[Ifeffit] max number of restraints

Victor.Streltsov at csiro.au Victor.Streltsov at csiro.au
Fri Apr 13 19:08:07 CDT 2007

> Hi Victor,
> It should be
>   restraint_sum = restraint1 + restraint2 + restraint3 + ...
> That is, a restraint should be a value that you'd like to me made as
> small as possible, but can take either sign.  The restraints are
> simply appended to the "vector to be minimized" in the least squares
> sense.
> I'm not sure that will fully solve the issue of having different
> results between 10+ individual restraints and fewer summed restraints.
>    But I'm interested to hear and see more....


>Given that individual restraints might be of either sign, you might
>consider adding them in quadrature and using the square root of that
>as the restraint.  As Matt said, the details matter, but I think that
>would be a serviceable work around for more than 10 restraints.


I am confused.
I thought I did exactly what Bruce said. I added them in quadrature and
used square root of that as the restraint in artemis:
After summing in quadrature:
restraint_sum = sqrt((restraint1)^2 + (restraint2)^2 +

I asked artemis "to build restraint from "restraint_sum"" and

artemis added line: res_restraint_sum=penalty(restraint_sum,n1,n2)*scale

This way of summing them seems closer to the way of adding them
individually squared to the "vector to be minimized", provided
artemis/ifeffit squares them before appending to the "vector" (you don't
need to square them before). I guess the questions is what artemis does
when asked to "build restraint from ..."? 


Dr Victor Streltsov
CSIRO Molecular & Health Technologies
343 Royal Parade 
Parkville VIC 3052 Australia 
Phone: +61 3 96627311 
Fax: +61 3 96627101 
victor.streltsov at csiro.au 

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