[Chimera-users] the matrix reported in 'fit in map'

Tom Goddard goddard at sonic.net
Mon Nov 13 10:13:59 PST 2017

Hi Qiang,

 The 3x4 matrix reported by Chimera has the 3x3 rotation in the first 3 columns and the translation in the last column.  I do not know EMAN2 conventions.  Chimera does not use or convert to Euler angles.  Keep in mind that the rotation is about the origin of the map coordinates which is set by the “Origin index” value (shown with Chimera Volume Viewer menu entry Features / Coordinates).  If you rotate your map about a different origin, then that becomes a non-zero translation and a rotation about the map origin.


> On Nov 10, 2017, at 8:36 PM, 周强 <zhouq2015 at mail.tsinghua.edu.cn> wrote:
> Dear Chimera developer group,
> I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. 
> Thank you very much.
> Qiang
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