Volume compressed to single plane

[zackg@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-02-27)
Description
Load a volume and display as "volume".  Apparently voxels now have no thickness so there is exactly one plane where the object will disappear.

This seems to be happening on all my datasets so I am attaching a video file showing the phenomenon.
If you have trouble reproducing it then contact me and I will send you an actual dataset I used.

Cheers,

Zack

Log:
UCSF ChimeraX version: 0.9 (2019-02-27)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/ParticleBase/IDPs/IDP L2071 CL17/Particle 3/20180613 - TitanX
- L2071 Clu17 Particle 3 grid A4/Stack 8 - EDS Tomo triple GEMS aka other
GEMS/Element Stacks Reconstructed/RGBs/HAADF.cxs"

opened ChimeraX session  

> view cofr false

> view orient cofr false

> view cofr false

> view orient cofr false

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Zack/Desktop/movie1.mp4

Movie saved to /Users/Zack/Desktop/movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/Zack/Desktop/movie2.mp4

Movie saved to /Users/Zack/Desktop/movie2.mp4  
  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon R9 M395 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: movie.mp4

movie.mp4​

[zackg@…]

Added by email2trac

[Eric Pettersen]

Reported by Zack Gainsforth

[Tom Goddard]

The data looks relatively smooth and I think it would look much better as a contour surface, choosing "Surface" from the menu over the histogram to use that style.

If you really want volumetric style rendering which is what the "Volume" style shows, ie. a semi-transparent grayscale rendering then there are a bunch of options it is useful understand. Look at the ChimeraX volume command "solid" style display options

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid

It is displaying correctly in your movie -- rendered as a stack of semitransparent planes. When viewed edge-on you see the edge of those planes. That is using projection mode 2d-z. You can instead use a stack of planes perpendicular to your view direction using command "volume #1 projectionMode 3d".

For tomography which can be pretty noisy and have features at different intensities you may want this volumetric style, but again, the movie you showed looks like it really should be rendered as a surface. Volumetric style does not do the lighting and shadowing that makes surfaces look much better.

[zackg@…]

Hi,

Ah OK, this was very helpful!

So, not a bug, but a user learning curve.

BTW, ChimeraX is really great, but you know that.  ;-)

Cheers,

Zack