One more option to get the average B-factor: phenix.model_vs_data model.pdb data.hkl will give you pretty complete statistics about your data, model and model-vs-data. Pavel. On 7/15/09 10:58 AM, Leo Sazanov wrote:
Hi, phenix.refine outputs "WILSON B" value into PDB header after refinement, which is not the same as average B-factor of all the atoms in the structure, and not exactly the same as Wilson B-factor from SCALA scaling. How exactly is Wilson B-factor for phenix header calculated and would it be possible to output there also the average B-factor of all the atoms in the structure? Also, deposition into PDB requires only Luzzati coordinate errors, while phenix produces only ML based ones. Presumably ML estimate is better than Luzzati?, but it looks like often people just ignore PDB input for errors. It seems that it would it be useful in future to have ML option in the PDB submission process? Or should Phenix produce Luzzati errors as well? (I know that one can calculate av. B-fac in other programs or ask PDB to add some data to the deposition, but if the idea is to streamline the process...) Thanks,