VMD-L Mailing List

From: Viswanadham Sridhara (muta.mestri_at_gmail.com)
Date: Thu Dec 15 2005 - 14:37:17 CST

Hi everyone,
I have a very basic question,
when you load 1ORQ.pdb file in VMD, does the z-axis of this loaded molecule
correspond to the z-axis of the bilayer system, assuming bilayer is in x-y
directions, or should I orient this protein and then embed in the bilayer?
And if you have to orient, how can we find out which way to embed, and
things?
By the way 1ORQ.pdb file is a KvpA potassium channel.
Thanks in advance,
Viswam. 

--
Viswanadham Sridhara,
Graduate Research Assistant,
Old Dominion University, "VIRGINIA".