<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,<div class=""><br class=""></div><div class="">I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question.</div><div class=""><br class=""></div><div class="">I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope). I want to visualize several elements together as different colors representing phases. In some cases, the boundary is fairly obvious and can be represented with an isosurface. </div><div class=""><br class=""></div><div class="">When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent. As an example, here is a silicon isosurface obscuring the other volumes inside it:</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="9989AF21-25C9-41DE-A33C-88B6861B335A" width="792" height="599" src="cid:010B4345-224C-4AAB-87EA-FBAE94143FBB@frontierlocal.net" class=""></div><div class=""><br class=""></div><div class=""><div class="">I’m setting the transparency using the colors dialog box:</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="972A47ED-5EDD-4FBE-9162-8DA0267DD6A1" width="224" height="358" src="cid:976B5763-FD2B-4B15-ABF4-8FE856506B4A@frontierlocal.net" class=""></div></div><div class=""><br class=""></div><div class="">For comparison, if I make the isosurface invisible to show the objects inside:</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="0869C0E9-23EC-4721-8F06-2612C5F570EA" width="792" height="599" src="cid:09AFFC98-5FC1-4744-A872-37C9744E0CC3@frontierlocal.net" class=""></div><div class=""><br class=""></div><div class="">If instead I use the transparency command:</div><div class=""><br class=""></div><div class="">volume #5 transparency 50</div><div class=""><br class=""></div><div class="">The isosurface turns black:</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="BBC3D90C-CEA1-4A81-92B0-2C08A29136AA" width="792" height="599" src="cid:818FF2F1-1E74-4543-9AC7-F4B4380AFA6A@frontierlocal.net" class=""></div><div class=""><br class=""></div><div class="">My question is: am I doing this incorrectly?</div><div class=""><br class=""></div><div class="">Thanks,</div><br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;">Zack Gainsforth<br class="">Space Sciences Laboratory, UC Berkeley<br class="">7 Gauss Way<br class="">Berkeley, CA 94720<br class=""><a href="mailto:zackg@ssl.berkeley.edu" class="">zackg@ssl.berkeley.edu</a></div>
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