<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Kavya,<div class="">I didn’t have a good example handy yesterday, but here is a more specific example, in commands:</div><div class=""><br class=""></div><div class="">open 5hvp</div><div class="">open 5hvp</div><div class="">mm #0:.a:.b #1:.b:.a pair ss<br class="">show :241.b</div><div class="">measure rotation #0 #1<br class=""><br class=""></div><div class="">This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP. The measurement is also reported in the Reply Log (open from Favorites menu):</div><div class=""><br class=""></div><div class="">Position of 5hvp (#1) relative to 5hvp (#0) coordinates:<br class=""> Matrix rotation and translation<br class=""> -0.32555997 0.82635225 -0.45951350 0.78339640<br class=""> 0.82635225 0.01248149 -0.56301524 15.06413576<br class=""> -0.45951350 -0.56301524 -0.68692152 28.23994571<br class=""> Axis 0.58070648 0.71150597 -0.39565040<br class=""> Axis point -5.75571422 -0.00000000 18.30836454<br class=""> Rotation angle (degrees) 180.00000000<br class=""> Shift along axis 0.00000000</div><div class=""><br class=""></div><div class="">I also attach an image below.</div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">----------<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""></div><div class=""><img apple-inline="yes" id="70F3B9A1-A5B7-4165-96DF-C8786EF645B4" src="cid:352366CF-BC50-4728-AB59-E2F3A6A7C66E@compbio.ucsf.edu" class=""></div><div class=""><br class=""></div><blockquote type="cite" class="">On Mar 29, 2017, at 10:10 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi Kavya,<br class="">I think I understood you, but I can only repeat the same answer. I do not know of any way to get the axis in Chimera except by first superimposing two copies of the dimer. Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2. Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.” <br class="">Elaine<br class=""><br class=""><blockquote type="cite" class="">On Mar 29, 2017, at 10:05 AM, Kavya Shankar <<a href="mailto:kavshank@umail.iu.edu" class="">kavshank@umail.iu.edu</a>> wrote:<br class=""><br class="">Hi,<br class=""><br class="">To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged.<br class=""><br class="">Thank you.<br class=""><br class="">Regards,<br class="">Kavya Shankar<br class=""><br class="">On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class=""><br class=""><blockquote type="cite" class="">On Mar 29, 2017, at 9:01 AM, Kavya Shankar <<a href="mailto:kavshank@umail.iu.edu" class="">kavshank@umail.iu.edu</a>> wrote:<br class=""><br class="">Hi,<br class="">Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures.<br class="">Thank you.<br class="">Regards,<br class="">Kavya Shankar<br class=""></blockquote><br class="">Hi Kavya,<br class="">Why not just match (superimpose) one monomer to the other and compare directly? At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching. However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis. If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2). This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest.<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html</a>><br class=""><br class="">After two models are superimposed, you can get the axis and rotation amount with command “measure rotation”<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class="">P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues<br class=""><br class=""><br class="">_______________________________________________<br class="">Chimera-dev mailing list<br class=""><a href="mailto:Chimera-dev@cgl.ucsf.edu" class="">Chimera-dev@cgl.ucsf.edu</a><br class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev<br class=""></blockquote><br class=""></blockquote><br class=""></div></body></html>