-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hello Jakob-- I'll try to fill in a bit while John is on vacation. > the system using only the long-range restraints (broken lines) . Is it > true that pasd somehow scales the violation energy to agree with the > total number of NOEs? not to my knowledge. > Does it have anything to do with the concepts of > "-noeCompletenessWeight" or "-scatterWeight" in the sa_protocols.tcl > script - I don't understand the meaning of these variables. > Obveously, I would like my calculations to converge using all NOEs, > have you had similar problems? I notice that you choose the number of > long-range violations as your criteria for convergence rather than the > total energy. Is this because there were to many structures with lower > total energy being incorrectly folded? We generally don't take energies too seriously in annealing protocols- number of violations and RMSD values are used instead. > > Do you have suggestion of what goes wrong in my case? Since I use > solid state data I have restraints between carbon atoms. The ambiguity > is rather large for my restraint ca. 4-5 degeneracy (as a geometric > average) after doing prefiltering. I think this should not be a problem. Why do you have such large ambiguity? Would it be possible to break these into separate peak assignments? This would be more consistent with the approach used in pasd/marvin. Anyway, clearly the algorithm needs to be tuned differently for your filtering protocol. Hopefully, John will have useful suggestions when he returns. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGyzg3PK2zrJwS/lYRAofbAJkBxIfNUicw12sVbrmDbhlhT2kgQgCcCFB4 FLgkf7Wu4fuhHjd5/NoMoCk= =nN/5 -----END PGP SIGNATURE-----
