[Chimera-users] About resolution and origin
goddard at sonic.net
Wed May 2 11:01:20 PDT 2012
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.
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.
> Hi friends,
> 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?
> Secondly, in the volume viewer...corrdinates I can know the origin
> index, but how can I know the origin?
> These questions may seem to be stupid, but I just want to know. So
> hope to hear from you very soon!
> Best Wishes,
> Yuhong Lee
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