<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""> The following page shows a “bent microtubule” model made with a Chimera Python script<br class=""><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html" class="">https://www.cgl.ucsf.edu/chimera/data/microtubule_aug2013/bent_mt.html</a></div><div class=""><br class=""></div><div class="">The bend makes it more complicated than a straight microtubule. Here is an explanation of how the Chimera “sym” command can make a straight microtubule model.</div><div class=""><br class=""></div><div class=""> These commands in Chimera (menu Favorites / Command-line to enter commands) make a straight microtubule from a PDB model as shown in the attached image.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 1jff</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sym #0 group h,9.8,27.7,13*shift,8,80.0 surf true axis x center 0,115,0 res 5</div><div class=""><br class=""></div><div class="">The sym command took the tubulin dimer (shown in red and blue in the image) and made copies in a helical pattern to look like a microtuble. The trick is to find the right helical parameters. I just did a few minutes trial and error to find the above. The “group” option says make a helix where each subunit is shifted 9.8 Angstroms from the previous one and by 27.7 degrees around the axis from the previous one, and make 13 copies (for a 13 protofilament microtubule). This makes a single turn of the microtubule. A microtubule does not have helical symmetry, the one turn achieves a shift of 1.5 subunits creating a seam where alpha and beta tubulin are touching in two adjacent protofilaments. So I just make one turn. Then the above command says shift that one turn by 80 Angstroms along the axis for each of 8 copies. The “surf true” option says show the copies as surfaces. Without that it will copy the atomic model and use a ton of memory. The helix axis is x (just judged by eye after opening tubulin dimer 1jff. The 1jff dimer seems to be centered not far from 0,0,0 so I shifted the helix axis 115 Angstroms along y to make the diameter about 23 nm. Here are the docs for the sym command:</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/chimera/current/docs/UsersGuide/midas/sym.html" class="">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html</a></div><div class=""><br class=""></div><div class=""> Here’s a web page where I did something more sensible to get better symmetry parameters — I fit the tubulin dimer to an EM map of a microtubule.</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/chimera/data/cellcomplexity06/tcell-demo.html" class="">http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><img height="629" width="326" apple-width="yes" apple-height="yes" apple-inline="yes" id="EFF60A4B-A94A-490B-8C1C-98CBF547FA4E" class="" src="cid:7A4F1C5F-BA8D-4454-ACA6-9642F2F925D1@cgl.ucsf.edu"></div><div class=""><br class=""><br class=""></div></div></body></html>