Dear Charles, 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. Since when I added # to those related to tensor, rdc etc, running anneal.py tooks much longer time. I don't konw why.
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. Have you got any references in using Xplor-NIH (vary tensors) to refine structures? I appreciated your help! Best wishes, Hongyan Quoting Charles at Schwieters.org: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Hongyan-- > > > I wonder whether xplor-NIH (anneal.py) does the job for refine tensor > > Da and Rh as the method used by Clore et al. (A robust method for > > determining the magnitude of the fully asymmetric alignment tensor of > > oriented macromolecules in the absence of structural information. JMR, > > 133:216-221, 1998). > > no- the anneal.py script allows the Da and rhombicity to be refined > along with molecular structure, while the cited paper provides a method > of determining Da and Rh in the absence of structural information. > > > It seems that all published papers using this method to refine Da and > > Rh. I have tried to use Module to get initial Aa and Rh and then using > > xplor-NIH anneal.py to calculate ten structures (with NOE and other > > constriants) and the set of Da and Rh of the lowest energy structure > > was input into Aria and then calculate structures using NOE > > constraints, RDC etc. To my surprise, I did not get well converged > > structures compared with those using Da and Rh directly obtained from > > Module. > > This indicates a convergence problem in anneal.py, a fact which is > hopefully apparent from the output of the script. I'd have to look at > the details of the script and restraints to figure out what went wrong. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> > > iD8DBQFGDMEbPK2zrJwS/lYRAg4UAJ4gYbazkY4+zDRhDAapkQ6Upi0qlwCghmuB > 2P9BMFHcVgGpauq+HflSeD4= > =gkHr > -----END PGP SIGNATURE----- > Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong
