From: Allen, Caley R (
Date: Fri Jun 17 2016 - 14:27:23 CDT

Good afternoon VMD experts and users.

I have what I believe to be a "simple" question.

After you load a membrane psf/pdb and then load a protein psf/pdb, how do you position the protein above the center of the membrane surface? Such that when you combine the coordinate files of the protein and membrane into one new psf/pdb pair, when you load them back into VMD the protein is still centered above the membrane system (i.e., the coordinates of the protein have been changed and remain changed). It would be great if I could control the orientation of the protein and the distance to/from the surface.

I have searched the archived vmd-list, read VMD tutorials (such as membrane proteins tutorial), and tried using tcl with commands such as "measure center ____" and "transaxis", and "vecscale", and have still not figured out how to do this.

If the solution has been posted somewhere and I missed it, please just point me in the right direction and I will proceed.

Thank you in advance.