Recent content by nitroamos

I implemented the test I described (i.e. rmsd) and it has the problem that rmsd can't distinguish between S1=R+T1 and S1=T1+R. That is, the order of the points matters to rmsd, but not to me. My new test is to compare the distance between all pairs of points...

Hello -- I have some reference object R (e.g. a protein), and I've got two transformations t1 and t2 (e.g. a transformation = quaternion + translation). In my case, t1 and t2 were obtained from symmetry operations. So after applying t1 to R I get object T1, and after applying t2 to R I get...

Here's somebody's http://nmr.cit.nih.gov/xplor-nih/xplorMan/node200.html" for their software. I'm interested in a mathematical discussion of what they're doing. If you click the links, you'll see they chose Euler angles -- are Euler angles the right way to go? What's the best point for rotating...

Hello -- I want to solve a very general type of minimization problem. I have 2 rigid bodies (e.g. molecules) which are exerting forces on each other, and I want to minimize the interaction energy (e.g. from a molecular forcefield with terms for things like Coulomb, van der Waals, etc). In...