui tool show "Volume Viewer"
> show sel surfaces
> undo
> hide sel surfaces
> select #1/D:77-414
2597 atoms, 2649 bonds, 338 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> transparency sel 50
> surface style #1 mesh
> surface style #1 solid
> hide #!2 models
> hide sel surfaces
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 2/P
> lighting soft
> select #1/P:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> color sel byhetero
> color sel light salmon
> color sel turquoise
> color sel dark turquoise
> color sel byhetero
> color sel orchid
> color sel hot pink
> color sel light green
> color sel pale green
> color sel light green
> color sel light blue
> color sel byhetero
> color sel light sky blue
> color sel sky blue
> color sel byhetero
> select clear
Drag select of 8 residues
> select clear
[Repeated 1 time(s)]
> select #1/P:77@CD
1 atom, 1 residue, 1 model selected
Drag select of 4 atoms, 1 residues, 3 bonds
> select clear
Drag select of 2 atoms, 2 residues, 2 bonds
> select #1/D:239@CG
1 atom, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> style sel sphere
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> ui tool show "Color Actions"
> color sel gold
> color sel byhetero
> select #1/D:344@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> color sel gold
[Repeated 1 time(s)]
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> color sel gold
> color sel byhetero
> select clear
> hbonds
3108 hydrogen bonds found
> hide #4 models
> select chain D
Expected an objects specifier or a keyword
> select D
Nothing selected
> select chain_ID=D
Expected an objects specifier or a keyword
> select chain_ID="D"
Expected an objects specifier or a keyword
> select #1/D:77-414
2597 atoms, 2649 bonds, 339 pseudobonds, 338 residues, 2 models selected
> select chain_ID="D"
Expected an objects specifier or a keyword
> select :.A
Expected an objects specifier or a keyword
> select :.D
Expected an objects specifier or a keyword
> select :D
Nothing selected
> select :.D
Expected an objects specifier or a keyword
> select :.P
Expected an objects specifier or a keyword
> select :.D
Expected an objects specifier or a keyword
> log metadata #1
No models had metadata
> log chains #1
Chain information for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb #1
---
Chain | Description
D | No description available
P | No description available
> select #1
2638 atoms, 2689 bonds, 353 pseudobonds, 344 residues, 2 models selected
> select #2
2624 atoms, 2675 bonds, 350 pseudobonds, 342 residues, 2 models selected
> select #3
2638 atoms, 2689 bonds, 353 pseudobonds, 344 residues, 2 models selected
> select #4
3108 pseudobonds, 1 model selected
> select #1
2638 atoms, 2689 bonds, 353 pseudobonds, 344 residues, 2 models selected
> select #1:D
Nothing selected
> select #1:.D
Expected an objects specifier or a keyword
> hbonds #1
1732 hydrogen bonds found
> show #4 models
> hide #4 models
> toolshed show
> ui tool show H-Bonds
> select #1/D
2597 atoms, 2649 bonds, 339 pseudobonds, 338 residues, 2 models selected
> hbonds sel color #aaff7f restrict cross reveal true
1366 hydrogen bonds found
> undo
Undo failed, probably because structures have been modified.
> hide sel atoms
Drag select of 1 atoms, 2 residues
> select #1/D:122
10 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 10 atom styles
> show sel atoms
> select #1/D:344
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
34 atoms, 34 bonds, 5 residues, 2 models selected
> select up
2597 atoms, 2649 bonds, 338 residues, 2 models selected
> select down
34 atoms, 34 bonds, 5 residues, 2 models selected
> select down
6 atoms, 5 bonds, 1 residue, 2 models selected
> show sel atoms
> select #1/D:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> interfaces
15 buried areas: #3/D #2/D 7468, #2/D #1/D 7468, #3/D #1/D 7400, #3/D #3/P
538, #3/D #1/P 538, #1/D #3/P 538, #1/D #1/P 538, #2/D #3/P 529, #2/D #1/P
529, #3/P #1/P 436, #2/D #2/P 393, #3/D #2/P 391, #1/D #2/P 391, #3/P #2/P
300, #1/P #2/P 300
> hbonds #1/D #1/P
1732 hydrogen bonds found
> show #4 models
> hide #4 models
> interfaces select #1/D contacting #1/P
12 contacting residues
> show sel atoms
> name
Missing or invalid "name" argument: Expected a text string
> name interface_res sel
registering illegal selector name "interface_res"
> name int_res interfaces select #1/D contacting #1/P
"interfaces select #1/D contacting #1/P": invalid atom specifier
[lots of the very long log deleted]
> show #2.2 models
> 2dlabels #2.2 xpos 0.397 ypos 0.194
> 2dlabels #2.6 xpos 0.650 ypos 0.581
> 2dlabels #2.14 xpos 0.637 ypos 0.775
> 2dlabels #2.5 xpos 0.383 ypos 0.718
> 2dlabels #2.5 size 14
> 2dlabels #2.5 size 16
> 2dlabels #2.5 xpos 0.385 ypos 0.733
> 2dlabels #2.2 size 16
> 2dlabels #2.3 size 16
> 2dlabels #2.3 xpos 0.289 ypos 0.219
> 2dlabels #2.3 size 16 bold false
> 2dlabels #2.11 size 16 bold false
> 2dlabels #2.11 xpos 0.384 ypos 0.025
> 2dlabels #2.11 size 16 bold false text ILE341
> 2dlabels #2.11 xpos 0.388 ypos 0.029
> 2dlabels #2.3 size 16 bold false text ASN239
> 2dlabels #2.3 xpos 0.281 ypos 0.245
> 2dlabels #2.2 size 16 bold true text SER344
> 2dlabels #2.1 size 16 bold true text HIS122
> 2dlabels #2.1 xpos 0.639 ypos 0.304
> 2dlabels #2.13 size 16 bold false text PHE190
> 2dlabels #2.13 xpos 0.423 ypos 0.646
> 2dlabels #2.5 size 16 bold false text GLY191
> 2dlabels #2.14 size 16 bold false text VAL163
> 2dlabels #2.6 size 16 bold false text LYS161
> 2dlabels #2.6 size 16 bold true text LYS161
> 2dlabels #2.14 size 16 bold true text VAL163
> 2dlabels #2.5 size 16 bold true text GLY191
> 2dlabels #2.13 size 16 bold true
> 2dlabels #2.3 size 16 bold true
> 2dlabels #2.11 size 16 bold true
> ui mousemode right translate
> ui mousemode right "move label"
> 2dlabels #2.8 xpos 0.579 ypos 0.137
> 2dlabels #2.7 xpos 0.558 ypos 0.262
> 2dlabels #2.10 xpos 0.415 ypos 0.508
> 2dlabels #2.9 xpos 0.557 ypos 0.550
> save binding_site.png width 1200 height 1200 supersample 3
> save binding_site.png width 800 height 800 supersample 3
> save binding_site.png width 1200 height 1200 supersample 3
> save binding_site.png width 2000 height 2000 supersample 3
> save binding_site.png width 500 height 500 supersample 3
> save binding_site.png width 1000 height 1000 supersample 3
> save binding_site.png width 1000 height 1000 supersample 5
> 2dlabels ASP88 size 16 bold true color green text ASP88
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels size 16 bold true color green text ASP88
> ui tool show "Color Actions"
> 2dlabels size 16 bold true color pale green text ASP88
> hide #2.15 models
> 2dlabels #2.16 size 16 bold true color pale green text ASP88 bgColor white
> 2dlabels #2.16 size 16 bold true color light green text ASP88 bgColor white
> 2dlabels #2.16 xpos 0.695 ypos 0.439
> 2dlabels #2.1 xpos 0.624 ypos 0.292
> 2dlabels #2.16 size 18 bold true color light green text ASP88 bgColor white
> 2dlabels #2.16 xpos 0.687 ypos 0.439
> 2dlabels #2.2 size 18 bold true color light green bgColor white
> 2dlabels #2.2 xpos 0.392 ypos 0.194
> 2dlabels #2.1 size 18 bold true color light green bgColor white
> 2dlabels #2.1 xpos 0.613 ypos 0.292
> 2dlabels #2.7 xpos 0.553 ypos 0.260
> 2dlabels #2.8 xpos 0.575 ypos 0.137
> save binding_site.png width 1000 height 1000 supersample 5
> graphics silhouettes color gray
> save binding_site.png supersample 5
> 2dlabels text P3 color cornflower blue size 16 bold true
> 2dlabels 2.17 text "P3" color cornflower blue size 16 bold true bgColor
> white
Expected 'all' or a 2d label name or a label models specifier or a keyword
> 2dlabels #2.17 text P3 color cornflower blue size 16 bold true bgColor white
> 2dlabels #2.17 xpos 0.533 ypos 0.658
> 2dlabels #2.17 text P3 color cornflower blue size 18 bold true bgColor white
> 2dlabels #2.17 text P3 color cornflower blue size 20 bold true bgColor white
> 2dlabels #2.17 xpos 0.530 ypos 0.654
> 2dlabels text P4 color cornflower blue size 20 bold true bgColor white
> 2dlabels #2.18 xpos 0.507 ypos 0.831
> save V:/projects/fusolisin/figures/fusolisin_figure.cxs
> select up
1 model selected
> select up
1 model selected
> save binding_site_new.png supersample 5
> save binding_site_new.png supersample 8
> save binding_site_new.png supersample 8 height 1400
> save V:/projects/fusolisin/figures/fusolisin_figure.cxs
——— End of log from Tue Jul 12 00:05:22 2022 ———
opened ChimeraX session
> clip back 5
[Repeated 1 time(s)]
> hide #!2 models
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> lighting full
> select /D:211
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /D:209
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /D:200
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:199
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:200
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:172
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /D:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select /D:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /D:209
19 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> select /D:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D:192
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select /D:165
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /D:165
15 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select /D:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /D:200
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add /D:199
12 atoms, 11 bonds, 2 residues, 2 models selected
> hide sel atoms
> select /D:209@CZ
1 atom, 1 residue, 1 model selected
> select add /D:211@CB
2 atoms, 2 residues, 2 models selected
> select add /D:165
9 atoms, 7 bonds, 3 residues, 2 models selected
> select add /D:192
14 atoms, 11 bonds, 4 residues, 2 models selected
> select up
38 atoms, 38 bonds, 4 residues, 2 models selected
> select up
311 atoms, 316 bonds, 42 residues, 2 models selected
> select down
38 atoms, 38 bonds, 4 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 38 atom styles
> select /D:258
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 9 atom styles
> select /D:165@N
1 atom, 1 residue, 1 model selected
> select /D:211@CA
1 atom, 1 residue, 1 model selected
> select add /D:165@N
2 atoms, 2 residues, 2 models selected
> select add /D:192@CB
3 atoms, 3 residues, 2 models selected
> select add /D:258@OE2
4 atoms, 4 residues, 2 models selected
> select add /D:209@CA
5 atoms, 5 residues, 2 models selected
> select up
47 atoms, 46 bonds, 5 residues, 2 models selected
> color sel byhetero
> select /D:187
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /D:188
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide sel atoms
> select /D:190
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 11 atom styles
> select /D:209@CA
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select /D:191
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> select /D:191
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:191
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> style sel ball
Changed 4 atom styles
> style sel sphere
Changed 4 atom styles
> select /D:211@CD2
1 atom, 1 residue, 1 model selected
> select add /D:165@CD
2 atoms, 2 residues, 2 models selected
> select add /D:190@CD2
3 atoms, 3 residues, 2 models selected
> select add /D:192@CA
4 atoms, 4 residues, 2 models selected
> select up
37 atoms, 37 bonds, 4 residues, 2 models selected
> style sel ball
Changed 37 atom styles
> select /D:258@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> style sel ball
Changed 9 atom styles
> name phobpocket #1/D:192,211,190,165
> select phobpocket
37 atoms, 37 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 37 atom styles
> name phobpocket #1/D:192,211,190,165, 258
> select phobpocket
46 atoms, 45 bonds, 5 residues, 1 model selected
> style sel sphere
Changed 46 atom styles
> select add /P:77@N
1 atom, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 2 bonds, 2 residues, 2 models selected
> hbonds sel
2 hydrogen bonds found
> hide sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
41 atoms, 40 bonds, 6 residues, 2 models selected
> select up
2638 atoms, 2689 bonds, 344 residues, 2 models selected
> select down
41 atoms, 40 bonds, 6 residues, 3 models selected
> select up
2638 atoms, 2689 bonds, 344 residues, 2 models selected
> select down
41 atoms, 40 bonds, 6 residues, 3 models selected
> hbonds sel
14 hydrogen bonds found
> color #1.4 #f9e559 models transparency 0
> select phobpocket
46 atoms, 45 bonds, 5 residues, 1 model selected
> style sel stick
Changed 46 atom styles
> style sel sphere
Changed 46 atom styles
> style sel ball
Changed 46 atom styles
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
11 atoms, 9 bonds, 2 residues, 2 models selected
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> select clear
> select phobpocket
46 atoms, 45 bonds, 5 residues, 1 model selected
> style sel stick
Changed 46 atom styles
> style sel sphere
Changed 46 atom styles
> save C:/Users/jvarg/Documents/huji/fusolisin/fusolisin_figure.cxs
——— End of log from Sat Jul 23 20:33:38 2022 ———
opened ChimeraX session
> clip front -5
[Repeated 3 time(s)]
> save 6mer_binding.png supersample 5 pixelSize 0.05
> clip front -5
> save 6mer_binding.png supersample 5 pixelSize 0.05
[Repeated 3 time(s)]
> save C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cx
No known data format for file suffix '.cx'
> save C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure.cxs
> save C:\Users\jvarg\Documents\huji\fusolisin\fusolisin_figure_surface.cxs
——— End of log from Sun Jul 24 00:35:18 2022 ———
opened ChimeraX session
> select /D:211@CE3
1 atom, 1 residue, 1 model selected
> select phobpocket
46 atoms, 45 bonds, 5 residues, 1 model selected
> hide sel atoms
> clip back -10
> clip back 20
[Repeated 2 time(s)]
> select #1/D
2597 atoms, 2649 bonds, 338 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> ui tool show "Color Actions"
> color sel light salmon
> color sel byhetero
> show sel surfaces
> coulombic sel
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.22, maximum 13.83
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting simple
> lighting shadows true
> lighting shadows false
> clip near 10
[Repeated 1 time(s)]
> clip near -10
> clip near 5
> clip near -5
[Repeated 1 time(s)]
> clip near -2
[Repeated 4 time(s)]
> clip near 1
> clip model #1/D true
> clip model #1/P false
> clip model #1 false
> clip model #1.1 true
> clip model #!1 false
> clip model #!1 true
> clip near -1
[Repeated 1 time(s)]
> mlp protein surfaces #1.1
Map values for surface "relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface": minimum -30.77, mean -6.378, maximum 21.71
Map values for surface "cap near": minimum -49.37, mean -9.307, maximum 41.72
> coulombic protein surfaces #1.1 offset 0
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -119.55, mean -2.01, maximum 27.46
Coulombic values for cap near #1.1.1: minimum, -2687.41, mean -0.60, maximum
9332.59
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> select #1/D
2597 atoms, 2649 bonds, 338 residues, 1 model selected
> coulombic sel
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.22, maximum 13.83
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic protein surfaces #1.1
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.46, maximum 4600.26
Coulombic values for cap near #1.1.1: minimum, -1218.72, mean 1.09, maximum
1147.31
> coulombic protein surfaces #1.1 offset 1
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -667.65, mean -1.52, maximum 297.80
Coulombic values for cap near #1.1.1: minimum, -7034.86, mean -0.94, maximum
3342.96
> coulombic protein surfaces #1.1 offset 10
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -73530.64, mean -0.56, maximum 13140.35
Coulombic values for cap near #1.1.1: minimum, -6824.58, mean -1.65, maximum
3156.92
> coulombic protein surfaces #1.1 offset 1.4
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.46, maximum 4600.26
Coulombic values for cap near #1.1.1: minimum, -1218.72, mean 1.09, maximum
1147.31
> color (#!1 & sel) white
> ui tool show "Color Actions"
> color sel white
> color sel yellow
> color sel white
> color zone #1.2.1 near protein distance 3 sharpEdges true update true
color zone: No surfaces specified.
> color zone #1.1 near protein distance 3 sharpEdges true update true
> coulombic protein surfaces #1.1
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.17, maximum 21139.05
Coulombic values for cap near #1.1.1: minimum, -1218.72, mean 0.97, maximum
1147.31
> coulombic sel
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -15.26, mean -1.23, maximum 13.83
To also show corresponding color key, enter the above coulombic command and
add key true
> color zone #1.1 near protein distance 3 sharpEdges true update true
> transparency #1.1 30
> color sel white target acpf
> color sel white
> color sel medium blue
> color sel white
> clip near 1
> clip near -2
> coulombic protein surfaces
Missing "surfaces" keyword's argument
> coulombic protein surfaces #/1.1
Invalid "surfaces" argument: invalid surfaces specifier
> coulombic protein surfaces #/1.1
Invalid "surfaces" argument: invalid surfaces specifier
> coulombic protein surfaces /1.1
Invalid "surfaces" argument: only initial part "/1" of atom specifier valid
> coulombic #1.1
> coulombic protein surfaces #1.1
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.17, maximum 21139.05
Coulombic values for cap near #1.1.1: minimum, -2887.66, mean -2.69, maximum
1017.62
> transparency #1.1 30
> transparency #1.1 50
> clip near -1
> coulombic protein surfaces #1.1
Coulombic values for relax_long_fusolisin_ISSQAS_0001_0078_top1.pdb_D SES
surface #1.1: minimum, -3348.00, mean -1.17, maximum 21139.05
Coulombic values for cap near #1.1.1: minimum, -3523.44, mean -3.76, maximum
548.46
> color sel white
> clip near -.01
> clip near -1
> clip near -10
> 10
Unknown command: 10
> clip near 10
> color sel white
> select #1/D
2597 atoms, 2649 bonds, 338 residues, 1 model selected
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1650, in
_update_graphics_if_needed
s[i].update_graphics_if_needed()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\structure.py", line 359, in update_graphics_if_needed
update()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 563, in update_selection
tmask = self._atom_triangle_mask(asel)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 351, in _atom_triangle_mask
logical_and(shown_vertices[t[:,0]], shown_vertices[t[:,1]], shown_triangles)
IndexError: index 196228 is out of bounds for axis 0 with size 195879
Error processing trigger "graphics update":
IndexError: index 196228 is out of bounds for axis 0 with size 195879
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molsurf.py", line 351, in _atom_triangle_mask
logical_and(shown_vertices[t[:,0]], shown_vertices[t[:,1]], shown_triangles)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9749
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20LS0015XS
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 8,437,047,296
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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 (4)
comment:1 by , 3 years ago
| Component: | Unassigned → Surface |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Update surface selection: index is out of bounds for axis |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
How should this be fixed? The code could return no vertex to atom map, this is what molecular surfaces that don't have sharp edges returns. In that case a selection of some atoms will not show the surface as selected. Or we could recompute the vertex to atom map for the new surface geometry. Gaussian surfaces don't associate atoms with vertices unless the surface is made with the sharp edges option. We also lose the association if atoms are deleted and the surface is not auto-updating (auto-updating is enabled by default). I'm a bit reluctant to handle this very rare case of color zone replacing the surface geometry with an auto-recomputation of the vertex to atom map.
comment:4 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Use no vertex to atom map if surface geometry was replaced by color zone. I tried recomputing the vertex to atom map but it gives a very jagged poor result after color zone with sharp edges.
Note:
See TracTickets
for help on using tickets.
The vertex to atom map for a molecular surface was somehow out of date. The surface vertices and triangles got updated creating a surface with more vertices but the vertex to atom map did not get updated. When the user selected chain D the code tried to map all surface vertices to their atoms so it could figure out the triangles to highlight for the selected atoms. But some surface vertex indices were too large for the vertex to atom map.
How did the surface geometry change without the vertex to atom map updating? It looks like it was from the "color zone" command with the "sharpEdges true" option, which changed the surface geometry. The MolecularSurface instance does not realize the geometry changed. I easily reproduced this error using color zone with sharp edges.