[chimerax-users] Distances in the 3D map - visualisation analysis

[Elaine Meng]

Hi Dmitry,
The ways to measure distances do not display arrows, although you can do that separately.

Measurement:

You can measure distances between pairs of atoms (or markers, effectively the same thing) or from an atom/marker to a surface.  That would require adding markers to the map, or at least one marker for the center, and possibly markers at the surface for precise control over the points used for measurement.  See Marker Placement and the "marker" command for the ways to place and move markers:
<https://rbvi.ucsf.edu/chimerax/docs/user/markers.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html>

The marker-marker distances can be added with the distance command, or Distances tool, or with the "mouse" etc. the same as for two atoms, see links in the "measurements" page.  These add a "distance monitor" pseudobond with distance label which you can show as dashed, but not with an arrowhead.
<https://rbvi.ucsf.edu/chimerax/docs/user/measurements.html>

The marker-surface distances can be measured with the tape-measure mouse mode
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure>

3D Arrows:

You can show 2D arrows with the "2dlabels" command, but not in 3D; the 2D arrows are for labeling figures.  To make 3D arrows you would either 
(1)  make a "bild" file (simple text format, file suffix .bild) describing the 3D shapes and then open it in ChimeraX.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#object>
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>
(2) use the "shape" command to add cones and cylinders that would form 3D arrows
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 29, 2021, at 3:09 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear colleagues, 
> I would like to measure the distances of within my 3D map - so I want to draw the arrows from the center of the map to the periphery in different directions and probably depth.
> (I want to have arrows and an length)
> Do you have any tips how to do that?
> Thank you
> Sincerely,
> Dmitry
> 
> 
> 
> 
> 
> 
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