tag:blogger.com,1999:blog-120256850987994647.post4487416988474829335..comments2020-03-11T06:48:09.112-07:00Comments on Protein Sequence and Structure Bioinformatics: How to calculate H atoms for Nitrogens in protein structuresAhttp://www.blogger.com/profile/14312808974629818240noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-120256850987994647.post-34542397249436345062010-10-07T15:30:24.624-07:002010-10-07T15:30:24.624-07:00Thanks for the comment. I modified the text above ...Thanks for the comment. I modified the text above to make it more clear that the H is for group i+1.Ahttps://www.blogger.com/profile/14312808974629818240noreply@blogger.comtag:blogger.com,1999:blog-120256850987994647.post-81066664398132553242010-10-07T05:52:20.887-07:002010-10-07T05:52:20.887-07:00Jmol uses the first of these (based on RasMol) for...Jmol uses the first of these (based on RasMol) for calculation of "hydrogen bond" dipole-dipole energies and, in Jmol 12, for DSSP analysis. <br /><br />For the CALCULATE HYDROGEN command itself and quaternion frame "N" analysis, however, Jmol uses the second of these.<br /><br />I realize the code says this, but it wasn't clear on first reading that this is the H position for group i+1, not group i.Bob Hansonhttp://jmol.sourceforge.netnoreply@blogger.com