[Chimera-users] About resolution and origin

Elaine Meng meng at cgl.ucsf.edu
Wed May 2 11:28:47 PDT 2012

Hi Yuhong,
If you are just looking at a map you got from EMDB, there might be information at the EMDB web site about the map resolution.  That information is supplied by the researchers who deposited the map.  You would enter the ID on this page
to see the summary, for example this one for EMDB #1023, which has resolution 42.2 angstroms.

What you see in Fit to Segments is not the resolution measured from a map.  It is a user input parameter for simulating a map from an atomic structure.  If you click the "Help" button on the dialog, the resulting manual page includes an explanation of this and the other settings in the dialog.

On May 2, 2012, at 11:01 AM, Tom Goddard wrote:

> 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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