Hi Sergio,

  As Elaine points out when you open the first atomic model in a ChimeraX session it sets "default" lighting with includes depth cue on.  It does this as part of "auto-styling" where it sets how a molecule is initially displayed (ribbons, sticks, spheres, which atoms, ...).  It enables "default" lighting when you open what it considers a small polymer, less than 5 chains and 200,000 atoms.  Larger atomic models use full or soft lighting which does not enable depth cue.

  We don't have any good way to tell ChimeraX to redefine what it considers "default" lighting.  But you could add a line to the ChimeraX Python code for the "lighting" command in your installation that would do that.  On a Mac the file you would change is

ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax/std_commands/lighting.py

and you would see lines

    if preset == 'default' or preset == 'simple':
        lp.shadows = False
        lp.multishadow = 0
        sil.depth_jump = 0.03
        lp.set_default_parameters(v.background_color)

and you would add one line to that keeping the indentation

    if preset == 'default' or preset == 'simple':
        lp.shadows = False
        lp.multishadow = 0
        sil.depth_jump = 0.03
        lp.set_default_parameters(v.background_color)
lp.depth_cue = False

Then the ChimeraX default lighting command will always have depth cue off.  Of course if you install a new ChimeraX you would have to change it again.

  When I try turning on and off depth cue in situations without clip planes it has such a minor effect I am surprised you even notice.  When do you find depth cueing problematic?

Tom

On Sep 19, 2024, at 6:11 AM, Sergio Pipaón Alcíbar via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello!!

My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs:

1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session.

2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following:

graphics silhouettes true
lighting soft
lighting shadows true
lighting depthCue false
~cofr

And these do not seem to run. Definitely not the lighting depthCue false.

Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false.

Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback.

I am currently running ChimeraX-1.8-rc2024.05.10.

Thank you guys!!

Sergio.

-- 
Sergio Pipaón Alcíbar (PhD Student)
Dept. of Macromolecular Structures, lab. S0 / Ext: 5347
National Center for Biotechnology (CNB - CSIC)
C/ Darwin, 3 28049, Cantoblanco-Madrid
email: spipaon@cnb.csic.es

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