When you have not moved the front and back clipping planes they are positioned in front and behind all the displayed models.  The front and back clip planes are usually not at the very front-most and back-most atom.  Here is how they are computed.  Each model has a rectangular bounding box which just touches the atom rendering at the x,y,z edges.  All those displayed model boxes are combined into one box that contains them all.  The center of that box plus or minus one box radius (= radius of sphere containing the box) is where the front and back clip planes are positioned when the clip planes have not been manually moved.  These rules for determining the front and back positions mean that usually there is a good bit of empty space between the front/back clip planes and the actual models since the molecules are not rectangular in shape and even if they were a sphere bounding the rectangular box is used to position the front/back planes (so that viewing from different directions does not move the clip plane in and out).

	Tom


On Nov 7, 2025, at 10:16 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

As it says exactly in the text that you sent, the start and end values are expressed as a position relative to the front and back global clipping planes (also called near and far clipping planes), where front is 0.0 and back is 1.0.

Maybe you didn't know what the clipping planes are. The near and far clipping planes are the vertical bars shown in the Side View.  They clip (slice away) parts of the view.  See the Side View help:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html>

0.2 is 20% of the distance between the near clipping plane and far clipping plane. 

I hope this helps,
Elaine
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 7, 2025, at 1:08 AM, Vincent CHAPTAL <vincent.chaptal@cnrs.fr> wrote:

Hi Elaine, 

following what you wrote, could be more precise on the meanings of start and end: 
Manual: 
depthCueStart  start
depthCueEnd  end
Set the position of the depth-cueing ramp. Depth-cueing shading increases linearly from start to end, each expressed as a position relative to the front (0.0) and back (1.0) global clipping planes (0.5 to 1.0 in simple lighting).

- What is the start really? Is it where the viewer/user seats on his chair? Because if I use your command I get a certain depthcue, but if I zoom on the structure and use the same command it doesn't change the depthcue. 
- Is 0.2 the relative start of the PDB file? 
- Where does it end? 
- is it related to the Side view bars? 

Thanks for these clarifications. 
Vincent

Le 07/11/2025 à 02:08, Elaine Meng via ChimeraX-users a écrit :
lighting depthCue true depthCueStart 0.2 depthCueEnd 0.8

-- 
Vincent Chaptal, PhD
CNRS research director
Team leader Drug Resistance and Membrane Proteins Lab

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