REFMAC (CCP4: Supported Program)

User's manual for the program REFMAC, version 5.0.36

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 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