[Chimera-users] Merge the protein sequences of two different chains

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 4 11:19:03 PDT 2012

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 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

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