3D projection of eigen vectors
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
Dear Prasanna, Sorry, there is no easy/automatic function to create porcupine plots in Chimera. You would need to calculate the vectors in some other program, then write out that information and manually convert the data into some input that Chimera understands. Here are some possibilities for that input: (A) the Chimera "Bild" file format; this format describes geometric objects such as the cones you could use to make a porcupine plot, and is fairly simple plain text: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> (B) the Chimera "shape" command can also create cones <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> (C) other object formats that Chimera can read include VRML <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 22, 2013, at 6:47 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
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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participants (3)
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Elaine Meng -
Prasanna Venkatesh -
Rebecca Swett