Solo blobs

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-18)
Description
Hi,

I love the new Measure and Color blobs tool! One suggestion - would it be possible to add an option to unshow the rest of the map, and just show that blob? Or to create a new surface model from that blob? This would be useful when showing for example ligand density in the context of a structure.

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> alias crosshairs_on log text crosshairs_on: displays crosshairs at center of
rotation and places cofr at center of view; cofr centerofview showpivot 5,0.2

> alias crosshairs_off cofr centerofview showpivot false

> alias cootmode volume style mesh step 1 squaremesh false meshlighting true
twosidedlighting false capfaces false; surface cap false; size stickradius
0.05; ~rib; disp; color gold target a; color byhet; lighting flat; lighting
depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set subdivision 1;
crosshairs_on; color #3333851effff target s; style stick; set bgcolor black

> alias cootmode_white volume style mesh step 1 squaremesh false meshlighting
true twosidedlighting false capfaces false; surface cap false; size
stickradius 0.05; ~rib; disp; color orange target a; color byhet; lighting
flat; lighting depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set
subdivision 1; crosshairs_on; color #00000000cccc target s; style stick; set
bgcolor white

> alias carve surface zone #* nearatoms sel distance $1 maxcomponents 1

> alias uncarve surface unzone #*

> alias focus view cofr false

> alias saturation_down color modify $1 saturation - 10

> alias saturation_up color modify $1 saturation + 10

> alias lightness_up color modify $1 lightness + 5

> alias lightness_down color modify $1 lightness - 5

> alias hue_up color modify $1 hue + 5

> alias hue_down color modify $1 hue - 5

> alias symclip clip near -$1 far $1 position cofr

> alias section clip near $1 far $1

UCSF ChimeraX version: 0.91 (2019-06-18)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/oliverclarke/Desktop/test4.cxs

opened ChimeraX session  

> crosshairs_on

crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  

> section 1

> section 1

> section 1

> section 1

> section -1

> section -1

> section -1

> section -1

> section -1

> select up

2 atoms, 1 bond, 1 model selected  

> select up

6 atoms, 5 bonds, 1 model selected  

> select up

38 atoms, 37 bonds, 1 model selected  

> select up

1161 atoms, 1169 bonds, 1 model selected  

> select up

148348 atoms, 151612 bonds, 1 model selected  

> select up

148348 atoms, 151612 bonds, 3 models selected  

> select up

148348 atoms, 151612 bonds, 3 models selected  

> select up

148348 atoms, 151612 bonds, 3 models selected  

> select down

148348 atoms, 151612 bonds, 1 model selected  

> select down

1161 atoms, 1169 bonds, 1 model selected  

> select down

38 atoms, 37 bonds, 1 model selected  

> select down

6 atoms, 5 bonds, 1 model selected  

> select down

2 atoms, 1 bond, 1 model selected  

> select down

1 bond, 1 model selected  

> select up

2 atoms, 1 bond, 1 model selected  

> select /I:805@N

1 atom, 1 model selected  

> crosshairs_on

crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  

> section -10

> section -10

> section -10

> focus

> symclip 10

> focus

> rainbow chains

> hide #!2 models

> symclip 20

> show #!2 models

> symclip 4

> focus

> symclip 10

> symclip 100

> ui mousemode rightMode "pick blobs"

> measure blob #!2.1 triangleNumber 659486 color #0000ccff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 560.19  
area = 979.72  
size = 44.819 14.785 12.425  
  

> measure blob #!2.1 triangleNumber 660376 color #2e5de9ff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 560.19  
area = 979.72  
size = 44.819 14.785 12.425  
  

> measure blob #!2.1 triangleNumber 660376 color #8f86a3ff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 560.19  
area = 979.72  
size = 44.819 14.785 12.425  
  

> measure blob #!2.1 triangleNumber 660376 color #972ec8ff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 560.19  
area = 979.72  
size = 44.819 14.785 12.425  
  

> measure blob #!2.1 triangleNumber 660376 color #236fe3ff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 560.19  
area = 979.72  
size = 44.819 14.785 12.425  
  

> measure blob #!2.1 triangleNumber 660376 color #08e968ff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 560.19  
area = 979.72  
size = 44.819 14.785 12.425  
  

> hide #!2.2 models

> hide #!2.3 models

> hide #!2.4 models

> hide #!2.5 models

> hide #!2.6 models

> hide #!2.7 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> measure blob #!2.1 triangleNumber 138095 color #d8841bff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 752.03  
area = 1173.2  
size = 40.009 14.134 12.121  
  

> measure blob #!2.1 triangleNumber 195267 color #8cd31cff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 60.835  
area = 100.5  
size = 8.8515 7.133 2.5093  
  

> measure blob #!2.1 triangleNumber 130370 color #831dd9ff outline true

Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob:  
volume = 3184.4  
area = 5100.3  
size = 83.011 31.912 26.701  
  

> select #2

3 models selected  

> select clear




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

[Tom Goddard]

It would be nice to be able to select a blob, ie part of a surface. Then you could run any commands on it you wanted, like copy it to a new model, hide the unselected part of the surface, color the selected part. But currently ChimeraX does not allow selecting of parts of surfaces. It is certainly possible, but could introduce complexity into the code. The measure and color blobs tool is a kind of hack way around the inability to select part of a surface, with the obvious limitation that you can't do everything you want with the blob.

I'm inclined not to add a ability to copy a blob to a new surface, because those rarely used features clutter the interface and reduce the overall usability of the tool. So it is the kind of feature I'd like to be able to add via a command. But since selecting a blob is not possible a command can't specify the blob. Maybe I can still add it to the command. The "measure blob" command that runs when you use the mouse mode (you will see it in the log) refers to the blob by specifying the number of one of its triangles. So it would be possible to click the blob, then run another "measure blob" command or maybe "surface copyblob #5 triangle 41287" to make the copy.

This needs some more thought.

[Tom Goddard]

Alexis Rohou is also interested in having a separate surface for a blob.

​http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2020-May/001137.html

[Tom Goddard]

Maybe worth adding a "copy blob" checkbutton option to the Pick Blobs gui that would make a new surface model from each blob when it is picked.