Stefan Hoorman wrote:
<snip>
I have tried using g_sgangle, but the problem is that it does not
calculate the principal axis of the helix. Since g_sgangle allows me to
choose at maximum 3 atoms per analysis, it is quite difficult to perform
such an analysis if one is to do this for 4 or five different systems
and dimers.
So, in this case, since g_bundle asks me to select a group of top and a
group of bottom atoms, I would need to create an index group with my
first group (top) being the top residues of both my helices and the
second group being the bottom residues of my helices. Or would I create
Per the documentation, that sounds right.
"The program reads two index groups and divides both of them in -na parts. The
centers of mass of these parts define the tops and bottoms of the axes."
-Justin
a first group for my first helix and a second group for my second helix?
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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