Ok, Painter and Merritt describe this situation in their Acta Cryst
(2006) D62 439-450 article entitled "Optimal description of a protein
structure in terms of multiple groups undergoing TLS motion." At
least with regard to fitting L parameters from previously refined
data, negative eigenvalues of L can happen as a result of deviations
from the rigid body assumption (deformations). In such cases, it
would seem that the resulting principle axes are meaningless. Painter
and Merritt provide a means of constraining the L parameters so as to
always yield positive eigenvalues, but it is unclear to me if Refmac5
refinement applies any such constraint.
Can anyone confirm this?
If this is the case, then principle axes of ANISO records generated
from TLSANL are also questionable for these particular bodies as are
thermal ellipsoids.
Richard Gillilan
MacCHESS
On Feb 25, 2007, at 8:10 AM, Richard Gillilan wrote:
After TLS refinement (which seemed to be stable and produced nice
R_free values), I have analyzed the rigid body results with TLSANL.
I get negative mean-square displacements along the axes of
libration WRT to orthogonal axes! Am I misunderstanding something
here? The units are (deg^2). I see this with two different
structures. Here is the output from TLSANL:
AXES OF LIBRATION WRT TO MEAN-SQUARE ANGLE
LIBRATION AXES MAKE TO
ORTHOGONAL AXES (IN ROWS) DISPLACEMENT ORTHOGONAL
AXES (DEG)
ABOUT AXES (DEG^2) X Y Z
0.842 0.197 0.502
-53.975 32.66 78.63 59.85
-0.494 0.657 0.570
193.421 119.60 48.97 55.24
-0.217 -0.728
0.650 -12.276 102.55 136.73 49.45
MEAN LIBRATION (TRACE/
3) 42.390
Anyone seen this happen before?
Richard Gillilan
MacCHESS
