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

[Elaine Meng]

Hi Mauricio,
I don't understand "the ability to superimpose the view of one chain" -- can you explain it in more words?  What is it that you want, that cannot be done currently?  Maybe it is already possible but I didn't explain it because I didn't realize that was what you wanted.

If you mean to make "cartoon style" work on just a chain instead of whole model, it may be unlikely since the settings it controls are per-model (not per-chain or per-residue).  However, it is already easy to split chains into separate models with "split."

Sorry if I am misunderstanding what you meant, however.
Elaine  
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 31, 2022, at 3:42 PM, Mauricio Losilla via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you very much for your prompt reply. Your workarounds were very helpful, I was able to tweak thickness and transparency, and arrived at a satisfactory display composition. Would you consider as a request feature the ability to superimpose the view of one chain?
> 
> Thank you!
> Mau
> 
> Mauricio Losilla, PhD
> Integrative Biology; and Ecology, Evolution, & Behavior
> Michigan State University
> he, him, his
> 
> 
> On Thu, Mar 31, 2022 at 11:43 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html*style__;Iw!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XapFhvyuc$ >
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44Xa-fKcbds$ >
> 
> 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://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html__;!!HXCxUKc!hKsk6lXSWeI6B9WmfXcRKCWrq70659PcqAPq2FBwdZzjDjOH6myV44XaI58NOwM$ >
> 
> 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>