<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Dieter,<div><br></div><div> You should be able to generate a smooth volume mask using "mask ones" and "vop falloff" in Chimera. Here's an example making a smooth cylinder mask</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>shape cylinder radius 100 height 100 caps true</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>mask ones #0 border 10</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>vop falloff #1 iter 100</div><div><br></div><div>The boundary smoothing "vop falloff" is described on this web page</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html">http://www.cgl.ucsf.edu/chimera/data/falloff-sep2012/falloff.html</a></div><div><br></div><div>Maybe you saw that page and got tripped up because it gave the wrong option name "step" instead of "iterations" in the vop falloff command -- I've fixed the web page.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><img height="401" width="557" apple-width="yes" apple-height="yes" id="ff997463-da10-4cd9-aa78-42a1a4ae1da0" src="cid:6A4C47BD-785D-40B4-9CE7-2EDC153E7E14@cgl.ucsf.edu"></div><div><br><div><div>On Nov 24, 2013, at 12:41 AM, Dieter Blaas wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br> I was wondering whether it is possible to generate binary raised cosine smooth masks with 'masked ones' followed by 'vop falloff' or anything alike. I'd like to generate an arbitrary mask (from a volume) with a smooth transition (over some few pixels) to 0 but I did not really find adequate parameters. Is this possible?<br>Thanks, D.<br><br>-- <br>------------------------------------------------------------------------<br>Dieter Blaas,<br>Max F. Perutz Laboratories<br>Medical University of Vienna,<br>Inst. Med. Biochem., Vienna Biocenter (VBC),<br>Dr. Bohr Gasse 9/3,<br>A-1030 Vienna, Austria,<br></blockquote></div><br></div></body></html>