Hello Ansari, and welcome to Jmol world Jmol does not use any connectivity table, and does not treat differently standard amino acids from other chemicals/residues/groups. It just makes bonds when the interatomic distance is below the sum of van der Waals radii of both atoms (there may be a tolerance value implicated, I don't remember for sure). There IS a table of radii for each element contained in Jmol code. You can check them out at http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/_documents/ (mostly you will want the radii.xls file in that folder) and visually at http://jmol.sourceforge.net/radii/ http://biomodel.uah.es/Jmol/radii/jmol_radii.en.html
And try to use proper capitalization: Jmol, not JMol (there has been controversy in the past with other programs, so the exact way is important) ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
