Hello Qianwen-- > > I have some questions about refinement a protein-DNA complex > structure combine NMR restraints and SAXS data. We first used the > script sry_final.inp (attachment) which is from the > eginput/deprecated/sry example in the xplor-NIH distribution to > calculated complex structure. In this step, the DNA bases are > grouped as rigid-bodies. Then we want to add SAXS data into this > script to refine the complex structure. So I found the script > refine.py in the eginput/saxsref example. But these two scripts were > written in different languages, the SAXS data module could not > directly used in the rigid-body refinement script sry_final.inp. > > So I want to how to add the SAXS data in the script sry_final.inp to > refine protein-DNA complex, because in this script we can fix the > DNA bases as rigid-bodies. If it counld not work, how to fix the > DNA-bases in the SAXS data script refine.py. Or if there are some > better solutions by which we can both fix DNA bases and introduce > SAXS data in the refinement.
Adding the SAXS setup to an old XPLOR script may be possible, but you're on your own. I am happy to assist in getting a Python-based script working, though. By default, the planar regions of nucleic acid bases are treated as rigid bodies, so you shouldn't need to do anything special there. The only setting which is not in the defaults (once protocol.torsionTopology is called) in the IVM setup of your .inp script is allowing the angle flex of the ribose rings- this will be the default in the future, though, as it does improve results. To enable it with current scripts, please call torsionTopology like this: # Argument flexRiboseRing below is a string that selects residues whose ribose # rings will have all endocyclic angles flexible. In general, all ribose rings # should be selected. protocol.torsionTopology(dyn, flexRiboseRing='resid 1:33') best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
