<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Dieter,<div><br></div><div> Chimera does not make masks with cosine falloff. The only mask smoothing in Chimera is "vop falloff". The algorithm is completely described in the Chimera manual (copied below) and basically amounts to a "heat equation" falloff -- the grid points outside the mask are assigned the average of the neighboring values, essentially the diffusion of heat from the masked ones region to the outside zeros region. This works for any shape.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div>"vop falloff volume-spec [ iterations M ] general-options</div><div><br>Smooth the boundaries of a masked map by replacing the value at each grid point outside the boundary with the average of the values of its six nearest neighbors, for M iterations (default 10). All grid points with values of zero before the first iteration are taken to be outside the boundary, thus assigned a new value at each iteration. Thanks to Greg Pintilie for the initial implementation."</div><div><br></div><div><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Dieter Blaas <br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [Chimera-users] generate raised cosine smoothed mask with "mask ones" and "vop falloff"</b><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">November 26, 2013 8:34:17 AM PST<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1.0);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Tom Goddard <br></span></div><br>
<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type">
<div text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi Tom,<br>
<br>
thanks for these explanations! I am still not sure whether such
a mask behaves like a mask made with e.g. xmipp_transform_mask or
with spider MA SOFT. I'd like to make an arbitrary mask (level 0
- 1) from a molecular volume which has a raised_cosine falloff.
When comparing a spherical mask made with chimera (as given below)
and with xmipp their histograms look quite different (probably
also a question of the choice of parameters). The difference
becomes much more striking when using a more irregular shaped
molecular assembly. I found the Chimera procedure when looking for
a method to make such masks as this is not provided in xmipp (only
a sphere or a crown with raised-cosine but not an irregularly
shaped mask). I want to use it in 3D-reconstructions......<br>
<br>
Best, Dieter<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
Am 25.11.2013 21:25, schrieb Tom Goddard:<br>
</div>
<blockquote cite="mid:1046690F-4B57-4A9F-A589-DD0F149AA10E@sonic.net" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
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 moz-do-not-send="true" 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><br>
</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>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
------------------------------
</pre>
</div>
<img name="Screenshot.png" id="fe3330a5-eeb5-44ff-b082-c86e8ca33c11" height="710" width="946" apple-width="yes" apple-height="yes" src="cid:D7769CF1-F382-4CE9-BA8C-29418B7647DF@cgl.ucsf.edu"></blockquote></div><br></div></body></html>