[Xplor-nih] costumizing PASD

[Jakob Toudahl Nielsen]

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

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