[chimerax-users] fine tuning depthcue

[Hunkeler, Moritz]

Hi Vincent,

the depthCue is in relation to your clipping planes, so you have to play with these values as well.

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html

“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). See also: clip”


By setting the clipping planes right at the ‘back’ and ‘front’ of you structure, you should get a very strong ‘fog gradient’ around the center with something like (if I understand your query correctly):

lighting depthcue true depthCueStart 0.45 depthCueEnd 0.5

Best,
Moritz


From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of vincent Chaptal via ChimeraX-users <ChimeraX-users at cgl.ucsf.edu>
Reply-To: vincent Chaptal <vincent.chaptal at ibcp.fr>
Date: Thursday, February 17, 2022 at 03:43
To: ChimeraX Users Help <ChimeraX-users at cgl.ucsf.edu>
Subject: [chimerax-users] fine tuning depthcue


        External Email - Use Caution
Hi,

I've been playing around a lot with depthcue-ing but I can't get it to do quite what I would like.

I want to display a protein structure, with a focus on one zone and a "heavy" depthcue to have a strong "fog" hiding much of the background (without deleting the residues in the back).

my script includes:
lighting full  #(sometimes I use soft too)
lighting shadows true intensity 0.3
lighting qualityOfShadows finer
lighting depthcue true depthCueStart 0.1 depthCueEnd 1.0


First, I have selected one residue and setting the rotation around it by using "cofr sel"

My max depthcue is with "depthCueStart 0.1 depthCueEnd 1.0". I've tried to change these numbers in many different ways, including negative or very large numbers) but I can't get it to be thicker.

Could you help me please. I missed the meaning of these values, so I'm blind on their use.
Thank you
Vincent
--


Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab



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