[Chimera-users] Depth-cued view

[Elaine Meng]

Hi Thiru,
It is much simpler to just use depth-cueing that automatically fades front to back, than to try to change the objects themselves.  With depth cueing, objects will automatically be darker in back when you are on a dark background, or they will fade into a white "mist" when you are using a white background.  Depth cueing is already turned on by default, but you can adjust parameters to make the effect stronger using the Effects tool (menu: Tools... Viewing Controls... Effects), and/or by moving the front and back clipping planes in the Side View tool (menu: Favorites... Side View).  The Effects tool is also a tab on the same dialog as the Side View.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#sideview>

The only reason to try to change the transparency for each layer of the structure is if you wanted to turn it sideways so that the gradient is in some other direction than front-to-back.  However, it could be difficult and tedious because you need to have some way ot specifying each layer of your structure.  So it depends on whether you know the model numbers, residue numbers, and/or atom names that could be used to uniquely specify each layer of atoms, and then write several "transparency" commands containing those specifications, one "transparency" command for each set of atoms to which you want to give a different transparency value.  You could also select the atoms by hand with Shift-Ctrl-click (and maybe up-arrow depending on if they are in residues) and then use "sel" to specify the atoms in the command, but it looks like there are many atoms per layer and that would probably also be difficult.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.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 23, 2022, at 7:31 AM, Thirumurugan Prakasam via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> I need to make some stacked COF with stacked view with descending order transparency as shown below within the same molecule 
> <image.png>
> 
> from a stacked view
> <image.png>
> Please let me know how I can select each 2D layer and decrease the transparency while going down. Please help me to make some nice images.
> Looking forward to hearing from you,
> Many thanks,
> Thiru