[Chimera-users] displaying specific residues

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 16 09:36:59 PDT 2010

On Aug 12, 2010, at 7:04 AM, Reza Heidari wrote:
> How can i display just some of residues (in form sphere)  on a protein (in form ball & stick), for example: Trp38, Val66, Ala80. Please help me, thanks a lot.

Hi Reza,
There are many ways to get the same final result.  I will give only two examples here.

You may want to look at the "Getting Started" tutorial and other tutorials for more information:

Example 1:
Show the command line by choosing from menu: "Favorites... Command Line"
If you don't want any ribbon, use command:   ~ribbon
Show all protein atoms/bonds and hide others with command:   show protein
(to show ALL atoms/bonds including nonprotein, use command:   display)
Change style of all atoms/bonds to ball&stick:   repr bs
Change style of specific residues to sphere:   repr sphere :38,66,80
(other commands such as color, display, ... also take these residue lists)

Example 2:
If you don't want any ribbon, use menu:   Actions... Ribbon... hide
Show all atoms/bonds with menu:  Actions... Atoms/Bonds... show
( If there is water and you want to hide it,
    menu:  Select... Structure... solvent
    menu:   Actions... Atoms/Bonds... hide
    menu:   Select... Clear Selection )
Change style of all atoms/bonds with menu: Actions... Atoms/Bonds... ball & stick
Display sequence window with menu:  Favorites... Sequence
      Click on Sequence window top bar, then inside that window,
      use mouse to choose residue 38; then it will be selected in the main window
Change selected residue to sphere with menu: Actions... Atoms/Bonds... sphere
Go back to Sequence window, choose next residue, etc.

For the future: general questions should go to chimera-users at cgl.ucsf.edu 
(chimera-dev is for programming questions)  and include a brief description in
the Subject line of the mail.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

More information about the Chimera-users mailing list