Greetings, Previously I have created a program which takes a sequence of hydrophobic or hydrophilic amino acids and folds it based of the HP protein folding model. The folded coordinates are given and displayed in a x-y-z grid format (as in an amino acid can only be located on integer x, y, z coordinates; no decimals). A typical folded protein resembles this:
http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg What I hoping to add is to use Jmol to display this protein. However, instead of simply a ball representing the amino acid, I would like to show each molecule of each amino acid. My current idea of how I would go about this is as such: - Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this into a string of hydrophobic or hydrophilic amino acids for my program to fold. - Once folded, replace each amino acid with it's actual molecules in Jmol, to do this I might - programmatically create a .pdb file for Jmol to read. To do this I would already have pdb files for all 20 amino acids stored, and displace their atoms to the grid coordinate given from the existing program. However, I would have to get the amino acids to be bonded together through peptide bonds, which seems tricky. Before I step into this large project, I would just like to ensure I'm on the right path and doing things the best/easiest way possible. I am quite new to Jmol and would very much appreciate any suggestions or things to look out for. If you have any questions, I am more than happy to answer them. Thank you for your time -- View this message in context: http://old.nabble.com/Help-with-Project-Direction-tp35329117p35329117.html Sent from the jmol-users mailing list archive at Nabble.com. ------------------------------------------------------------------------------ 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
