From: John Stone (
Date: Fri Oct 28 2005 - 10:43:27 CDT

  I've forwarded your questions to the authors of the multiple alignment
plugin, hopefully they will get back to you on this shortly.

  John Stone

On Thu, Oct 27, 2005 at 03:01:42PM -0700, Shachi Gosavi wrote:
> 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.

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