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: [log in to unmask]
> 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
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