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Hello Hongyan--
> The problem for me is to choose which program to refine my protein
> structures using RDC. Xplor-NIH anneal.py script did gave rise to
> well-converged structures but there seems no much differences with or
> without RDC, both in RMSD and structures. However, in Aria, I do see
> the differences when RDC is used (lower RMSDs and slightly different
> helical angles). When I used anneal.py to calculate structures without
> RDC, I just input a empty rdc.tbl, not sure if
> it is OK.
that should be ok. Better to just comment-out the lines referring to rdcs
> Since when I added # to those related to tensor, rdc etc, running
> anneal.py tooks much longer time. I don't konw why.
not exactly sure what you mean. It does take longer when rdcs are
included.
>
> My people did use the method as described by Clore et al to refine Da and Rh
> even if they have an initial structres (since they don't fit well with RDC
> data). I think the old-verion of Xplor-NIH could not float tensor, how
> to get a good set of Da and Rh is also important issue.
anneal.py requires a decent approximation to Da and rhombicity- this can
be gained by the approach in J. Magn. Reson. 133, 216-221 (1998).
If you have good starting structures you can use protG/calcTensor.py (or
protG/grid_search.inp if you want to wait longer) to determine values of
Da and Rh. Otherwise, please use the above reference. Once you have a
good initial guess at Da, Rh, anneal.py and refine.py can fine tune
things.
hope this helps--
Charles
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