[chimerax-users] Transparency for atoms selected only

[Elaine Meng]

Hi Gabriele,
You're welcome!

In the "Usage" lines in the command help pages, where it says "spec" or "atom-spec" is where you put the specifier of which atoms, residues, models to act upon.

Usually "spec" or "atom-spec" is a link that goes to this page explaining the many ways to specify, including the word "sel" which means the current selection:

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

Best,
Elaine

> On Nov 20, 2020, at 6:58 PM, Gabriele Cerutti <gc2695 at columbia.edu> wrote:
> 
> 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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