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

Hsih-Te Yang paulhtyang at gmail.com
Wed Apr 4 14:39:50 PDT 2012


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 at 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
>
>
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