RFE: option to always draw a specific model on top

[Elaine Meng]

Mauricio Losilla would like an option to draw a specific model on top, as per these earlier messages on chimerax-users:

<​https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-March/003537.html>
Hi,
I am new to ChimeraX, thank you for making this great software available.

I loaded a pdb file that has 2 amino acid chains aligned (chimerax.png).
These chains are a model (gray) and template (purple).

As you can see, the two chains look weaved or blended. I would much prefer
to display the uninterrupted template around to model, to visually
represent their fit. Is there a way to do this?

I am attaching a second image (ideal_display.png, generated elsewhere) with
the visual outcome I am after (the purple chain is the template, the
rainbow-colored chain is the model).

Thank you
*Mauricio Losilla, PhD*
Integrative Biology; and Ecology, Evolution, & Behavior
Michigan State University
he, him, his

... my first answer suggesting making one transparent and the other one fatter:
<​https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-March/003538.html>

...and subsequent request and further clarification from Mauricio
<​https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-March/003541.html>

From: Mauricio Losilla via ChimeraX-users <chimerax-users@…>
Subject: Re: [chimerax-users] display options for model with 2 chains
Date: April 1, 2022 at 8:17:42 AM PDT
To: ChimeraX Users Help <chimerax-users@…>
Reply-To: Mauricio Losilla <losillam@…>

Hi Elaine,

I am sorry, I didn't explain myself well, I will try to do it here. I was able to use all your tips successfully: I split the chain in two models, and tweaked the thickness, width, and transparency at will. It worked great! I am attaching the result [result.png]. I think it accomplishes my original goal fairly well: to visually represent the fit of the gray protein to the purple template.

However, the purple chain still looks sewed into the gray chain. In the image, this is better seen in the horizontal beta sheets at the center. The ideal display I was after is that of the image with the rainbow-colored chain and the purple template I sent in my original email. There, the purple chain always looks "on top" of the rainbow chain. That is what I meant yesterday with "the ability to superimpose the view of one chain".

In case it is helpful, the reference image and the PDB file came from I-TASSER.

I am new to ChimeraX (and to 3D shapes of molecules in general), so I apologize if I am not making much sense.

Thank you!

[Elaine Meng]

Now that I look carefully at ideal_display.png I see that it also is "threaded" in some places. However, it is a lot less noticeable because the rainbow ribbon is paper thin, what we called "flat" ribbon in Chimera. ChimeraX does not have this ribbon style option, although you can approximate it by making the thickness of the ribbon very small instead of the default 0.4 Angstroms.

[Tom Goddard]

Drawing one model entirely on top of another would not achieve the desired look since the on-top model would appear to cross in front of other parts of the not-on-top model in a paradoxical way like an Escher drawing. So I don't think this is what Mauricio needed. Instead the issue was different smoothing of beta-strands and coils in ribbons.

[Tom Goddard]

Seems the problem here was that Mauricio did not know that beta strand ribbons were smoothed while coils were not smoothed. Told him about this and the smoothing controls using the cartoon command. And he used transparency of the ribbon to show the superimposed coil. Does not appear anything else is needed.