Currently, FirstGlance in Jmol suggests hydrogen bonds whenever a nitrogen or oxygen is within 3.5 Angstroms of another nitrogen or oxygen. This crude method fails to take into account whether or not either atom actually has a hydrogen to donate, and the angle of the acceptor to the donor.
If the model contains all hydrogens (or once Jmol can add them), is Jmol capable of selecting donor-acceptor pairs using not only distance, but angular criteria? For example, in 3hyd, see http://proteopedia.org/wiki/index.php/User:Eric_Martz/Sandbox_10 [Leu1]:A.N #1 is donating [Leu1]:A.H3 #11 to HOH8 #135 at 126.4 degrees (donor to acceptor distance 2.8 Angstroms), or to HOH10 #137 at 154.9 degrees (D-A distance 3.1 A). Can I select one or the other (and which would be the stronger hbond?) based on these angles? What would the script commands be? Thanks, -Eric ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
