From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 28 2005 - 10:43:27 CDT

Hi,
  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
  vmd_at_ks.uiuc.edu

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.

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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