VMD-L Mailing List

From: Kapil Amarnath (kapilamar85_at_gmail.com)
Date: Fri Aug 12 2011 - 11:19:31 CDT

Hi all,

I am working with a membrane protein that is asymmetric and arbitrarily
located and rotated in space. I would like to orient the protein "flat" onto
the x-y plane of the coordinate system used in the pdb file, with the center
of the protein at (0,0,0), and I would to obtain the coordinates of the
protein in its new location/orientation. Is there any way to use VMD to
obtain the necessary translation vector and rotation matrices for doing so?
 Is this information even contained in the pdb file?

Thanks,
Kapil