More than whteher Jmolis capable or not, my icreasing concern is whether this makes sense.
> I would say this goes far beyond the capability of Jmol. You will > need way more sophisticated tools to do those "adjustments" > Since I'm doing this project through my University, I'm not sure if > I'm legally allowed to let you help with the physical code portion. > I'll have to get back to you. However, If this is allowed, I would > gladly embrace your help. Well, after all, your email was entitled "Help" ;-) I understand. > The HP Protein Folding Model is a simplified model which computers > can use to fold proteins. I realize what the basis and limitations are. Is this "HP" an algorithm you have developed, is it published? > This is a problem I've thought about, as some amino acids such as > phenylalanine are much larger than say, glycine. The goal I'm > personally going for is to get as close as we can to the folded > model, while obeying molecular structure. We might have to edit the > Jmol structure if overlap occurs. Not only overlap, but unrealistic bonding distances. I'm not sure this is sensible. > This goes as before. We can attempt to rotate the peptide bond as > much as possible to get the closest match. You see? Speaking of rotating the bonds as much as possible is scary. Peptide bonds do have their prefered orientations. > The results given from the finished project also are not expected to > give entirely realistic proteins. Certainly not. > However, the results we do obtain > can be directly compared to an experimentally found .pdb of proteins. Not necessarily; too many constraints in the approximation. I'm not sure any comparison can be made. > To evaluate the results of the algorithm > before, we simply had to observe that hydrophobic residues appeared > in the middle, and hydrophilic residues on the outside. That you are already seeing with your lattice model. You don't need the residues structures. Anyway, I wish you good luck, but I'd say think it twice before embarking into this. · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain ------------------------------------------------------------------------------ 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
