<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="">For a density map you can control the number of surface triangles and vertices by choosing the subsampling “step” size in the Volume Viewer dialog. Step 2 will use every other grid point along x,y,z axes and result in a coarser mesh. For molecular surfaces computed from atoms, change the vertex density as described here<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-January/005889.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jul 31, 2018, at 5:53 AM, עמיחי הולצר wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="rtl" class=""><div dir="ltr" class="">And another question - there is "<span style="white-space: pre-wrap;" class="">Surface and Mesh options" under the "Features" tab, so one can control the smoothing of the surface, thickness, etc. How can I control the number of nodes of the surface? I mean, I want the mesh </span><font class=""><span style="white-space:pre-wrap" class="">not to be so dense. Is it possible?</span></font></div><div dir="ltr" class=""><font class=""><span style="white-space:pre-wrap" class=""><br class=""></span></font></div><div dir="ltr" class=""><font class=""><span style="white-space:pre-wrap" class="">Thanks again!</span></font></div></div><div class="gmail_extra"><div dir="ltr" class=""><br class=""><div class="gmail_quote">2018-07-31 13:38 GMT+03:00 עמיחי הולצר :<br class=""><blockquote class="gmail_quote" style="margin:0 .8ex;border-left:1px #ccc solid;border-right:1px #ccc solid;padding-left:1ex;padding-right:1ex"><div dir="rtl" class=""><div dir="ltr" class="">When I save it as OBJ file, how can I watch it in chimera again as a molecule with "atoms" and "bonds" (like CONECT line in pdb file)?</div><div dir="ltr" class="">I see that OBJ file look like a xml file, and contains coordinates and edges, but does it reflect the mesh?</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">Thanks,</div><div dir="ltr" class="">Amichai</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote"><div dir="ltr" class="">2018-07-30 19:37 GMT+03:00 Tom Goddard :</div><blockquote class="gmail_quote" style="margin:0 .8ex;border-left:1px #ccc solid;border-right:1px #ccc solid;padding-left:1ex;padding-right:1ex"><div style="word-wrap:break-word;line-break:after-white-space" class="">Hi Amichai,<div class=""><br class=""></div><div class=""> Chimera computes density map isosurfaces using the marching cubes algorithm. It can be saved in various file formats for example OBJ, others are described with the export command</div><div class=""><br class=""></div><div class=""><span class="m_5485483688103864686m_-3332512580404104184Apple-tab-span" style="white-space:pre-wrap"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/export.html" target="_blank" class="">https://www.cgl.ucsf.edu/chime<wbr class="">ra/docs/UsersGuide/midas/expor<wbr class="">t.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class=""><div class="m_5485483688103864686h5"><div class="">On Jul 29, 2018, at 3:06 AM, עמיחי הולצרwrote:</div><br class="m_5485483688103864686m_-3332512580404104184Apple-interchange-newline"></div></div><div class=""><div class=""><div class="m_5485483688103864686h5"><div dir="rtl" class=""><div dir="ltr" class="">Hi Chimera support,</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">I have 2 questions:</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">1. How does Chimera calculate the mesh from the density map?</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">2. How can I save the mesh as a file?</div><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">Thanks a lot,</div><div dir="ltr" class="">Amichai Holzer</div><div dir="ltr" class="">Huji</div></div></div></div>
______________________________<wbr class="">_________________<br class="">Chimera-dev mailing list<br class=""><a href="mailto:Chimera-dev@cgl.ucsf.edu" target="_blank" class="">Chimera-dev@cgl.ucsf.edu</a><br class=""><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev" target="_blank" class="">http://plato.cgl.ucsf.edu/mail<wbr class="">man/listinfo/chimera-dev</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br class=""></div>
</div></div></blockquote></div></div></div>
</div></blockquote></div><br class=""></div></body></html>