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

Kenward Vaughan kenward at kvaughan.family
Mon Mar 11 15:57:45 PDT 2019

On Mon, 11 Mar 2019 10:21:23 -0700, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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

Hi Andrea!

Another way to approach this would be to simply use Focus on the selected atoms/residues (Actions > Focus).  If you play with the fore- and background cutoff planes under "Side view" (Favorites > Side view -- play with the vertical red lines) you may get the right amount of fading and foreground clipping to get a feeling similar to what you are seeking.  

Changing the background from black to white can also change one's perception!  :)


> 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
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