[phenixbb] Weird Hydorgen refinement
pafonine at lbl.gov
Mon Aug 22 18:22:03 PDT 2011
> The pdb did have anisou records for H's. I believe that is because in
> some previous runs I had only selected chain 'A' - I left out "and not
> elemnt H" - which I believe caused the H's to get refined
Ok, that would be the explanation.
> I am trying to get rid of the ANISOU records and Ill run refinement
> ps. I am getting ready to deposit the coordinates and I dont want to
> keep hydrogens in the model, how can I get rid of them? I ve been
> using pyMol to remove them, but pymol gets rid of all the info
> -including symmetry -that phenix adds...
Any post-refinement changes to the model are very bad. By doing so you
invalidate the reported in REMARK 3 statistics, such as R-factors, atom
counts, etc. This is explained in details here:
phenix.model_vs_data: a high-level tool for the calculation of
crystallographic model and data statistics. P.V. Afonine, R.W.
Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson,
D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams
J. Appl. Cryst. 43, 677-685 (2010).
In general, phenix.pdbtools is the tool to manipulate PDB files:
phenix.pdbtools model.pdb remove="element H"
will remove all H atoms. If you do so then re-run the refinement so you
get correct numbers.
More examples of PDB tools usage:
More information about the phenixbb