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@csiro.au