> I realize what the basis and limitations are. Is this "HP" an > algorithm you have developed, is it published?
No I certainly didn't develop it. HP Protein folding has been around in the literature for a while. Some examples below: Bui, T.; Sundarraj, G.; An Efficient Genetic Algorithm for Predicting Protein Tertiary Structures in the 2D HP Model. Genetic and Evolutionary Computation Conference. 385-392. 2005. Hoque, M.; Chetty, M.; Sattar, A.; Protein Folding Prediction in 3D FCC HP Lattice Model Using Genetic Algorithm. IEEE Congress on Evolutionary Computation. 2007. > I would say this goes far beyond the capability of Jmol. You will need way > more sophisticated tools to do those "adjustments" > More than whether Jmol is capable or not, my increasing concern is > whether this makes sense. > Not only overlap, but unrealistic bonding distances. I'm not sure > this is sensible. > You see? Speaking of rotating the bonds as much as possible is scary. > Peptide bonds do have their preferred orientations. > Not necessarily; too many constraints in the approximation. I'm not > sure any comparison can be made. > Anyway, I wish you good luck, but I'd say think it twice before > embarking into this. I'm beginning to feel this project may be too ambitious. Is there some other 3D visualization tool you know of, which does have such capability? Aside from difficulty, do you feel this is a worthy endeavour? I'm starting to worry that even if I did obtain molecularly 'valid' structures, they would be so different from the folded hp model that most meaning would be lost. Please don't be afraid to post your opinion, I'd rather figure out now than months into this. Thanks, Aaron Germuth ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
