Hi, Elaine:
 
Thanks for your kind reply that is very informative.
 
Eventually, I found the solution to mapping the epitopes to reference/merged protein which is combined by text editor. Please see the enclosed results analysed by "Blast 2 seqs" (HTY_HA_B2Seq).

I spent a couple of days to study the docs of "Chimera". Finally , I came out of the command lines to map epitops to protein structure:

open 3LZG
split #0
preset apply int 3
col magenta r #0.1:322-330
col magenta #0.2:1-11
=========================

However, I found a very unexpected region which is colored by the epitope segment. See the "red question marks" in the PPT file (HTY_HA_Chimera.pdf)
Thanks again,
Hsih-Te
On Wed, Apr 4, 2012 at 2:19 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Hsih-Te,
Welcome to Chimera!

Can you explain more about what you want to do?  Are the chains in two different PDB files or in the same PDB file, and why do you want a single chain in Multalign Viewer?  Did you just want one chain stuck on the end of the other, or mixed together somehow?

You may be able to do what you want without merging any chains.  You can just show the sequence of each chain in a separate window (Favorites.. Sequence), and both of those will automatically interact with your structure: if you highlight some residues in the sequence window, the corresponding part of your structure will be selected and vice versa.

If you really need a merged single chain, the details depend on what you have to start with.  Multalign Viewer editing does not allow merging chains directly, so you might have to do text-editing manually (in your favorite text editor outside of Chimera).

Elaine
-----
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 3, 2012, at 9:10 AM, Hsih-Te Yang wrote:

> Dear all:
> I am a new beginner of Chemira software package.
> By using "Multalign Viewer", I would like to merge the protein sequences of two different chains (200~300 a.a.). After that, I want to map some epitopes (8 ~ 20 a.a.) to this merged sequence.
> How can I do? Thanks for any kind help further.
> Hsih-Te