Hi all, I just tried to reset my B values to the wilson B before TLS refinement (in an attampt to shake some model bias that I am sure is hiding somewhere in my temperature factors...). My start model was a TLS-refined PDB file from phenix.refine (hence with ANISOU cards). I issued the following command:
phenix.refine my_model.pdb my_data.mtz modify_start_model.adp.set_b_iso=60 output.prefix=my_model_resetB main.number_of_macro_cycles=0
As far as I can tell, this should reset my B values to 60 and then exit. However, when I look at the resultant PDB file the Bs for all the solvent molecules 60 but for the protein they are not; rather the protein Bs are almost identical to the starting PDB file. If I try to remove the TLS-derived ANISOU cards by adding the command line option "adp.convert_to_isotropic=true" the result is the same (except the output PDB file no longer has ANISOU cards). However, if I strip out the ANISOU cards from my starting pdb file and _then_ run the above command the resultant PDB file _does_ have the correct values for both protein and solvent. It seems like modify_start_model.adp.set_b_iso=60 does not work when atom has an ANISOU card. The behaviour I would *expect* would be for the adp be reset to an 'isotropic' 60 (i.e. set the diagonal elements to 1 and the off-diagonals to 0). Is this a bug, or am I doing something silly? Cheers, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549