<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Cynthia,<div class=""><br class=""></div><div class=""> The description of making a microtubule model in an earlier Chimera post</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011646.html" class="">http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011646.html</a><br class=""><div><br class=""></div><div>was just applied helical symmetry to a tubulin dimer. It is a made-up model not based on fitting actual data. To do it right start with a microtubule electron microscopy map. Fit your tubulin, or kinesin or other motor atomic model into the map. Find the map symmetry (helical pitch, center, axis direction) and apply that symmetry to the atomic model. You might be able to get the map symmetry parameters with the Chimera "measure symmetry" command</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry</div><div><br class=""></div><div>Here is a tutorial making a ParM helical filament model.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html" class="">http://www.cgl.ucsf.edu/chimera/data/singapore-jul2012/parm.html</a></div><div><br class=""></div><div>Send questions to chimera-users so others will be able to find the answers in the future.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 16, 2020, at 10:06 AM, Cynthia Page wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Tom,<div class=""><br class=""></div><div class="">I have found your Chimera user group entry: How to make a microtubule model pretty helpful, thanks for posting this. I am especially naive with Chimera and would like to ask you assistance in making decorated microtubule models as reference maps or cryoem analysis. I can post our conversation to the Chimera group if you think it would be useful.</div><div class=""><br class=""></div><div class="">I would like to make reference maps for The MiRP/Moors Lab procedure. MiRP interfaces with Relion to perform “helical" reconstruction of molecules bound to microtubules from cryo-em data.</div><div class=""><br class=""></div><div class="">I have been playing around with you command </div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: Courier;" class=""><span style="font-kerning: none" class="">sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5</span></div></div><div class=""><span style="font-kerning: none" class=""><br class=""></span></div><div class=""><span style="font-kerning: none" class=""><br class=""></span></div><div class=""><span style="font-kerning: none" class="">While as you know it works fine with PBD ID 1jff, I cannot figure out how to get results from other PBD ID’s, those with Kinesin molecule and alpha/beta tubulin. I think the key is "</span><span style="font-family: Courier;" class="">axis x center 0,115,0</span><font face="Courier" class="">”</font> portion of this command, and the orientation of molecule as download from the PDB, but for the life of me I cannot figure out how to change the axis coordinates to orient the alph/beta/kinesin correctly. Can you tell me how to do this? I have been using PDB ID’s 3J8Y, and 2P4N.</div><div class=""><br class=""></div><div class="">Thank you in advance for your time,</div><div class=""><br class=""></div><div class="">Cynthia Page</div><div class="">Research Assistant</div><div class="">University of Colorado, Boulder</div><div class=""><br class=""></div><div class=""><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>