<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=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Tiru,<div class=""><br class=""></div><div class="">If the center of symmetry is at 0,0,0 for your model and it just needs 6 rotated copies placed use Chimera command<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sym #0 group c6</div><div class=""><br class=""></div><div class="">where #0 is the model number of your monomer. If you do not know the center of symmetry or how the monomers interface with each other (ie their orientation in the hexamer), then that is a protein-protein docking problem and the sym command does not solve that. For that case you would need to fit in a cryoEM or X-ray map of the hexamer, or align the monomer to a known homologous hexamer, or find some amazing oligomeric structure prediction tool.</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><div class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 1, 2021, at 11:24 AM, Tiru Hcu <<a href="mailto:tiru.hcu09@gmail.com" class="">tiru.hcu09@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="auto" class="">Hi Tom, <div dir="auto" class=""><br class=""></div><div dir="auto" class="">Thank you for your response. My protein symmetry is a hexamer. Please would you mind sharing a little elaborate how to to do in chimera. Thank you. </div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Best regards,</div><div dir="auto" class="">Tiru</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 1 Sep 2021, 21:10 Tom Goddard via Chimera-users, <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;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 style="white-space:pre-wrap" class=""> </span>tom</div><div class=""><br class=""><div class=""><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" target="_blank" rel="noreferrer" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><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" target="_blank" rel="noreferrer" 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" rel="noreferrer" 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" rel="noreferrer" 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" rel="noreferrer" 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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