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

[Mauricio Losilla]

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>
>
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