[chimerax-users] Access to git repository

[Tom Goddard]

Hi Ilhan,

  The ChimeraX source code for map outline boxes is Python and is in the ChimeraX distribution.

	on Windows: chimerax/bin/Lib/site-packages/chimerax/map/volume.py
	on macOS: ChimeraX.app/Contents/lib/python3.7/site-packages/chimerax/map/volume.py
	on Linux: chimerax/lib/python3.7/site-packages/chimerax/map/volume.py

A trick to display an outline box mesh is make a copy of your map (one time point, "save grid.mrc model #1.1") and open it, display mesh style and set the threshold level to less than the lowest value in the map.  Here's what I see for some lightsheet microscopy of an immune cell.  Ugly, mesh has triangles.  But also having a whole box of mesh lines looks busy.



So I made a single plane with ChimeraX command "shape rectangle", positioned it over the microscopy with move selected mouse mode, and showed it as mesh style with "surface style #3 mesh".  Still has the ugly diagonal lines.



So I wrote some Python to hide the diagonals.  I put this on the ChimeraX recipes web site as an example.

	https://rbvi.github.io/chimerax-recipes/hide_diagonals/hide_diagonals.html <https://rbvi.github.io/chimerax-recipes/hide_diagonals/hide_diagonals.html>

and I will try to put it into the ChimeraX distribution today as the "surface squaremesh" command.



This last view I used "camera ortho" to get orthographic projection.  The standard ChimeraX camera mode is perspective projection and makes this closer look bigger which is not good if you want to measure distances.

You could also possibly use "shape rectangle" to make a scale bar.

If you still want access to the ChimeraX GitHub repository, send me your github user name and I can add you.

	Tom

> On Oct 19, 2020, at 4:00 AM, Tomris, I. (Ilhan) <i.tomris at uu.nl> wrote:
> 
> Dear sir/madam,
> 
> At the moment I am utitilizing ChimeraX to render 3D images of lightsheet data I have obtained (see attachment of 3D render). It is a pretty nice software package, although there is something I would like to implement into chimerax. A bounding box/outline box with gridpoints on it to indicate the size of the rendered volume, additionally I would also like to implement a scalebar of some sort. Hence I was wondering whether I could get access to the git repository so I could attempt to use the "Outline box" already present and put grid points on it?
> 
> <image.png> 
> Kind regards,
> 
> Ilhan
> <chimerax render.mp4>_______________________________________________
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