Re: [phenixbb] will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb?

Thanks Pavel: I tried the following code for PDB 1SX3: ******************* phenix.tls 1SX3.pdb combine_tls=true ******************** but it ended up with: *********** ======================= TLS groups from PDB file header ======================= Sorry: Bad TLS selection: start index > end index. ******************* Not sure whether something wrong with the PDB file or the script. By the way, do I have to specify the selection or phenix.tls will automatically do it based on PDB header? Thanks! Hailiang

Hi Hailiang,

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For the pdb file generated by refmac which contains only the residual-B, will phenix.fmodel automatically generates and takes into account the TLS B by reading the TLS REMARK from pdb? Thanks a lot!

phenix.tls

is the tool to convert between total and residual ADPs. It can recognize Refmac and phenix.refine formats of TLS records.

phenix.model_vs_data does this internally to compute correct R-factors and ADP statistics.

phenix.fmodel takes the PDB file as is, so it is your responsibility to provide the correct input B-factors.

Pavel.