[chimerax-users] Transparency for atoms selected only

[Gabriele Cerutti]

Hi Elaine,
That's exactly what I needed:

transparency sel 70 target a

I was not able to put the "sel" specifier in the right place, and I had a
hard time trying to find the solution in the documentation.
Thanks for your prompt response!
Best,

Gabriele


On Fri, Nov 20, 2020 at 7:12 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Gabriele,
> It would be useful to give more detail on what exactly you tried and what
> you want. I don't know if you were using the menu, or the "color" command,
> or the "transparency" command and whether you mean the atomic
> representation (sticks, balls, ...), ribbons, and/or molecular surface.
>
> However, here is an example of changing the transparency of the atomic
> representation of selected atoms only, using the transparency command and a
> value of 70%.  Example commands:
>
> open 2gbp
> select ligand
> transparency sel 70 target a
>
> You can use command "help transparency" to show the help page for the
> command:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>
>
> In commands, you use "sel" to mean the selected atoms.  See:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
>
> The Actions menu automatically applies to the selected parts, but it does
> not have an option for changing transparency of atomic representations.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Nov 20, 2020, at 4:02 PM, Gabriele Cerutti <gc2695 at columbia.edu>
> wrote:
> >
> > Hello,
> > I am trying to display transparency only for selected residues in my
> protein model but I am having a hard time trying to restrict the
> transparency only to the selected set of atoms (it sets the transparency to
> all residues).
> > Do you have any suggestions and/or examples about this?
> > Thanks,
> > Gabriele
>
>
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