[chimerax-users] display options for model with 2 chains

[Elaine Meng]

Hi Mauricio,
Some ideas are to:

- make the gray ribbon transparent
and/or
- make the purple one thicker

I can't tell from your question whether they are in two separate models or not.  Even if they're together in one PDB file they can be defined as separate models (as is done for NMR ensembles, e.g. PDB 1kfp).  If the purple one is model #1 and the gray one is #2, could be something like:

cartoon style #1 width 1 thick 1 xsect round
transparency #2 50 targ r

...of course, you could use different width/thickness and transparency values.  

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>

The cartoon style command works on whole models, so you would need them to be in separate models for that approach.  If your current PDB file does not have them in separate models, you could either text-edit it to add MODEL and ENDMDL records, or (probably easier) use the "split" command after opening it.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.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 Mar 31, 2022, at 10:02 AM, Mauricio Losilla via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
> <ideal_display.png><chimerax.png>