[Chimera-users] IMOD scaling and alignment

Tom Goddard goddard at cgl.ucsf.edu
Tue Jun 5 17:08:28 PDT 2007

Points placed in IMOD may not have proper scale and alignment when 
opened in Chimera together with the original MRC map.  There are some 
IMOD settings that can fix this.

Jeff wrote:
> great,
> I don't know if I replied earlier or not, but if the issue comes up 
> with anyone else, setting the magnitude of the IMOD model (which a 
> user would typically do in the IMOD tool 3dmod) to be equal in 
> magnitude to the pixel size listed in the MRC header of the 
> desired/corresponding volume map is enough to ensure the proper 
> scaling; the default for units in 3dmod appears to be nm, while in MRC 
> files it is generally Angstroms. Applying a translation equal to the 
> origin offset that chimera uses in the MRC header is then sufficient 
> to co-register the two.
> -J

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