One way you can show those in chimera is a broadened ribbon image, or morphed animation. Generate several pdbs of your protein with per-residue displacement along the eigenvectors in something like R, and then open them all in chimera, displace as backbone trace rounded ribbon. the overlay will show the eigenvectors and eigenvalues as broadened stacks of ribbons in the direction and magnitude of the motion. If you morph between the conformations, you'll get a nice animation of the displacement along any principal component.

Rebecca Swett
Wayne State University
357 Chemistry
Detroit, MI 48201

Lab Phone 313-577-0552
Cell Phone 906-235-0768

On 3/22/2013 9:47 AM, Prasanna Venkatesh wrote:

Dear support member,

I would like to know the steps or command lines that I should follow to make 3D projection of eigen vectors like Tube representation or porcupine plots in Chimera. Thank you in advance.

Regards,

Prasanna

Ph.D student

Ajou university, South Korea
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