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Notice to REFMAC USERS

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

When using TLS 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 depositors have finished the final round of refinement without including "tlsout addu" keywords, and did not see ANISOU records in the coordinates, only the residual B factor had been generated in the coordinate file. For this situation, the residual B factor needs to be updated to the full B factor in order to properly run validation checks, and the two following update options are given:

• 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