tag:blogger.com,1999:blog-7844526396210378482.post3732962069946922503..comments2024-01-31T09:23:26.925+00:00Comments on Noel O'Blog: What does the pairwise RMSD of all possible conformations look like?Noel O'Boylehttp://www.blogger.com/profile/03288289351940689018noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-7844526396210378482.post-66415350738679929192010-05-19T15:34:32.590+01:002010-05-19T15:34:32.590+01:00Good that you minimized the RMSD first. I suspect...Good that you minimized the RMSD first. I suspect your graphs may look a little different after considering automorphs, as many hydrogen atoms are symmetry equivalent to others. You could try heavy atoms only and see if the plot changes much. :-)Evan Boltonnoreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-74072729102327834192010-05-18T14:09:56.323+01:002010-05-18T14:09:56.323+01:00The RMSD was after Kabsch alignment and it include...The RMSD was after Kabsch alignment and it included hydrogen atoms (these are not usually included in 'real life'). Automorphs were not considered - at some point I may need to sort this out.Noel O'Boylehttps://www.blogger.com/profile/03288289351940689018noreply@blogger.comtag:blogger.com,1999:blog-7844526396210378482.post-59226944645130319572010-05-18T13:45:20.541+01:002010-05-18T13:45:20.541+01:00Reading this post left me with lots of questions.....Reading this post left me with lots of questions... :-)<br /><br />How exactly did you do your RMSD? Was it simple pairwise comparison? Did you allow rigid body rotation and translation to minimize the RMSD between conformers? Did you consider automorphs (symmetry equivalent atoms)?Evan Boltonnoreply@blogger.com