<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">There is a Python script on the Chimera scripts page called xyzsdmap.py that does this with a slightly different file (no first column C, and 3 columns for sdev).<div class=""><br class=""></div><div class=""><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts" class="">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a></div><div class=""><br class=""></div><div class="">You could edit the file, and use that script.</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><blockquote type="cite" class=""><div class="">On Sep 14, 2017, at 10:36 AM, George Tzotzos 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; -webkit-line-break: after-white-space;" class="">I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below). <div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">727</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156); min-height: 13px;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""></span><br class=""></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 25.54114723 39.11305046 0.03241467</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 26.54114723 40.11305046 0.03353754</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 28.54114723 40.11305046 0.03223133</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 29.04114723 37.61305046 0.03259914</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 30.04114723 41.11305046 0.03254872</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 31.54114723 28.11305046 0.03995054</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 32.04114723 38.11305046 0.02878203</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">C 3.46464014 33.04114723 42.61305046 0.02801451</span></div></div><div class=""><br class=""></div><div class="">Is there a way to visualise in Chimera the protein together with volumetric map?</div><div class=""><br class=""></div><div class="">Thank you in advance for any advice</div><div class=""><br class=""></div><div class="">George</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><br class=""></div></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="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>