Hi John,
Is it possible to set the maximum B-factor limit during adp refinement ( like in CNS... 5-100)
In phenix.refine you can reset B-factors (selected or all) before refinement: 1) you can ransomize them; 2) set to a value; 3) set to Wilson B. To do so, look modify_start_model scope: refinement.modify_start_model { adp { randomize = None set_b_iso_to = None set_biso_to_wilson_b = None convert_to_isotropic = False shift_b_iso_by = None } selection = None write_modified = None } Example: phenix.refine data.mtz model.pdb modify_start_model.adp.set_b_iso_to=20 modify_start_model.selection="chain A and resid 10-20" This will set B=10 for the residues from 10 to 20 in chain A. Make sure to refine your model after such manipulation. Also, large B may indicate either lack of density or potential big movements so you may want to use TLS model.
Regarding rmsd question.. after model building and refinement ...i took the model and ran only xtal_pdbsubmission in cns. And that gave the difference rmsds (phenix 0.007 & cns 0.0218) thats why i got confused.
If you prepare this in CNS, you can manually replace the values. Also, make sure to put PHENIX (phenix.refine) as a program used. Let me know if you have any questions! Cheers, Pavel.