[Chimera-users] color by height

Tom Goddard goddard at sonic.net
Mon Jul 8 17:41:07 PDT 2013

Hi Pedro,

  Here's a method to color a density map surface with colors varying along the viewing direction.  Use the following command (note the "-" at the end) to report the orientation of the model

matrixget -

then use Favorites / Reply Log to see the reported orientation and use the first 3 numbers of the last row of the 3 by 4 matrix as the coloring axis in the Surface Color dialog (with color by height), or in the scolor command.  That vector is the axis pointing out of the screen expressed in coordinates of the model.  The reason this method gives the desired axis is that the first 3 columns of the reported 3 by 4 matrix are a rotation mapping the model coordinates to the screen coordinates.  The inverse of that matrix maps screen coordinates to model coordinates and the axis we want is obtained by mapping the screen z axis to model coordinates, and that is the last column of the inverse matrix.  Since the inverse of a rotation matrix equals the transpose of that matrix, the desired axis is the last row of the 3x3 rotation matrix.


On Jul 4, 2013, at 7:34 AM, p.j.depablo <p.j.depablo at gmail.com> wrote:

> Hi everybody
> I am interested in coloring an EM volume by height. In this option you can change the origin and the axis of coloring. Specifically, I rotate t the structure untill a  desired orientation. Then, I would like to choose the axis of coloring to be the same as the view axis, but can not find the viewing axis coordinates. Is there possible to find this informaton anywhere?
> Thank you in adavance.
> Pedro
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