[Chimera-users] Volume transformation based on Phenix symmetry operators

Tom Goddard goddard at sonic.net
Thu Nov 12 16:37:40 PST 2015

Hi Kyle,

  You could use the Chimera “matrixset” command:

	http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/matrixset.html <http://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/matrixset.html>

You would put the rotation and translation in a file in a 3 by 4 matrix format with the first 3 columns being a rotation (applied about 0,0,0) and the 4th column being a translation that happens after the rotation.  I’m not quite sure what you need to use for the rotation sicne your output has “tran_orth" and “center_orth” and it may be that the 3x3 rotation you have may need to be transposed depending on Phenix conventions.

  To use matrixset I would open two copies of the density map in Chimera.  Don’t move the maps with the mouse or there transforms will be changed.  Then use matrixset <filename> to change the transform of one copy (model #0).


> On Nov 12, 2015, at 3:25 PM, Morris, Kyle  wrote:
> Dear Chimera developers and community,
> I have a volume and an associated symmetry operator identified by another software package for this map.
> I would like to transform the map according to the symmetry operator to inspect what the symmetry related map looks like, does anyone know how to do this based on the appended matrix?
> Thanks in advance for your help!
> Best wishes,
> Kyle
> ==================================
> From Phenix:
> new_operator
> rota_matrix   -0.0877   -0.5114    0.8549
> rota_matrix    0.9251   -0.3601   -0.1206
> rota_matrix    0.3695    0.7803    0.5047
> tran_orth   578.6845  434.1862  -508.9168
> center_orth  918.6495  790.3525  1034.0200
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