REFMAC (CCP4: Supported Program)

User's manual for the program REFMAC, version 5.*

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 more details of TLS parameters see Martyn Winn's page on TLS in REFMAC (external link).

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 Å². 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