REFMAC (CCP4: Supported Program)
User's manual for the program REFMAC, version 5.0.*
Input and output files - TLS parameter files
Input and output
TLS files are ASCII files containing details of the TLS groups and the values
of the corresponding T, L and S tensors. For details of TLS parameters see bla-bla.
TLSIN
The input TLS file (logical name TLSIN) may contain only information about
TLS groups without values of T, L and S tensors.The possible records are:
- TLS <title>
- This must be the first record for each TLS group, and indicates
the start of a new group. <title> is a short description of
the group.
- RANGE <from> <to> [<selection>]
- This record describes which atoms are included in the TLS group.
<from> and <to> consist of the chain identifier followed
by the residue number in the format (A1,I4), for the beginning and end
of a particular segment. Several segments can be included in a TLS group
by including several RANGE records. The values of <from> and
<to> should be enclosed in quotes, e.g. 'A 131'. The optional
<selection> specifies an atom selection for a particular segment.
The possibilities are "ALL" (all atoms - default), "MNC" (main chain
atoms only), "SDC" (side chain atoms only) or a particular atom type
up to 3 characters, e.g. "CB".
- ORIGIN <origin_x> <origin_y> <origin_z>
- The origin used for the calculation of TLS parameters in the
coordinate system of XYZIN. This defaults to the centroid of the
group, and this record can normally be omitted.
- T <T11> <T22> <T33>
<T12> <T13> <T23>
- Starting values for the translation tensor in Ų.
Normally, this would be omitted, and the program will start with all values
zero.
- L <L11> <L22> <L33>
<L12> <L13> <L23>
- Starting values for the libration tensor in degree². Normally,
this would be omitted, and the program will start with all values zero.
- S <S22 - S11> <S11 - S33>
<S12> <S13> <S23> <S21>
<S31> <S32>
- Starting values for the screw rotation tensor in Å * degree.
Normally, this would be omitted, and the program will start with all values
zero.
TLSIN - Format
The format is essentially the same as that used by the program RESTRAIN.
A simple example with two TLS groups representing two domains
of a single chain:
TLS Chain A NAD binding domain
RANGE 'A 1' 'A 137' ALL
RANGE 'A 303' 'A 340' ALL
TLS Chain A Catalytic domain
RANGE 'A 138' 'A 302' ALL
TLSOUT
The output TLS file (logical name TLSOUT) contains
refined TLS parameters (details of TLS group, origin of TLS group, T, L, S tensors).
TLSOUT - Format
The format is essentially the same as that for TLSIN,
with the T, L and S records holding the refined parameters,
and the ORIGIN record holding the calculated origin, if not specified in TLSIN.
In addition, the output file contains a record "REFMAC" denoting that
the file has been output by REFMAC. Example of output TLS file:
! Output from REFMAC
TLS Chain A
RANGE 'A 1.' 'A 300.' ALL
ORIGIN -3.680 0.700 11.039
T -0.0161 -0.1041 -0.0362 0.0121 0.0497 0.0194
L 1.9572 2.9920 2.5163 0.3999 -0.3219 0.1108
S 0.0066 -0.0199 0.0299 -0.0444 -0.1246 -0.0684 0.0286 0.0062
TLS Chain B
RANGE 'B 1.' 'B 175.' ALL
ORIGIN 4.104 26.003 64.557
T 0.0619 0.0104 0.0481 -0.0128 0.0051 -0.0226
L 2.5549 4.4075 3.5760 0.5356 0.7041 0.2892
S 0.1170 -0.1274 -0.0305 0.2005 -0.0652 0.1453 -0.1772 0.1566