On Friday 28 November 2008, Ben Akiyama wrote: > Hi Everyone, > > I am measuring and comparing torsion angles in several solved crystal > structures of RNA helices using AMIGOS. I was wondering if anyone knows > of a program that can give me an idea of the error in these measurements > based on coordinate error, b-factors, etc.
If you mean real torsion angles, the only quantitative way to do this is to do full-matrix refinement, invert the matrix, and derive error estimates from the off-diagonal terms. That is not something you can do after the fact from a previously refined structure. On the other hand, perhaps you can provide more information about what exactly is the question you want to answer. For example, if you are interested in how reliable the assignment of sugar puckers is, looking at torsion angles is not a good way to go about this. I think you'd be better off counting satisfied/unsatisfied hydrogen bonding partners for the ring oxygens. Also, your mention of AMIGOS throws me off a bit. That program calculates a pseudo-atom simplified representation of the model, right? If you are asking about the pseudo-torsion angles associated with pseudo-atoms, then I think there are no actual "measurements" directly associated with them in the first place. Perhaps the paper describing AMIGOS discusses the issue of how sensitive the simplified representation is to small variation in the original coordinates? That's actually an interesting question, but I don't have any intuitive feel for the answer. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
