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Opened 3 years ago
Last modified 3 years ago
#7325 closed defect
Update surface selection: index is out of bounds for axis — at Version 1
| 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 (1)
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 |
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