VMD-L Mailing List

From: Shachi Gosavi (shachi_at_ctbp.ucsd.edu)
Date: Thu Oct 27 2005 - 17:01:42 CDT

Hi,

I am new to VMD and I am trying to do a multiple structural alignment of
three proteins with the same fold. Can you tell me how the Q is calculated
for such an aligment. The manual says that it's based on Qalign and gives
a formula for a pairwise Q. I have the following questions:

1) Q seems to be -ve if an amino acid doesn't have a matching one in any
of the other two proteins. What happens if there is a matching amino acid in
one of the other two proteins and but not the other?

2) The three proteins that I have all have different sizes. How do you
average over the paiwise alignments that you get?

3) Is it possible to plot a Q vs residue index plot?

Thanks,
Shachi.