[Chimera-users] about transformation matrix

Tom Goddard goddard at cgl.ucsf.edu
Tue Jul 27 15:10:33 PDT 2010

Hi Julio,

   The matrixget command gives the placement of the map in Chimera world 
coordinates.  If you simply shift or rotate the map with the mouse this 
changes.  That is not what you want.  You want the placement of the map 
that was fit relative to the map it was fit into.  That is what the Fit 
in Map dialog reports in the Reply Log.  Use that.

   For transformations expressed at 3 by 4 matrices Chimera does the 
rotation first (about 0,0,0) then the translation.


> Hi,
> I am doing fitting of two maps and am getting different values of the transformation parameters: the ones given in the window where I specify the options (these seem to be correct), and those given by using the command "matrixget" --- these give a very large translation vector, and moreover, I don't see any relation between that vector and the correct translation.
> Also, could you tell me what is the order used in Chimera: rotation, then translation?  or  translation, then rotation?
> Thank you very much.
> Julio Kovacs

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