<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Elaine,<div><br></div><div>Thanks so much for all the advice. I'm still having trouble getting the match/alignment command to work and I'm not quite sure what I'm doing wrong but I think it's in my pdb format. I have attached two files with four atoms in each that I would like to overlay and get the rms deviation for. Maybe you could look at the files and let me know where my formatting mistake is. The files are attached and the coordinates are listed below. They both open in Chimera and work fine but I think maybe the problem lies in chain id #'s or something.</div><div><br></div><div>Thanks again for your help,</div><div>Dave</div><div><br></div><div><br></div><div>1st pdb file: <span class="Apple-style-span" style="font-family: 'Lucida Grande'; ">2to1_coordinates_test.pdb</span></div><div><br></div><div><div>HETATM 114 B2 CE2 22 8.649 -5.055 13.615 1.00 1.00 B</div><div>HETATM 115 B3 CE2 22 10.976 -7.450 8.675 1.00 1.00 B</div><div>HETATM 117 S1 CE3 22 8.845 -8.275 11.641 1.00 1.00 S</div><div>HETATM 118 S2 CE3 22 10.227 -5.377 10.923 1.00 1.00 S</div><div>END</div><div><br></div><div><br></div><div>2nd pdb file: <span class="Apple-style-span" style="font-family: 'Lucida Grande'; ">Cycle_coordinates_test.pdb</span></div><div><font class="Apple-style-span" face="'Lucida Grande'"><br></font></div><div><font class="Apple-style-span" face="'Lucida Grande'"><div>HETATM 96 B2 CE2 Z 1 -3.480 14.686 -11.018 1.00 1.00 B</div><div>HETATM 97 B3 CE2 Z 1 -5.877 19.992 -9.560 1.00 1.00 B</div><div>HETATM 99 S1 CE3 G 1 -6.701 16.412 -10.234 1.00 1.00 S</div><div>HETATM 107 S9 CE3 G 1 -3.731 17.766 -10.322 1.00 1.00 S</div><div>END</div><div><br></div><div></div></font></div></div></body></html>