[Chimera-users] Planes feature in the Volume Viewer

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 5 20:00:16 PST 2008

Hi Jeff,
I believe plane numbering is by the grid index value, which starts  
from 0 along each axis for the full data set, at least in all the  
example data sets I checked.  You can see the grid index ranges for  
your current data set in the "Region bounds" section of Volume Viewer  
(show this section by checking the "Region bounds" box in the  
Features menu).
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 5, 2008, at 5:07 PM, William Jeffrey Triffo wrote:

> hi,
> when using the Planes tool in Volume Viewer, are the planes numbered
> from 0 or 1? I loaded a contour using the IMOD import, where I had  
> drawn
> the contour on slice 12 of a volume; however, it appears that the  
> plane
> that transects the contour in Chimera is '11' when using the Planes
> tool. I tried to test the enumeration by exceeding bounds (150 slices
> are in the volume, so was expecting an error for an entry of '150'  
> if it
> was enumerated from zero), but it appears that slice indices  
> outside the
> range of the loaded volume just default to the limit in either  
> direction
> (typing in '200' just sets it to the highest-enumerated slice).
> -- 
> -------------------------------------------------------------
> Jeff Triffo
> Auer Group, Donner Lab, Lawrence Berkeley National Laboratory
> Raphael Group, Bioengineering Department, Rice University
> Medical Scientist Training Program (MSTP), Baylor College of Medicine
> phone (Berkeley): 510-486-7940
> fax   (Berkeley): 510-486-6488

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