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Hello Lei--
> 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.
Load the parameters using (assuming a param filename of file.par) in
refine.py somewhere after the import protocol line:
protocol.initParams('file.par')
For the topology, one approach is to directly apply the patch in
refine.py:
protocol.initTopology('file.top') #file.top contains patch named ZNPA
xplor.command("""
!place appropriate patch parameters here:
patch ZNPA reference= ... end
""")
Alternatively, you could generate a psf file externally and use that
instead - see eginput/PSF_generation/testNAG.py in the Xplor-NIH
distribution.
best regards--
Charles
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