[Chimera-users] Re: About resolution and origin

Tom Goddard goddard at sonic.net
Wed May 2 20:34:30 PDT 2012

Hi Yuhong,

   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.


> Hi friend,
> Thanks for you kindly answer.
> 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 
> "(http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates). 
> 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.
> Hope to hear from you very soon.
> Yuhong Lee
> ------------------------------------------------------------------------
> *发件人:* Tom Goddard
> *收件人:* Yuhong Li **
> *发送日期:* 2012年5月3日, 星期四, 上午 2:01
> *主题:* Re: [Chimera-users] About resolution and origin
> 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.
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#symmetry
>   Tom
>> 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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