[chimera-dev] displaying specific residues

[Elaine Meng]

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:
<http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html>

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