[chimera-dev] Origins in CCP4 and MRC maps

[Bernard Heymann]

Hi Tom

Thanks for the clarification. It turns out I had no idea how the new  
origin fields are interpreted. It is also not clear from the limited  
documentation how it should be interpreted and there are no example  
images to see how it is done. So I decided to just follow your  
explanation and fix it in Bsoft such that it displays correctly in  
Chimera.

Thanks again

Bernard

On Oct 23, 2007, at 2:24 PM, Tom Goddard wrote:

> Hi Bernard,
>
>  The Chimera origin reported in the Volume Viewer dialog is not the  
> array index of physical origin.  It is the physical coordinate of  
> array index 0,0,0.  So it is the inverse of how you are  
> interpreting it.  We've been using this definition since about  
> 2000, before your 2006 paper on conventions for EM maps.  With this  
> understanding your example of a 100^3 map with physical origin at  
> array index (50,50,50) and 2 angstroms/voxel the index (0,0,0)  
> physical coordinate is (-100,-100,-100) which you say Chimera  
> reports for a CCP4 map.
>
>  Chimera uses the xorigin, yorigin, zorigin header values (words  
> 50-52) in MRC2000 format instead of the nxstart, nystart, nzstart  
> header values (words 5-7).  You probably have (50,50,50) in the xyz  
> origin fields while
> Chimera expects (-100,-100,-100) in those fields.  The MRC  
> documentation
>
>    http://www2.mrc-lmb.cam.ac.uk/image2000.html
>
> unfortunately does not describe the meaning of those origin fields,  
> though I suspect your interpretation is correct as it agrees with  
> nxstart,nystart,nzstart definition and would just provide floating  
> point equivalents of those integer values.  Perhaps there is better  
> MRC documentation defining xorigin,yorigin, zorigin.  Chimera  
> writes MRC2000 files and fills the origin fields with the physical  
> coordinate of index (0,0,0).
>
>  These different interpretations of the meaning of the origin  
> fields are a big problem.  How are the xorigin,yorigin,zorigin  
> fields in MRC2000 actually being used?  I know Chimera and EMAN  
> both interpret it as a physical coordinate of array index (0,0,0).   
> From your comments I assume BSOFT interpets it as the array index  
> of the physical coordinate origin.  What other software is using  
> these fields and how do they interpret it?
>
>  It would be a big problem to change the origin definition in  
> Chimera because users have written many MRC2000 files using Chimera  
> that would no longer be positioned correctly if the meaning of the  
> origin fields is changed.  Chimera does not write information in  
> the MRC labels header fields indicating which version of Chimera  
> wrote the file.  That was a mistake.  So there is no way of telling  
> which interpretation should be used for a Chimera-written MRC  
> file.  EMAN currently writes a label line saying EMAN and the date  
> and time the file was written.
>
>    Tom

Bernard Heymann, Research Fellow
Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH
Bethesda MD 20892-8025
Tel. 301-451-8241, Fax. 301-480-7629



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