[Chimera-users] thermal ellipsoids
pett at cgl.ucsf.edu
Mon Jul 6 17:22:46 PDT 2009
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.
UCSF Computer Graphics Lab
On Jul 5, 2009, at 11:37 PM, Michael K. Gilson wrote:
> 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
> I'll be happy to provide screenshots or other information.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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