TLSANL | obtain total B factors



Notice to REFMAC Users



Depositors using REFMAC with TLS should make sure that the ATOM records contain the full (and not residual) B factor before depositing an entry.

When TLS is involved in refinement using a script, the keyword "tlsout addu" should be added to produce a coordinate file containing the full B factor. The latest REFMAC interface (in CCP4i) has a button "Add TLS contribution to XYZOUT" in the folder of 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 factors have 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 three following update options are given:


Option 1: Convert your file so it contains full B factors using this server

Upload the PDB coordinate file below and click "RUN" to create an updated PDB file with full B factors. The file uploaded should have residual B factors, and correct residue ranges for the TLS groups in the header section.

Coordinate



Option 2: Convert locally using script

Run tlsanl_script.csh pdbfile
(note: CCP4 should be installed on your local machine prior to running the script)



Option 3: Convert using CCP4i package

  • 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 CCP4'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.

Please note that options 2 and 3 will fail if the "TLSD waters add" keyword (the default for REFMAC 5.5) was used during refinement. To correct this problem, use the "TLSD waters exclude" keyword during refinement. Otherwise, the residue range definitions for each TLS group must be manually updated to include the waters that belong in that group prior to using options 2 or 3. Further information can be found at the CCP4 Wiki.


Questions regarding CCP4 should be sent to ccp4@ccp4.ac.uk.


Question, Comments, and suggestions should be sent to deposit@deposit.rcsb.org.