[Chimera-users] Sequence alignment

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 1 11:14:21 PST 2005

Hi David,
I'd like to add that although the "Chimera selection" region will  
always keep track of the current Chimera selection, you can copy the  
region to another name to preserve it (click Copy on the Region  
Browser).  We've been using the word "region" to mean boxed areas on  
the sequence alignment, and a single region can actually include more  
than one disjoint box.

Here is an example of why you'd want to copy the region: if you  
wanted to keep a region with all residues near a ligand, you could  
first select those residues and then Copy the "Chimera selection"  
region to another name, say, "binding site."  Then even when you  
change the current Chimera selection, the "binding site" region will  
stay the same.  You will want to make the border and interior colors  
of the copy or copies different from one another, however, so it will  
not be visually confusing.  You can also toggle between showing and  
not showing a region in the alignment with the "Shown" checkboxes in  
the Region Browser.

On Dec 1, 2005, at 9:48 AM, David G. Morgan wrote:

> Hi,
> 	I'm learning to use the sequence alignment tools in chimera.  I
> know that I can highlight sequences in the alignment window and select
> residues in the structure, but is it possible to do the opposite?  In
> other words, I'd like to box or otherwise select some residue(s) in  
> the
> structure and have that region highlighted or otherwise marked in the
> aligned sequence window.
>                     David Gene Morgan
>              Advanced Microscopy & Proteomics
>                 Molecular & Cellular Biology
>              University of California at Davis
>                     530 752 2693 (lab)
>                     530 752 3085 (FAX)
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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

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