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
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@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
On Mon, 11 Mar 2019 10:21:23 -0700, Elaine Meng <meng@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! :) Kenward
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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
� In a completely rational society, the best of us would aspire to be _teachers_ and the rest of us would have to settle for something less, because passing civilization along from one generation to the next ought to be the highest honor and the highest responsibility anyone could have. - Lee Iacocca
Dear Elaine, thanks a lot for all this detailed explanation! Best regards Andrea ________________________________ Da: Elaine Meng <meng@cgl.ucsf.edu> Inviato: lunedì 11 marzo 2019 17:21 A: Acco . Cc: chimera-users@cgl.ucsf.edu Oggetto: "bring to front" selected residues 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@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
participants (3)
-
Acco . -
Elaine Meng -
Kenward Vaughan