[Chimera-users] About resolution and origin

Tom Goddard goddard at sonic.net
Wed May 2 11:01:20 PDT 2012

Hi Yuhong,

   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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