[chimerax-users] Stack thickness question and cine playing?

[Elaine Meng]

Hi Jason!

With (1), I'm not sure what is happening... from the orthoplanes image you sent, one guess is that the 3 axes of the data are not along X,Y,Z and so a larger XYZ box is shown.  Or maybe the slices are placed too far apart, which may be defined (or misinterpreted from) the input files.  Or if you simply meant that the scale of the data is wrong, that can be reset with the "volume" command "voxelSize" option.  

I understand that this may be private data, but if there is example data you can share, it would help in defining and possibly solving this problem.  You could send it to just me rather than chimerax-users if that helps.

(2) If the data are recognized as a volume series, then the series can be played with a slider or the "vseries" command.  What kinds of data can be recognized and how to specify that are described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.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 Feb 25, 2022, at 9:16 AM, Rubenstein, Jason via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 
> Hi!  Two questions:
> 
> 	• This 3D dataset is only about 30 mm thick in the Z direction.  When ChimeraX is displaying it, it shows the thickness about 50x too thick.  Any way to adjust this?
> <image.png>
> 
> 	• this is a "4D" dataset, with 20 phases of 3D stacks.  Any way to "play" the cine?
> Thanks!
> 
> Jason Rubenstein, M.D.
> Codirector, Cardiac MRI
> Associate Professor, Medical College of Wisconsin