Selection suggestions

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-05)
Description
Hi,

Suggestion:

Would it be possible to add a "Previous/Next selection" pair of menu items to the "Select" menu? It would be very useful to be able to step through the selection history - particularly if one has just made a complicated atom selection in the GUI and then accidentally scrubbed it by selecting something else.

Another idea is to automatically save selection/color pairs - so if I color a particular selection a named color (e.g. "color sel cornflower blue"), that color/selection pair is auto-saved somewhere so I can easily adjust the color later. Maybe a panel similar in style to the model panel, but for selections, with color wells and selection checkboxes? Not sure if that is workable but it would certainly be handy...

Cheers
Oli

Log:
UCSF ChimeraX version: 0.9 (2019-06-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1bl8 format mmCIF fromDatabase pdb

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> close all

> open /Users/oliverclarke/Dropbox/Downloads/model_moved.pdb_modified.pdb

Summary of feedback from opening
/Users/oliverclarke/Dropbox/Downloads/model_moved.pdb_modified.pdb  
---  
warnings | Duplicate atom serial number found: 819  
Duplicate atom serial number found: 820  
Duplicate atom serial number found: 821  
Duplicate atom serial number found: 822  
Duplicate atom serial number found: 823  
103573 messages similar to the above omitted  
  
Chain information for model_moved.pdb_modified.pdb #1  
---  
Chain | Description  
A B G I | No description available  
F | No description available  
H J O | No description available  
  

> close all

> open
/Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb

Chain information for
last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #1  
---  
Chain | Description  
A B G I | No description available  
C D E K | No description available  
F H J O | No description available  
  

> ribbon

> ~display

> color "dim gray"

> camera ortho

Expected some numbers or a keyword  

Expected some numbers or a keyword  

> help cofr

> cofr centerOfView showPivot true

> cofr centerOfView showPivot false

Expected a keyword  

Expected a keyword  

> cofr centerOfView showPivot 10,1

> cofr centerOfView showPivot 10,0.1

> cofr centerOfView showPivot 10,0.5

> cofr centerOfView showPivot 5,0.3

> help alias

> alias crosshairs cofr centerofview showpivot 10,0.3

> crosshairs

> alias crosshairs_on cofr centerofview showpivot 10,0.3

> alias crosshairs_off cofr centerofview showpivot false

> crosshairs_off

> crosshairs_on

> crosshairs_off

> help sel

> help color

> open /Users/oliverclarke/Dropbox/best_new_4cmc_combined_4.2_filter.mrc

Opened best_new_4cmc_combined_4.2_filter.mrc, grid size 512,512,512, pixel
1.06, shown at level 0.0146, step 2, values float32  

> lighting soft

Expected an objects specifier or a keyword  

Expected an objects specifier or a keyword  

Expected an objects specifier or a keyword  

> select :1-3610&/B

26110 atoms, 26703 bonds, 13 pseudobonds, 1 model selected  

> color sel "cornflower blue"

> select up

26162 atoms, 26757 bonds, 13 pseudobonds, 1 model selected  

> select clear

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

Expected an objects specifier or a keyword  

Expected an objects specifier or a keyword  

Expected an objects specifier or a keyword  

> select :3639-end&/B

8783 atoms, 8975 bonds, 10 pseudobonds, 2 models selected  

> color sel "forest green"

> select clear

> select :4300-end&/B

3863 atoms, 3973 bonds, 6 pseudobonds, 2 models selected  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel orange

> select :4957-end&/B

755 atoms, 779 bonds, 5 pseudobonds, 1 model selected  

> color sel firebrick

> select clear

> select clear

> select /O:105

8 atoms, 7 bonds selected  

> select /O:104

8 atoms, 7 bonds selected  

> select up

33 atoms, 32 bonds selected  

> select up

815 atoms, 831 bonds selected  

> select clear

> help color

> select /O:65

9 atoms, 8 bonds selected  

> select up

65 atoms, 65 bonds selected  

> select up

815 atoms, 831 bonds selected  

> select /O:64

5 atoms, 4 bonds selected  

> select up

65 atoms, 65 bonds selected  

> select up

815 atoms, 831 bonds selected  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel gold

> select clear

> select clear

> select /D:30

9 atoms, 8 bonds selected  

> select up

76 atoms, 75 bonds selected  

> select up

1161 atoms, 1169 bonds selected  

> color sel "medium purple"

> select up

148348 atoms, 151612 bonds selected  

> select clear

> select up

Nothing selected  

> select up

Nothing selected  

> select :3911-3938&/B

242 atoms, 248 bonds selected  

> select :3611-3638&/B

218 atoms, 223 bonds, 1 pseudobond, 1 model selected  

> color sel cyan

> select clear

> select protein

148072 atoms, 151348 bonds, 68 pseudobonds, 1 model selected  

> color zone #2 near protein distance 20

> hide #!1 models

> lighting soft

> surface dust #2 size 5

> surface dust #2 size 10

> show #!1 models

> select clear

> select /D:122

8 atoms, 7 bonds selected  

> select up

91 atoms, 90 bonds selected  

> select up

1161 atoms, 1169 bonds selected  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel gold

> select /O:64

5 atoms, 4 bonds selected  

> select up

65 atoms, 65 bonds selected  

> select up

815 atoms, 831 bonds selected  

> color sel "dark magenta"

> select /B:3628

11 atoms, 10 bonds selected  

> select /B:3633

7 atoms, 6 bonds selected  

> select up

74 atoms, 74 bonds selected  

> select up

35111 atoms, 35903 bonds selected  

> select /B:3632

7 atoms, 6 bonds selected  

> select up

74 atoms, 74 bonds selected  

> select up

35111 atoms, 35903 bonds selected  

> select down

74 atoms, 74 bonds selected  

> select /B:3638

8 atoms, 7 bonds selected  

Unknown command: selbetween  

> select :3611-3638&/B

218 atoms, 223 bonds, 1 pseudobond, 1 model selected  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel gold

> select /D:30

9 atoms, 8 bonds selected  

> select up

76 atoms, 75 bonds selected  

> select up

1161 atoms, 1169 bonds selected  

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel "dark cyan"

> color sel cyan

> select clear

> hide #!1 models

> color zone #2 near protein distance 20

> show #!1 models

> hide #!2 models

> select #1

148348 atoms, 151612 bonds, 160 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Hi Oliver,

Generically setting (or unsetting) a selection state in ChimeraX is considerably more difficult than Chimera, due to the fact that there was a limited set of kinds of things in Chimera that could be selected, whereas in ChimeraX a bundle can define a new model type with its own graphics and its own selection possibilities. Therefore, instead of putting entries in the Selection menu for Undo/Redo, I rely on the Edit menu's Undo/Redo for at least remedying selection booboos like you describe.
As you can imagine, this also makes auto-magical saving of used selections unlikely. Besides, if you care about a selection state, you should name it with "name frozen sel some-mnemonic-name". This will allow you to use it by name in commands later and make it appear in the "Named Selections" section of the Selection menu. It will also be saved in sessions, and can be listed with "name list".

--Eric