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Dear Elaine,</div>
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thanks a lot for all this detailed explanation!</div>
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Best regards</div>
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Andrea</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>Da:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Inviato:</b> lunedì 11 marzo 2019 17:21<br>
<b>A:</b> Acco .<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Oggetto:</b> "bring to front" selected residues</font>
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<div class="PlainText">Hi Andrea,<br>
There is nothing exactly like what you describe. Some possibilities are:<br>
<br>
(1) hide all atoms except for the residues you are interested in<br>
and/or<br>
(2) make the rest of the structure transparent, with only the residues you are interested in as nontransparent<br>
<br>
See for example the image tutorials:<br>
Glycoside Hydrolases<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html</a>><br>
Similar Binding Sites<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html</a>><br>
<br>
See also the “getting started” tutorials:<br>
<<a href="http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html">http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html</a>><br>
<<a href="http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html">http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html</a>><br>
<br>
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.<br>
<br>
For (1) you could<br>
(a) with nothing selected, use menu: Actions… Atoms/Bonds… hide<br>
(b) select residue(s) of interest. Thre are several ways to select, see<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/selection.html">http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/selection.html</a>><br>
(c) use menu: Actions… Atoms/Bonds… show <br>
This could also all be done with commands, e.g. show the Command Line from the Favorites menu, enter:<br>
~display<br>
show :15.A,28-30.A<br>
(… that would show residues 15 and 28-30 of chain A)<br>
<br>
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<br>
(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).
<br>
(b) use the “transparency” command on the selection, for example: transparency 70,a,r,s sel<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html</a>><br>
...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.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Mar 11, 2019, at 1:54 AM, Acco . <scarsoacco@hotmail.com> wrote:<br>
> <br>
> Hello,<br>
> 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?<br>
> Thank you in advance for your help<br>
> Sincerely,<br>
> Andrea<br>
<br>
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