[Chimera-users] Alignment

[Suda Parimala Ravindran]

Hi Bodvael,

Please check out my answer in blue color for your query.

I have never used Chimera so please bear with me. I have this short peptide
sequence (8 aa) that I want to locate in the secondary structure of a
protein which I have opened in chimera. Is there a way to highlight the
sequence in a particular color in the 3D model and/or only have the
aminoacid numbering in this region?
**
Yes, you can highlight the desired region using Chimera. After loading your
structure, goto

*Tools -> Sequence -> Sequence *

to display the sequence. Here, you can find that by default, alpha -
helices are highlighted in yellow, sheets in green in the sequence window.
Now, to highlight the region of your interest, just drag on the residues
that you want. You can see that the residues you have selected are
highlighted in green in the structure window. Now goto
*Actions -> Color -> choose a color of your choice

*
To have the amino acid numbering, goto *

Actions -> Label -> Residue -> Specifier (you can select 1-letter code +
specifier to have the amino acid residue and residue number labelled).
*


I have never used Chimera so please bear with me. I have this short peptide
sequence (8 aa) that I want to locate in the secondary structure of a
protein which I have opened in chimera. Is there a way to highlight the
sequence in a particular color in the 3D model and/or only have the
aminoacid numbering in this region?

I am unsure, if you can display the strand numbers in Chimera. The best way
is to identify the N- and C- terminal and count the strand from N-
terminal.
*
-Suda *



On Tue, Nov 15, 2011 at 7:12 AM, bodvael email <bodvael at gmail.com> wrote:

> Hi,
>
> I have never used Chimera so please bear with me. I have this short
> peptide sequence (8 aa) that I want to locate in the secondary structure
> of a protein which I have opened in chimera. Is there a way to highlight
> the sequence in a particular color in the 3D model and/or only have the
> aminoacid numbering in this region?
>
> Also, I would like to view a linear alignment of the entire
> protein sequence with my peptide sequence of interest. I was able to do
> that and see that the peptide sequence falls in a beta-sheet (green color).
> Is there any way know which strand it is exactly? It is supposed to be in
> strand 5 but I don't know how to display strand numbers, or verify with
> certainty that it is indeed strand 5 and not strand 6 for example.
>
> Thanks,
> Bodvael
>
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>
>
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