ms wrote:
Hi,
I am using g_mindist to see how close get C-alphas to each other in my
chains. What I do is selecting C-alpha two times when prompted. I have
only a quick question, just to be sure: The script doesn't take into
account the distance between *neighbouring C-alpha*, isn't it?
I don't see why they wouldn't be. I suppose you'd have to look into the code to
be sure. But if you choose C-alpha for analysis, then I would imagine all of
those atoms are going to be considered.
If there are specific interactions you are looking for, create specific index
groups for those residues, otherwise I don't know if you're going to gain much
from this analysis, because the minimum distance within a protein may always
occur between two specific atoms, oscillating about a certain value.
-Justin
thanks!
m.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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