I am doing structure RDC/SAXS refinement with refine.py in xplor0nih on a protein that contains three Zn atoms. My input NMR structure (from ARIA/CNS) has the Zn atoms in the pdb, the XPLOR output pdb files also generate Zn atoms but not bonded or angled to the protein structures.
I have the patch files and parameter files ready (from ARIA/CNS), but I do not know where to add them in the refine.py. In the ARIA protocol, I added the patches in the generate.inp but I can not find it in Xplor-nih. Lei Zeng
