I failed to mention that this particular group is a small set of
terminal residues (48 atoms I think) that are part of a poorly-
resolved HIS tag, so it turns out not to be a meaningful part of the
model anyway. I was just surprised to see negative values reported.
The other body (different structure) that gives a negative value has
as the smallest mean-squared displacement -0.27. I take it that this
simply means that the mean-squared displacement is near zero and that
I am seeing numerical error. It seems strange to encounter a near-
zero displacement in some direction, but one of the examples in the
TLS documentation shows exactly this behavior as well. Here are the
parameters:
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
0.633 0.420 0.650 4.952 50.71
65.17 49.45
-0.363 0.903 -0.230 -0.268 111.29
25.44 103.27
-0.683 -0.091 0.724 10.899 133.12
95.21 43.59
MEAN LIBRATION (TRACE/3) 5.194
On Feb 26, 2007, at 4:40 PM, Winn, MD (Martyn) wrote:
I'd also comment that the absolute values are quite large. Well, I
have no
knowledge what groups you've chosen, but for domain-sized groups,
typical
values are 1-10 deg**2. Values can be larger for smaller TLS
groups. This is
just a rule-of-thumb, but would make me suspicious whether the TLS
refinement
was really stable in this case.
Regards
Martyn
-----Original Message-----
From: CCP4 bulletin board on behalf of Richard Gillilan
Sent: Sun 2/25/2007 1:10 PM
To: [email protected]
Subject: [ccp4bb] TLSANL: negative mean-sq displacements?
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
