TLSANL (CCP4: Supported Program)
NAME
tlsanl
 analysis of TLS tensors and derived anisotropic U factors
SYNOPSIS
tlsanl xyzin
input.brk
tlsin
input.tls
xyzout
output.brk
[ axes
output.in ]
[Keyworded input]
The program analyses TLS tensors and is intended for use with the
output of RESTRAIN or
REFMAC.
TLSIN
An ASCII file containing details of the TLS groups and the values
of the corresponding T, L and S tensors. See the
RESTRAIN documentation for
details of the file format. In addition to the records described
there, the file may contain a line "REFMAC" denoting that
the file has been output from the refinement program
REFMAC, which has a different order
of tensor elements.
XYZIN
Input coordinates in PDB format. ANISOU records are ignored. ATOM records
may contain the full B factor (as output by RESTRAIN) or only the
residual B factor (which doesn't include the contribution from the TLS
parameters, as output by REFMAC). The program interprets the B factors
according to the keyword BRESID.
XYZOUT
Output coordinates and anisotropic tensors in PDB format. The ATOM
records may contain the full B factor, the residual B factor, or the
TLScomponent of the B factor according to the keyword
ISOOUT. The ANISOU records contain the full
anisotropic displacement parameters, irrespective of the ISOOUT keyword.
AXES
Output file containing the axes for translation, libration,
screwrotation, reduced translation and nonintersecting
screwrotation. The file is in a suitable format for including in a
MOLSCRIPT .in file. See AXES
keyword below.
Available keywords are:
ANISO,
BINPUT,
BRESID,
ISOOUT.
AXES.
END,
ANISO
Do anisotropic tensor analysis (default: don't). The principal axes of the
anisotropic tensor are determined for each atom in each TLS group and written
to the log output. If the tensor is nonpositive definite, then a warning
is given. The anisotropic tensor includes the isotropic contribution as well
as the contribution from the TLS parameters.
BINPUT [true  t  false  f]
If true (default), assume PDB file contains isotropic B factors.
Else, assume PDB file contains isotropic U factors (smaller by 8*pi**2).
BRESID [true  t  false  f]
If true, assume the ATOM records in XYZIN contain only residual B factors,
and don't include the contribution from the TLS parameters. If false (default),
assume the ATOM records contain the full B factor, including the contribution
from TLS.
ISOOUT [FULL  RESI  TLSC]
Determine whether the ATOM records in XYZOUT contain B factors calculated
from the TLS parameters (TLSC), residual B factors (RESI), or the sum
of both (FULL). Default is FULL.
AXES [ < scale > ]
A file (logical name AXES) is output containing the axes for
translation, libration, screwrotation, reduced translation and
nonintersecting screwrotation, for each TLS group. All axes are calculated
in an orthogonal frame with respect to the centre of reaction. The file is
in a suitable format for including in a MOLSCRIPT .in
file.
Each axis is written as a pair of coordinates (in the coordinate
system of the input PDB file) representing the beginning and the end
of the axis. For the intersecting axes, the intersection is at the
centre of reaction of the TLS group. The length of each axis is proportional
to the magnitude of the corresponding motion. The proportionality factor can be
adjusted by the argument < scale >, which defaults to 10.
END
Terminate input.
PROGRAM OUTPUT
For each TLS group included in the file TLSIN, the program outputs information
about the TLS tensors in several representations. Two coordinate origins
are considered:
 The origin used in refinement, and given by the ORIGIN record in TLSIN.
 The centre of reaction, which is the origin that makes S symmetric.
TLS tensors with respect to this origin are flagged with a prime (').
Three axial systems are considered:
 Orthogonal axes, as used in XYZIN and TLSIN
 Libration axes, i.e. the principal axes of the L tensor. TLS tensors
in this axial system are flagged with a caret (^).
 Rigidbody axes.
The values of the T, L and S tensors are given with respect to both
origins, and in the first two axial systems. The L tensor is in general independent of
the origin, and in particular is the same for both origins considered here. In the axial
system defined by the libration axes only, the diagonal elements of
S are also independent of origin.
The values of the T and S tensors held in TLSIN thus depend on the origin chosen for
their calculation. The Centre of Reaction, however, is independent of the original
origin, and hence so are quantities calculated with respect to the Centre of Reaction.
The rigid body motion can also be described as 3 screw motions about 3
nonintersecting axes parallel to the libration axes, together with a
reduced translation tensor (see Schomaker and Trueblood (1968)).
The program gives the absolute position of these screw axes and the pitch of
the screw motion along them, followed by the reduced translation tensor.
For files generated by RESTRAIN, defaults
can be accepted, although the ANISO keyword might be useful:
tlsanl XYZIN foo_in.pdb TLSIN foo_in.tls XYZOUT foo_out.pdb <<eof
ANISO
END
eof
For files generated by REFMAC, the BRESID keyword
will be needed:
tlsanl XYZIN foo_in.pdb TLSIN foo_in.tls XYZOUT foo_out.pdb <<eof
BRESID
END
eof

B.Howlin, S.A.Butler, D.S.Moss, G.W.Harris and H.P.C.Driessen,
"TLSANL: TLS parameter analysis program for segmented anisotropic refinement
of macromolecular structures.",
J. Appl. Cryst., 26, 622624 (1993)

V.Schomaker and K.N.Trueblood Acta Cryst., B24, 63 (1968)
SEE ALSO
restrain,
refmac
AUTHORS
Huub Driessen, David Moss, Ian Tickle et al., Birkbeck College.
Contact: Ian Tickle (tickle@mail.cryst.bbk.ac.uk), Martyn Winn (m.d.winn@dl.ac.uk)