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Hello Olivier-- > Thank you for the explanation. I understood that there might be an > issue not with the docking itself but more probably between the > individual domains and their respective RDC's from the full protein > RDC experiment. As I wrote earlier, I am currently trying to refine > individual domains including RDC from the full protein experiment. I > have been using the standard refining script that you provide in the > eigeninput directory, and yet R-inf look quite high (~ 20 ) if I keep > Da and R fix, but it becomes much better if I allow those values to > change (Da changes from 5.5 to ~12 (or -12)). I was wondering if, in > that case, it does make sens or not to allow Da and R to vary ? If > not, there is a real issue (whatever it is) with my RDC dataset or at > least with the way I handle them. I have recompared HSQC spectra from > individual and linked domains (I have been working only lately on the > project), but the changes are not important. So, I would have thought > that RDC values would have maybe only slightly modify orientations of > secondary structures. All of this is really intriguing. > An R-inf value of 20% may be appropriate, if you have relatively large errors. Are the svd Da and rhombicity of the individual domains still consistent after your new procedure? That Da change is rather huge. Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkqTBNoACgkQPK2zrJwS/lazkwCfcPlfQFcC6LVdWOl9oDLd73Hh l4YAn3QZuhPBK+C5ikxh45li2o/v8ikl =M0gw -----END PGP SIGNATURE-----
