Notice to REFMAC USERS

Depositors using REFMAC should make sure that the ATOM records contain the full (and not residual) B factor.

When TLS is involved in refinement, the keyword tlsout addu should be added in the final round of refinement to produce a coordinate file containing the full B factor. The latest REFMAC interface has a button “Add TLS contribution to XYZOUT” in the folder TLS Parameters which will add this keyword.

If the file has already been refined using TLS parameters, and REFMAC did not include ANISOU records in the coordinates, then only the residual B factor has been included in the coordinate file. This needs to be changed to the full B factor in order to properly run validation checks.

Depositors can add the full B factor to the coordinates by using one of two options:

Option 1:

• Find the file of TLS parameters TLSOUT that corresponds to the coordinate file, or if necessary extract the TLS parameters from the PDB file using the CCP4 program tlsextracti
• Use CCP4’s tlsanl to put the full B factor in the PDB coordinate file, available in the interface as the task “Analyse TLS parameters”. Be sure to set the keyword BRESID T in this script

Option 2:

• Run tlsanl_script.csh pdbfile