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Hello Hongyan-- > It seems that I cannot find any tutorial for this software and the manual is > indeed very difficult to understand. There's a tutorial here: http://nmr.cit.nih.gov/xplor-nih/doc/current/python/tut.pdf > > I wonder what is the difference between refine.py and anneal.py (both said to > refine structures using NOE, RDC, J-coulpling). refine.py refines a rough model structure, while anneal.py determines structure from a random extended model. If you have a starting structure, you should use refine.py. > I have tried both sample > anneal.py and my own anneal.py got warning message : TorsionTopology Warning: > Tensor containing AXIS 500 and ANI OO is not specified and software is still > running. I am not sure if I need axis.psf and axis.pdb file in my dir and how > to define residue number for tensor in rdc.tbl. (I used 999 for the tensor as > that used in Aria, and didn't define tensor.psf, but the xplor-NIH still runs > without problems, however I am not sure if the results are reliable.) you shouldn't get that message, and you should not usually specify any extra axis coordinates or psf info. > > In terms of determination of Da and Rh, which script should be used? > Grid_search.inp or calTensor.py? What is the difference between > these. use calcTensor unless you want to wait longer. Both scripts determine the best tensor parameters given a set of input structures, but calcTensor uses singular value decomposition (linear algebra). > I have refined my structure using RDC in Aria with fixed Da, Rh and I got a > better convergences, however, Aria can not float Da Rh, that is why I am > switching xploy-NIH. But my initial run (anneal.py) didnot give me a better > converged structures, is something wrong somewhere? It seems so. I would also use refine.py instead. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFF8W7cPK2zrJwS/lYRAvqtAJ9JjUdabhpulNFjziGae9eVa5/bIwCfbQc/ WprUu81OAlQHmmZGx7ANwXw= =0PgF -----END PGP SIGNATURE-----
