[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....
>--Matt
>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.
>B
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 +
(restraint3)^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 ..."?
Victor
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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