[Chimera-users] "bring to front" selected residues

[Elaine Meng]

Hi Andrea,
There is nothing exactly like what you describe.  Some possibilities are:

(1) hide all atoms except for the residues you are interested in
and/or
(2) make the rest of the structure transparent, with only the residues you are interested in as nontransparent

See for example the image tutorials:
Glycoside Hydrolases
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html>
Similar Binding Sites
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html>

See also the “getting started” tutorials:
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html>

The details depend on what items you are showing: atoms/bonds, ribbons, and/or molecular surfaces, and whether you have multiple models open or just one model.  A common situation is that you have just one model and it is shown as ribbons with some of the atoms/bonds also shown.

For (1) you could
(a) with nothing selected, use menu: Actions… Atoms/Bonds… hide
(b) select residue(s) of interest.  Thre are several ways to select, see
<http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/selection.html>
(c) use menu: Actions… Atoms/Bonds… show 
This could also all be done with commands, e.g. show the Command Line from the Favorites menu, enter:
~display
show :15.A,28-30.A
 (… that would show residues 15 and 28-30 of chain A)

For (2) it depends on what you want to make transparent: atoms, ribbons, and/or surfaces.  If you have your residues of interest selected, you could
(a) invert the selection so that they are now unselected and everything else is selected (for example, using one of the “invert” options in the Select menu).   
(b) use  the “transparency” command on the selection, for example: transparency 70,a,r,s sel
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
...the “a” “r” and “s” are for atoms, ribbons, molecular surfaces, respectively. You can use only the letters for what you want to make transparent.

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 11, 2019, at 1:54 AM, Acco . <scarsoacco at hotmail.com> wrote:
> 
> Hello,
> I am a beginner with Chimera and I am looking for how to "bring to front" the residues that I have selected displaying the remaining structure of the protein in kind of blurred view. Is it possible to do this?
> Thank you in advance for your help
> Sincerely,
> Andrea