VMD-L Mailing List
From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Tue Oct 07 2014 - 11:16:31 CDT
I don't there would be anything wrong as long as the averaging is done
while calculating the correlation of motion between residues, i.e., the 2
subunits in the dimer are aligned and 2 sets of coordinates per frame are
taken for each residue while calculating the correlation in motion between
residues. Having said that, it is important to realize that the differences
in pathways are related to the stochasticity in the pathways for
communication between the residues (resulting from stochasticity in
correlation values). This stochasticity is real and there is nothing wrong
in reporting it according to me.
Genius is nothing more or less than doing well what anybody can do badly. -
On Tue, Sep 30, 2014 at 9:22 PM, mason H <tailermason_at_gmail.com> wrote:
> I am working with an enzyme that is a dimer. I performed 'Dynamical
> Network Anaysis' on the enzyme. For each subunit, I generated a "contact
> map" (--- that is, I have two subunits, and I have two contact.dat files).
> I am now doing pathway analysis (using 'subopt').
> When I look at the pathway between two nodes on one subunit, it
> produces a certain set of 'pathways.'
> When I look at the pathway between the same two nodes in the other
> subunit, the pathways are similar, with some slight differences.
> I noticed that 'subopt' uses the 'contact.dat' file.
> Can I average the data from my two 'contact.dat' files to produce one
> "Average_contact.dat" file? -- Can I then perform subopt on this average
> contact map to create average pathways?
> I know this is technically feasible (I have done it) -- but is it
> As long as I also separately report the pathways of each subunit (perhaps
> in "supplemental info") Can I display the "average" pathway data in a
> Thank you