<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 Albert,<div class=""><br class=""></div><div class=""> You need finer phi and theta steps to get a smoother appearance. I found that 10 degree steps gives chunky appearance, while 3 degree steps givs smooth appearance. Chimera does not have code to make an arbitrary surface smoother.</div><div class=""><br class=""></div><div class=""> Maybe you are interested in making these surfaces all in Python instead of using BILD. Here is how it is done in our newer ChimeraX program.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics" class="">http://plato.cgl.ucsf.edu/trac/chimera/wiki/SphericalHarmonics</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="C543760C-73D4-4E52-B903-A499FC8FAA51" width="801" height="374" src="cid:939E450C-16C8-49F4-BC2F-7A8E2E5F7291" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 28, 2020, at 1:54 AM, Albert Smith-Penzel <<a href="mailto:Albert.Smith-Penzel@medizin.uni-leipzig.de" class="">Albert.Smith-Penzel@medizin.uni-leipzig.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hello,<div class=""><br class=""></div><div class="">I have a question about improving user defined graphics in Chimera.</div><div class=""><br class=""></div><div class="">For background (maybe not necessary for answering):</div><div class="">I’m working with nuclear magnetic resonance and MD simulation, and so I want to plot dynamically averaged spin-spin (H–C) dipole tensors, obtained from MD, on top of the corresponding H–C bonds. I’ve been relatively successful, but while one has a very high-resolution picture of the molecule itself, the tensors themselves are visibly triangulated.</div><div class=""><br class=""></div><div class="">How I get this plot:</div><div class="">Each tensor is expressed first in spherical coordinate (theta, phi, r). In python, I run Delauney from scipy.spatial on theta and phi to get a list of vertices that can be used for triangulation of the tensor. Then, for each tensor, I convert theta, phi, and r into cartesian coordinates, shift the center so that the tensor sits on top of the correct bond. Finally, I create a .bild file where I write out each triangle using the coordinates and vertices. Tensors have negative and positive values (red and blue in the plot), and so I only take triangles for which r for all vertices is positive, and then in a second step, take only triangles where all vertices are negative. This all gets written to the .bild file, and then opened in chimera on top of the molecule (see picture).</div><div class=""><br class=""></div><div class="">The question:</div><div class="">The result is certainly acceptable, however, there is clearly a quality difference in the molecule rendering vs. the tensor rendering (obviously, because the tensors are just made of triangles that I’ve created in python). Is there a better way to bring the surface data describing the tensors into chimera that would then allow usage of some sort of smoothing within chimera for a nicer image? (And possibly with a relatively simple data format….)</div><div class=""><br class=""></div><div class="">Thanks for your help!</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Albert Smith</div><div class=""><br class=""></div><div class=""><span id="cid:9956C594-C972-4C35-8662-7C00F4B5029B@wlan.intern.uni-leipzig.de"><example_triangulation.png></span></div></div></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>