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Hi-- Well I'm glad we seem to get the right answer some of the time... > I have been using a standard annealing script with TAD from CNS 1.0 that > included sani restraints (only 1 class, HN). Most of the structures had > no sani violations larger than 1 nor 0.1, as listed in the header of pdb > file. However, when I loaded the structures in vmd-xplor and displayed > the dipolar couplings (using the same DFS, Da and R values as for the > calculations), there were usually several violations larger than 1 or > even 2. I was quite surprised by this discrepancy. :( I listed all the > rdc, as calculated by CNS, using the sani print statement (with > threshhold = 0) and indeed, the values differed quite a bit between CNS > and vmd-xplor. I thought that this was perhaps some peculiarity of CNS, > but a sani print statement in xplor-nih (version 2.9.2) gave me > calculated values of rdcs identical to those from CNS, and different > from vmd-xplor!!! the SANI code in Xplor-NIH and CNS is pretty much identical, so it's not surprising that they give the same answer. > This does not look quite right, does it? Since I was getting two > different sets of calculated rdcs, I wrote my own program to calculate > them from pdb files with ANI residue. My calculated values agree very > well with vmd-xplor values. This suggests that rdcs calculated by the > sani statement in xplor are not quite correct - which makes my very > suspicious about any sani calculations!!! Another option for you would be to use the DIPO term in Xplor-NIH- you might see how that does. Of course we'd like to fix any bugs in the SANI term. If you could send me psf, pdb files and a table of SANI assignments which differ I will look into this. It's best if you could tar these up and ftp them to dcb.cit.nih.gov/pub/incoming regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFAJ9PWPK2zrJwS/lYRArKWAJ9s60+Bajf5xCuwnnDmkEbBI+A8/QCfUc6d 97nmT0DLmHjVPjd0gbOjJX8= =N8Gx -----END PGP SIGNATURE-----
