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

[Elaine Meng]

Hi Hsih-Te,
In 3lzg, the protein chain A (#0.1 after splitting) ends at 325.  When you color residues 325-330 it includes a nonprotein residue NAG 330, which is a glycosylation on a different area of the chain.

One way to see what you are coloring is to display the atoms of those residues when the surface is not shown, for example:

alias epi1 #0.1:322-330
color magenta epi1
show epi1

You can put the mouse over the atoms to see the residue name and number.

Or, you could check first to see what residues are in some chain of your protein structure by using the Sequence tool (under Favorites menu) to show the sequence of that chain and then putting the mouse cursor over the sequence to see what the structure residue numbers are.

Some other advice for making your figure...

(1) 3lzg has two hemagglutinin trimers, the first one is chains A-F, the second one is chains G-L.  Might as well delete the second copy before splitting and doing the other stuff, for example commands:

open 3lzg
delete :.g-l
split

(2) instead of using the preset to show the surface with orange-white-blue coloring by hydrophobicity, just show the surface and color it one color.  Then it will be easier to see the epitope locations when you color the epitopes some other colors.  For example:

surface
color tan,s
alias epi1 #0.1:322-325
alias epi2 #0.2:1-11
color magenta epi1
color cyan epi2

I like to use aliases because it is then easier to try other colors or do other things to those sets of residues without typing the residue numbers again.

(3) After you have the structure coloring as you like it, you can use a publication preset to make the surface smoother and color the background white. It will keep the structure coloring the same.

I hope this helps,
Elaine

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On Apr 4, 2012, at 2:39 PM, Hsih-Te Yang wrote:

> 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