Hello, Huan Jmol uses 2 methods:
1st if the pdb file contains HELIX and SHEET records, Jmol uses those. 2nd if that is not the case, Jmol will calculate secondary structures using the DSSP algorithm Even in case #1, you can force calculation with DSSP (and see the difference) using the command calculate structure dssp There is also another option, calculate structure ramachandran which I guess does what you expected, i.e. use the dihedral angles All of those do not depend on hydrogens, I believe. See documentation at https://chemapps.stolaf.edu/jmol/docs/#calculate Also this: http://proteopedia.org/wiki/index.php/Secondary_structure#How_Jmol_Deter mines_Secondary_Structure Cheers! · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
