[Chimera-users] Re: About resolution and origin

Yuhong Li leon1991 at yahoo.cn
Wed May 2 19:17:09 PDT 2012

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 <goddard at sonic.net>
收件人: Yuhong Li <leon1991 at yahoo.cn> 
抄送: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu> 
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.



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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