[Chimera-users] Alignment

bodvael email bodvael at gmail.com
Mon Nov 14 17:42:16 PST 2011


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.

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