[phenixbb] Few questions
pafonine at lbl.gov
Thu Mar 15 07:57:14 PDT 2007
> 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
1) you can ransomize them;
2) set to a value;
3) set to Wilson B.
To do so, look modify_start_model scope:
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
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
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!
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