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 do not see ANISOU records in the coordinates, only the residual B factor has 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:

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 tlsextract.
• Use CCP's tlsanl to put the full B factor in the PDB coordinate file, available in the GUI interface as the task "Analyse TLS parameters". Be sure to set the keyword BRESID T in this interface.

Option 2:

• Run tlsanl_script.csh pdbfile

Further information can be found at the CCP4 Wiki.

Question, Comments, and suggestions should be sent to deposit-help@mail.wwpdb.org or through the use of the communication interface in the deposition system.