[Key-worded input file]

Using rigid groups defined in TLSIN, it can fit TLS values to the observed U values. These are output in TLSOUT, and residual U values are output in XYZOUT. The so-called L2 norm is used as the residual for fitting U's calculated from TLS tensors to the observed Us obtained from refinement.

The program can also analyse the input anisotropic U values in terms of Rosenfield's rigid-body postulate. Output plots give an indication of whether groups of atoms (as defined in TLSIN) have U values conforming to rigid-body-like displacements. A postscript plot is also produced which may hint at possible rigid groups.

The plots against residue may be useful for visualising U values obtained from the program TLSANL. However, the rigid group analysis is less useful, since in this case the U values will have been obtained from a rigid group description in the first place.

Input coordinates with anisotropic U values held in standard ANISOU records. The elements of U are assumed to appear as integers representing 10000*Uij in orthogonal coordinates, and in the order U11, U22, U23, U12, U13, U23.

The program will check for non-positive-definite anisotropic U values, and report any found to the log file. Non-positive-definite means that one of the eigenvalues is less than or equal to zero, which in turn means that one of the radii of the thermal ellipsoid has vanished.

For all pairs of atoms, the absolute difference in the projection as a fraction of the mean projection (the "delta" value) is calculated, and all such differences are binned (see the keyword DUBINS). These "delta" values are displayed graphically in a postscript plot (file PSOUT, default anisoanl.ps). Light shading implies low "delta" value, consistent with the atoms belonging to the same quasi-rigid group. Dark shading means the atoms are unlikely to belong to the same quasi-rigid group. Atom selection can be done with the file TLSIN - only atoms specified in this file are used in the calculation. For example, clearer results may be obtained if only CA atoms are used. See Tom Schneider's article for an example of this kind of plot.

The distribution of "delta" values is included in the log output (see keywords DUBINS and DURANGE). Possible quasi-rigid bodies should be defined using the TLSIN file (see example below). The distribution is plotted for all pairs of atoms within each quasi-rigid body, and a final plot gives the distribution for pairs of atoms from different groups. If the choice of rigid bodies is good, the differences should be significantly smaller within groups than between them. A subset of atoms can be chosen using the atom selection field in TLSIN (e.g. "CA" may be useful for large rigid groups).

- Uiso
- The equivalent isotropic U factor calculated as 1/3*trace(U).
- R2FROMORIG
- The square of the distance from the local origin. If the FITTLS option is being used, then the local origin is taken to be the origin of the TLS group to which the atom belongs. Otherwise, the local origin is taken to be the centroid of the chain to which the atom belongs (i.e. the mean atomic coordinates of that chain). The values of R2FROMORIG are divided by a scaling factor (currently 3000) for convenience of plotting.
- Anisotropy
- This is defined as the ratio of the smallest to the largest eigenvalue of U.
- PROLMEAN
- This factor is defined as the ratio of the middle to the largest eigenvalue of U. If the thermal ellipsoid corresponding to U is oblate (disc-like), then this factor will be close to 1. If however it is prolate (cigar-like), then this factor will be close to the value of the anisotropy
- URADMEAN
- The projection of U onto a radial vector from the local origin (see above) to the atomic position.
- UTANGMEAN
- The average value of U projected on to a plane perpendicular to the radial vector.
- UISOMEAN2, ANISOMEAN2, PROLMEAN2
- If TLS groups have been fitted, then the values of Uiso, A and PROLMEAN as derived from the fitted TLS parameters are also given.
- Radial distribution of Urad and Utang
- In a separate graph, Urad and Utang are plotted against R**2. For rigid body motion, Urad should be constant, and Utang linear in R**2.

anisoanl xyzin holo_adh.pdb tlsin holo_adh.tls \ xyzout holo_resid.pdb tlsout holo_out.tls <<eof FITTLS RIGIDBODY OFF PLOT MAINCHAIN END eof

anisoanl xyzin 1exr.pdb tlsin 1exr.tls <<EOF FITTLS OFF RIGIDBODY DUBINS 8 10 DURANGE 0.2 PLOT OFF END EOFwhere the rigid groups are defined in 1exr.tls as:

REFMAC TLS Chain A RANGE 'A 16.' 'A 16.' CG CD1 CD2 CE1 CE2 CZ TLS Chain A RANGE 'A 19.' 'A 19.' CG CD1 CD2 CE1 CE2 CZThe two rigid groups are two PHE side chains. This example gives a clear indication of the two phenyl groups acting as rigid-bodies. Similar results can be obtained for domain-size quasi-rigid bodies, though never as clear-cut.

In this case, the postscript plot is unhelpful - it is more helpful for looking at larger groups of atoms.

- arginine kinase transition-state analogue complex at 1.2A
- Yousef M.S., Fabiola F., Gattis J.L., Somasundarama T. and Chapman M.S. (2002)
*Acta.Cryst.*,**D58**, 2009 - calmodulin
- Wilson, M.A. and Brunger, A.T. (2003)
*Acta.Cryst.*,**D59**, 1782 - GroEL
- C Chaudhry, A L Horwich, A T Brunger and P D Adams (2004)
*J. Mol. Biol.*,**342**, 229

RASTEP (Raster3D Thermal Ellipsoid Program) - plotting of thermal ellipsoids.

- Martyn Winn,
*CCP4 Newsletter*March 2001,**39**

ANISOANL - analysing anisotropic displacement parameters - R.E.Rosenfield, K.N.Trueblood and J.D.Dunitz,
*Acta Cryst*,**A34**, 828 - 829 (1978)

Rigid-body postulate. - T.R.Schneider,
*Proc. CCP4 Study Weekend*, 133 - 144 (1996).

Application of rigid-body postulate to protein SP445. - V. Schomaker and K.N.Trueblood,
*Acta Cryst.*,**B24**, 63 - 76 (1968)

Original description of TLS. - V. Schomaker and K.N.Trueblood,
*Acta Cryst.*,**B54**, 507 - 514 (1998)

Description of THMA program for small molecules, which fits TLS parameters (and more) to refined U values.