Dear Charles and Xplor users, Charles has been suggested me to use their ensemble approach of PRE data (Iwahara 2004 JACS), however, I still don't understand some part of it and have some concerns.
Instead of getting a refined structure, I am trying to have some sets or contacts of conformation in a denatured protein with PRE restraints. One of the currently used methods is applied in Michele Vendruscolo's group (e.g. Dedmon et al, 2005 JACS, 127, 476-477). They calculated up to 20 copies of extended protein together with long distance restraints by means of CHARMM program. One similar way in Xplor should be "ensemble.inp", I think. However, there is no "ensemble" parameter in PMAG (as in ensemble.inp "NOE ensemble on end end") if I want to use delta R2 directly. If I want to convert PRE into distance, it is also troubled me, because I am not sure whether one can use the same energy function correctly. For example, equation (18.6) in the Manual (potential = biharmonic) and equation (13) in Iwahara 2004 JACS, is that possible convert the standard error of delta r2 into upper bound and lower bond limits? Besides, the script from Iwahara 2004 JACS is simulated annealing with multiple ligand to average the conformation ensemble, right? I am wondering where the ensemble calculation is called in this script, and in which kind of restraint, in dintance or in relaxation rate? (as equations (13) (15) in Iwahara 2004 JACS) Thank you very much!! Jie-rong -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20080415/100066f3/attachment.html
