The user enters in a sequence of h's and p's, which starts off as a linear chain of amino acids. After folding, the linear chain usually takes on a 'globular' form. Each amino acid is represented as a single red (hydrophobic) or blue (hydrophilic) sphere. The folding model does not deal with anything at the level of atoms, only amino acids. I hope this answers your question.
Aaron Germuth ---------------------------------------------------------------------------- This sounds very interesting. When you do the folding, do you do it strictly in terms of residue locations in space? That is, no real atoms? Or is there at least a backbone to work with? I'm not sure what you mean by minimization. Keep in mind this program is just an educational model and is not meant for proteins thousands of amino acids long. In fact, attempting to fold a protein even one hundred amino acids long would take over a day. I intend to use this only on very small proteins. Aaron Germuth ----------------------------------------------------------------------------- It seems to me there will be a significant amount of minimization to be done. That is beyond the scope of Jmol. Jmol can minimize small sections of a model, but not a full protein. ------------------------------------------------------------------------------ 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
