Allow angle command to specify 4 atoms defining two vectors

[a.rohou@…]

The following bug report has been submitted:
Platform:        macOS-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202311100228 (2023-11-10 02:28:59 UTC)
Description
Would be nice if the angle command can handle two vectors each specified by 2 atoms as produced by the measure rotation command.  Alexis Rohou asked about this on the mailing list.

Log:
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.8.dev202311100228 (2023-11-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1a0m format mmcif fromDatabase pdb

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #1  
---  
Chain | Description | UniProt  
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16  
  
Non-standard residues in 1a0m #1  
---  
NH2 — amino group  
  

> open 1a0m format mmcif fromDatabase pdb

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #2  
---  
Chain | Description | UniProt  
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16  
  
Non-standard residues in 1a0m #2  
---  
NH2 — amino group  
  

> open 1a0m format mmcif fromDatabase pdb

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #3  
---  
Chain | Description | UniProt  
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16  
  
Non-standard residues in 1a0m #3  
---  
NH2 — amino group  
  

> hide #1 models

> ui mousemode right "move picked models"

> view matrix models
> #2,0.9754,0.0088688,0.22027,-1.4601,0.010358,0.99624,-0.085978,0.54331,-0.22021,0.086144,0.97164,2.6281

> view matrix models
> #3,0.99924,-0.0074237,0.038152,-0.2029,-0.0047722,0.95073,0.30999,-1.7616,-0.038573,-0.30994,0.94997,3.5352

> measure rotation #1 toModel #2

Position of 1a0m #1 relative to 1a0m #2 coordinates:  
Matrix rotation and translation  
0.97539816 0.01035780 -0.22020704 1.99724537  
0.00886880 0.99624323 0.08614393 -0.75471730  
0.22027203 -0.08597760 0.97164195 -2.18527415  
Axis -0.36395769 -0.93141016 -0.00314857  
Axis point 10.92789172 -0.00000000 7.82074200  
Rotation angle (degrees) 13.67759194  
Shift along axis -0.01708096  
  

> measure rotation #1 toModel #3

Position of 1a0m #1 relative to 1a0m #3 coordinates:  
Matrix rotation and translation  
0.99924439 -0.00477223 -0.03857308 0.33070150  
-0.00742372 0.95072827 -0.30993650 2.76894441  
0.03815161 0.30998867 0.94997446 -2.80454632  
Axis 0.99241912 -0.12282619 -0.00424467  
Axis point 0.00000000 10.22663235 7.30814392  
Rotation angle (degrees) 18.19972295  
Shift along axis -0.00000000  
  

> angle #4,5

Must specify exactly 3 atoms/centroids or two measurable objects (e.g.
axes/planes)  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
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      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
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      System Firmware Version: 515.0.0.0.0
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      SMC Version (system): 2.41f2

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          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Tom Goddard]

From: Alexis Rohou via ChimeraX-users <chimerax-users@…>
Subject: [chimerax-users] measure rotation showAxis does not create a measurable object
Date: November 16, 2023 at 5:19:20 PM PST
To: ChimeraX Users Help <chimerax-users@…>
Reply-To: Alexis Rohou

Hello again,

I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.

Two of my axes are #4 and #5.

When I try to measure the angle with "angle #4 #5", I get the error:
"Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"

I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.

Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?

Cheers,
Alexis

[Tom Goddard]

Done.

Made angle command accept 3 or 4 atoms or centroids (although the centroids part has been broken since at least ChimeraX 1.6.1, ticket #10187, and needs fixing).

This allows measuring the angle between two rotation axes produced by the measure rotation command (e.g. for axes #3 and #4 use "angle #3,​4").

[Tom Goddard]

Added to 1.7 release candidates and daily builds.