Dear Xplor-nih users, I am using PASD (which I think is a very elegant method) to calculate the structure of a protein with known structure using solid state NMR data. I have derived the peak assignments with our new method which uses statistical data and secondary designition based on chemical shifts. For each individual peak assignment within each restraint I have also derived an assignment likelihood for each assignment. I use these likehoods in the PASD process and hence start from the pass2 step in the procedure. Since my use of PASD is somewhat different from normal use, I would like to play around with a few parameters, e.g. a longer duration of the first heating phase in pass2 etc... Is this possible? what would be the syntax? I notice there is a flag "-numStructs" for the pass2 procure, but I am not aware of other possible flags/options - is this true? So far my results are disapointing, the structures I derive are mostly elongated, despite that there a several restraints with long-range assignments with significant likelihood between the two ends of the chain in a parallel beta-sheet. I also notice that only a few (typicallly 50 out of 266) restraints are active at the end of pass2 - is this normal/good? What is the violation energy for an inactive restraint - is it 0.0?. I was wondering if the structure could be trapped in an elongated structure with most of the restraints inactivated, do you think this is possible?
Any help would be very much appreceated. Best regards, Jakob ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
