<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Smith,</div><div class=""><br class=""></div>Do you know the symmetry of the oligomer you are trying to make? Is it just a matter of applying positions that you already know? Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)? If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation).<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 Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thank you, Elaine and Kevin, for your response. <div class="">The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. </div><div class=""><br class=""></div><div class="">Thank you. </div><div class=""><br class=""></div><div class="">Best </div><div class="">Smith</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <<a href="mailto:kjude@stanford.edu" class="">kjude@stanford.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class=""><div class=""> Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server</div><div class=""><br class=""></div><div class=""><a href="https://rosie.rosettacommons.org/symmetric_docking" target="_blank" class="">https://rosie.rosettacommons.org/symmetric_docking</a></div><br clear="all" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><span class=""><div class="">--<br class=""></div><div class="">Kevin Jude, PhD (he/him/his)<br class=""><div class="">Structural Biology Research Specialist, Garcia Lab</div><div class="">Howard Hughes Medical Institute</div></div><div class="">Stanford University School of Medicine</div><div class="">Beckman B177, 279 Campus Drive, Stanford CA 94305</div><div class="">Phone: <a href="tel:%28650%29%20723-6431" value="+16507236431" target="_blank" class="">(650) 723-6431</a></div></span></div></div></div></div></div></div></div></div></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class="">Hi All,<div class="">Apologies for the nonrelated question!!</div><div class=""><br class=""></div><div class="">Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you </div><div class=""><br class=""></div><div class="">Best</div><div class="">Smith</div></div>
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