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Hello Hongyan-- > I used formatconverter to convert NOE format from Cyana to CNS, it works fine > for my other protein without metal ions. I still believe that something wrong > with PSF file. Since in the metal cluster, Cd-S distances and angles were > fixed, but in this protein, for each Cd, both Cd-S distances and > angles varied according to our Cyana structures and published structures. > you might do a survey of the pdb to find the observed range of these bond lengths and angles. You are correct that you should allow the values to vary in this structure if they are not found to be constant. > I got Cd radius of gyration value from parameter files of CNS > (ion.param), not sure where to get proper value. if the selection you specify in initCollapse is globular (it should be), then the default Rg it calculates should be reasonable. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFGI4SLPK2zrJwS/lYRAo3BAJ9WiBJ6uwiZGKjo4LAuwASxAOT/XACfennz MKp4ugdoKf6bvvEKMimAFbA= =mbu0 -----END PGP SIGNATURE-----
