It turns out that the math that transformed a uniform sphere into an ellipsoid was over-complicated and wrong.  That'll teach me to crib code from other programmers in the lab. ;-)  Also, I wasn't taking the square root of the eigenvalues like I should have, since the U matrix is in units of length squared.

I committed fixes for both problems and if tonight's build works then they'll be in the daily build available tomorrow.  Check that the date in the table is at least July 6th.  Otherwise the build failed and you'd have to try again the next day.

--Eric  

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu

On Jul 5, 2009, at 11:37 PM, Michael K. Gilson wrote:

Hi,

Chimera and PyMol are showing very different thermal ellipsoid
orientations for the same PDB file, and I have reason to believe that
the PyMol display is the right one.
Here are the first two lines of the PDB file I am reading in:

Atom      1 O1   CUC     1       3.345   1.613   0.172
ANISOU    1 O1   CUC     1      619    156    528    150     43     -6
ATOM      2 O2   CUC     1      -1.699   0.125   2.792
ANISOU    2 O2   CUC     1      497    355    848    128    -68    204

I would appreciate help with this because Chimera appears to provide
more detailed control of the coloring of the ellipsoids than PyMol does.

I'll be happy to provide screenshots or other information.

Regards,
Mike

_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users