[Chimera-users] rmsd and display queries

[Elaine Meng]

On Jun 8, 2007, at 12:06 AM, bala wrote:

> Hi Elaine,
> Thank you for your inputs. I think i didnt mention my second query  
> reg. substructure creation clearly,
> I hve a 20 mer duplex RNA, i want to visualize only a few base  
> pairs at the middle. Is there any way that i can select, display  
> and do actions only the portion of interest and undisplay other  
> portion
> Bala

Hi Bala,
Of course.  The general procedure is to

(1) select what you are interested in
(2) invert the selection so now it contains only what you are *not*  
interested in
(3) hide or delete the selection (if you're confident you won't want  
the other parts, deleting will make later steps simpler)
(4) if you only hid rather than deleting, now select the parts of  
interest again, and use the Actions menu to work with those parts

There are many different ways to do each step, too many to describe  
in this mail.  Below, I'll just give an example using commands, but  
be aware that selection can also be done with Ctrl-click and arrow  
key operations, or with the Select menu, or using the Sequence tool:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html

Commands example:

open 6bna
sel :4-8.a,5-9.b
sel invert
delete sel

Then carry on with what is left, using commands or the menu as you  
prefer.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html