[Chimera-users] question about Chimera

Richard Collins rcollins at sickkids.ca
Sun Apr 9 12:56:33 PDT 2017

Hi Elaine

Yes this helps, thanks.  I used control-click to select residues.

Is there a way to adjust the transparency of ribbons, helices and amino acids?

What I am trying to do is find all the residues along the tunnel of my molecule. It is a solid protein with a tunnel through the middle.  Using the SURFACE function shows only the outer surface.

I am wondering if there is a way to show only the tunnel surface and not the outer surface?  For now  I am using the PER-MODEL CLIPPING to slice through the middle.

Richard Collins
Lab Research Project Coordinator
Department of Cell Biology
Peter Gilgan Centre for Research and Learning
Room 199420, bench HH
Hospital for Sick Children
686 Bay St.
Toronto, ON
M5G 0A4
T (ext): 416 813-8474
T (int): 308474
E: rcollins at sickkids.ca

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Sunday, April 09, 2017 12:42 PM
To: Richard Collins
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] question about Chimera

Hi Richard,
Of course you can color and show/hide individual residues and atoms in Chimera.  Otherwise it would not be very useful!!  It is probably the first thing to learn, and there are many different ways depending on your style of working.

The two main approaches are:
- “select” the residue, which outlines it in green, and then use the Actions menu to do something to your selection
-  use commands like “color” and “display” specifying the residue directly by residue number and chain (show Command Line from Favorites menu)

However, there are many ways to select a residue, including with Ctrl-click in the graphics window or a command or in the Sequence window, and conversely, you can act on the current selection with commands too. You should take a look at the “getting started” tutorial, which has two sections with examples of these two general approaches.

There are lots of other tutorials too:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 8, 2017, at 2:34 PM, Richard Collins <rcollins at sickkids.ca> wrote:
> Hello
> I would like to highlight certain residues of interest in my molecule, preferably by colorizing them in Chimera.  Is there a way to do this?
> Richard Collins


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