Dear Charles, Thank you very much for your reply. Following your suggestion I used a histogram method to estimate Da and rhombicity. I also included RDCs corresponding only to well-structured regions of the protein for now. Structures and energies look a little better. One thing I am noticing is that Da value in all calculated structures hits the maximum of -50. Why this value has been selected as DaMax? Is it unrealistic to have Da larger than that? Thank you, Irina.
Hello Irina-- > > I would greatly appeciate your helpful suggestions. We would like to use > RDCs > (only HN) in addition to NOEs to calculate the structure of symmetric > dimer. I > have already calculated NOE-based structures, and use them to estimate Da > and > R parameters using gridsearch.inp. However, the values I get depend very > much > on the starting values of Da and R. calcTensor.py gives me numbers > different > from those that I get by using gridsearch.inp. None of those numbers give > me > an improved structures, when I input them in anneal.py and energies > increase > significantly (up to 12000-20000 kcal/M). What can be the reason for this > behavior? my guess is that your structure is not well-enough defined to be able to be able to determine Da and rhombicity. You will need tp use an alternate method- like JOURNAL OF MAGNETIC RESONANCE 133, 216-221 (1998) or JOURNAL OF MAGNETIC RESONANCE 149, 271-275 (2001) I plan on releasing a script which implements one of these algorithms sometime in the near future. best regards-- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFGH8I2PK2zrJwS/lYRAmcKAKCAnaaeuU82flbggeGaW3JPgVMUTwCfbERH 3rM+yb67GoJk6kDCmF654ao= =x2pe -----END PGP SIGNATURE-----
