[chimerax-users] Useful tools ideas/requests

[Elaine Meng]

Hi Shayne,
We're glad you like ChimeraX!

Currently there are no options for using different coloring of different box edges of the volume, or automatically generating a time stamp.

You could manually annotate with date/time using "2dlabels":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html>

For your mock coverslip, the throwaway volume  is a reasonable approach.  Another possibility is to draw a rectangle (flat, no thickness) such as for with "shape rectangle":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#rectangle>

And perhaps this is too much of a hassle, but perhaps you could draw very thin cylinders of the desired colors along box edges with "shape cylinder":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#cylinder>

If you just want to keep track of axes and it doesn't have to be shown on the box itself, you can show axes arrows by opening this BILD object file:
-------------- next part --------------
A non-text attachment was scrubbed...
Name: axes.bild
Type: application/octet-stream
Size: 117 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20221019/d70c93a5/attachment.obj>
-------------- next part --------------

Colors, sizes, coordinates, etc. can be edited.  See format description link below.  Creating a BILD file in a text-editor and then opening it in ChimeraX is another approach for generating 3D objects.  Unlike the "shape" command it does include a rectangular box. Unfortunately, however, these objects have problems with transparency rendering.
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>

And then there are other formats like COLLADA, VTK, ...
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#object>

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 19, 2022, at 12:01 PM, Shayne Quinn via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them.
> 
> 1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes?
>      For example box lines in x-blue, y-green and z-red to help keep orientation
>      (I have included a mock version in the attachment)
> 
> 2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. 
>      So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment.
> 
> 3) Is there a time stamp feature similar to the scale bar function that has already been implemented?
> 
> Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool!
> 
> Cheers,
> Shayne Quinn
> <Chimera Session.PNG>