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

[Hsih-Te Yang]

Good morning, Elaine:

You really solved my problem as well as I expected. The Chimera is such a
powerful software with kind support to the scientist who doesn't know much
about structure biology.
Thank you again.

Cheers,
Hsih-Te

On Wed, Apr 4, 2012 at 7:00 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
>
>
>
> 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
>
>
>
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