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Hi Yuhong,<br>
<br>
If by "origin of the map" you mean the x,y,z physical coordinates
(e.g. in Angstroms) of grid index 0,0,0 then you would calculate
that using the grid index of the xyz origin (called the "origin
index") and the grid plane spacing. For example if the grid plane
spacing is 3 Angstroms, and the origin index is 50,50,50, then the
x,y,z position of grid point 0,0,0 is -150,-150,-150. The x,y,z
position of any grid point can be computed similarly.<br>
<br>
Tom<br>
<br>
<br>
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<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 moz-do-not-send="true"
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>
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<hr size="1"> <b><span style="font-weight:bold;">发件人：</span></b>
Tom Goddard<br>
<b><span style="font-weight: bold;">收件人：</span></b>
Yuhong Li <b><span style="font-weight: bold;"></span></b><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>
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<div> 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 moz-do-not-send="true" 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>
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