<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: 'times new roman', 'new york', times, serif; "><span>Hi friend,</span></div><div><span>Thanks for you kindly answer. </span></div><div><span>But maybe I didn't make my origin question clear. Let me explain it. According to the chimera documentation, "Origin index refers to the grid indices of the XYZ origin "(<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates</a>). But the origin I mentioned before actually refers to the origin of the map. And apparently they are different, So I want to know where can I obtain "the origin of the map" instead of the origin index.</span></div><div><span>Hope to hear from you very
soon.</span></div><div><span>Yuhong Lee</span></div><div style="font-family: 'times new roman', 'new york', times, serif; "><br></div> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div style="font-size: 12pt; font-family: 'times new roman', 'new york', times, serif; "> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">发件人：</span></b> Tom Goddard <goddard@sonic.net><br> <b><span style="font-weight: bold;">收件人：</span></b> Yuhong Li <leon1991@yahoo.cn> <br><b><span style="font-weight: bold;">抄送：</span></b> "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> <br> <b><span style="font-weight: bold;">发送日期：</span></b> 2012年5月3日, 星期四, 上午 2:01<br> <b><span style="font-weight: bold;">主题:</span></b> Re: [Chimera-users] About resolution and origin<br> </font> </div> <br><meta
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Hi Yuhong,<br>
<br>
I don't know what kind of map you have. If it is a
single-particle electron microscope reconstruction, then the most
common way to determine resolution is Fourier shell correlation.
The original 2-d micrographs are divided into two sets and two 3-d
maps are computed and then you see how far out in frequency the maps
agree. Chimera does not do 3-d reconstructions so this would have
to be done before analysis in Chimera. In the Chimera Fit in Map
dialog it will suggest a default resolution under Options "Use
simulated map from atoms at resolution...". The default is 3 times
the grid plane spacing. Often the map grid spacing is chosen to be
about 1/3 the resolution -- a level of oversampling that provides
nicer visualization.<br>
<br>
I don't understand your origin question. Maybe you mean how do
you find the center of symmetry of a symmetric map. The measure
symmetry command can do that. For example, "measure symmetry #0" if
your map is model #0. Here is documentation.<br>
<br>
<a rel="nofollow" class="yiv2112036025moz-txt-link-freetext" target="_blank" href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#symmetry">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#symmetry</a><br>
<br>
Tom<br>
<br>
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<div>Hi friends,</div>
<div>Firstly, I was wondering how to know the resolution of my
map since one day I opened volume viewer...tools...fit to
segments. And I found that there displaying "density map
resolution". So my question is whether that number is the
correct resolution of my map?</div>
<div>Secondly, in the volume viewer...corrdinates I can know the
origin index, but how can I know the origin?</div>
<div>These questions may seem to be stupid, but I just want to
know. So h<span style="font-size:12pt;">ope to hear from you
very soon!</span></div>
<div>Best Wishes,</div>
<div>Yuhong Lee</div>
</div>
<br>
</blockquote>
<br>
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