Create/Edit TLS File
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Main Page - Using the CCP4 software - Refinement with CCP4 - Create/Edit TLS File
TLS refinement requires a definition of the TLS groups to be used, and outputs the TLS parameters found for each group. This information is held in special TLSIN / TLSOUT files. Refmac now has a default assignment of TLS groups, so a TLSIN file is no longer absolutely required, but it is recommended to try different TLS models and you will need a TLSIN file for that purpose.
These files are simple ASCII files which can be hand-edited, but they can also be created and edited with the "Create/Edit TLS File" task. You should first specify the starting point:
- "from scratch" i.e. with no prior information
- "starting from chain list in PDB file". You are requested to supply a PDB file, and the task will create a TLS group for each chain in the PDB file. This is in fact the default in Refmac5, but the task enables you to tweak the exact definitions to be used.
- "starting from an existing TLS file". This allows you to tweak the definitions used in a previous TLS file.
- "starting from TLS REMARKS in PDB file". This uses the jiffy program TLSEXTRACT to extract TLS group definitions and parameters from REMARK 3 lines in a PDB file. This route would typically used when starting from a structure downloaded from the Protein Data Bank (assuming that TLS refinement was actually used for the structure in question).
You also need to specify whether to edit only the group definitions (as at the start of TLS refinement) or whether you want to include TLS parameters for each defined group.
You should then add or change the values in the TLS group definitions folder. You can have one or more groups, and each group can consist of one or more atom ranges. If TLS parameters are included for each group, these are displayed, but obviously it is not a good idea to edit them!
See also the TLS Motion Determination site for a more sophisticated way of preparing TLSIN and XYZIN files for Refmac5.
--Martyn Winn 15:59, 24 May 2008
