<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 Mike,<div class=""><br class=""></div><div class=""> An icosahedral capsid has twenty 3-fold symmetry axes. Are the 3-fold symmetric spikes aligned with the 3-fold symmetry axes of the icosahedron? If they are then imposing the icosahedral symmetry will make the antibody binding to each spike 3-fold symmetric. If the spike 3-fold symmetry axes are not aligned with the icosahedron 3-fold symmetry axes (seems unlikely) then you would need to know where the spike 3-fold symmetry axes are and in that case I’d suggest fitting an antibody to a single spike using C3 symmetry with an explicitly specified axis vector.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 26, 2018, at 4:43 PM, Kent, Michael S wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">I have an EM map for a virus that includes an antibody bound to the envelope proteins. The envelope proteins <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">are trimers of dimers with C3 symmetry</span> that form spikes on the surface of the virus. I fit an atomic model for the spikes to the map using icosahedral symmetry, following the very helpful<span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/" target="_blank" class="">symmetric fitting video tutorial</a>. Now I am trying to fit a model for the antibody into the spike regions of the map. I need to impose C3 symmetry for the antibody for the fit into each spike, in addition to imposing icosahedral symmetry to include all the spikes. How can I impose both of these in the fit? <br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Thanks,<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class="">Mike Kent<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration: none;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px; caret-color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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