I wouldn't call it numerical error, as such. Refmac doesn't
restrain/constrain the T, L or S values at all. In particular, the L
value can refine stably and accurately to a negative value.
Refmac is refining a set of ADPs constrained to fit a certain functional
form with parameters T, L and S. That functional form is derived from a
rigid body model. If L goes negative, then the assumption of a rigid
body breaks down. But you still have a set of ADPs that describe your
data.
So with an L eigenvalue = -0.268 you can probably say that you are close
to a rigid body model with virtually no libration about one axis. The
rigid body model is only a rough assumption - you should have the same
caveats if you have L = +0.268
With L = -53.975, you may well have numerical instabilities, or you are
so far from a rigid body model that the results are meaningless. And
your individual ADPs are probably bad as well.
Cheers
Martyn
On Tue, 2007-02-27 at 09:23 -0500, Richard Gillilan wrote:
> 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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