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

Tom Goddard goddard at sonic.net
Tue Nov 14 10:33:31 PST 2017

Hi Qiang,

  Glad you figured this out.  Chimera uses whatever map origin is specified in the map file, and this may not follow the EMAN2 convention of putting the origin at the center of the map.  You can change the map origin in Chimera using Volume Viewer panel menu entry Features / Coordinates, and you could save a new map with that origin with Volume Viewer menu File / Save Map As….


> On Nov 13, 2017, at 8:10 PM, 周强  wrote:
> Hi Tom,
> Thank you very much for your kind reply. 
> I have tested the Chimera matrix in EMAN2 Transform class as you described. The rotation part is consistent between Chimera and EMAN2. The translation part is also consistent if the origin index is set to the center of the map. ( For even images, the center is at (nx/2,ny/2) where the first pixel is at (0,0). For odd sized images, the center is at ((nx-1)/2,(ny-1)/2). The same concept extends to 3-D.  http://blake.bcm.edu/emanwikiEman2TransformInPython ).
> Qiang
>> -----原始邮件-----
>> 发件人: "Tom Goddard" <goddard at sonic.net>
>> 发送时间: 2017-11-14 02:13:27 (星期二)
>> 收件人: "周强" <zhouq2015 at mail.tsinghua.edu.cn>
>> 抄送: 
>> 主题: Re: [Chimera-users] the matrix reported in 'fit in map'
>> 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.
>> 	Tom
>>> 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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