[Xplor-nih] PASD: converting restraints to xplor

[John Kuszewski]

Hi Robert,

Try -cutoff instead of -likelihoodCutoff.  That should correct the  
problem.

--JK


On May 5, 2008, at 12:40 PM, Robert Schneider wrote:

> Dear Xplor developers,
>
> I have another question regarding a PASD script in Xplor 2.18. After
> everything ran as desired now so far, I wanted to try and see what  
> I get
> out of a structure calculation using marvin restraints converted to
> xplor if I also include peak assignments with likelihoods lower  
> than the
> standard 0.9. So I re-ran convert_restraints_to_xplor.tcl with a lower
> cutoff:
>
> removeLowLikelihoodPeakAssignments \
>      -pot $3dc625 \
>      -likelihoodCutoff 0.5
>
> but the xplor_noes file I get out is identical to that produced with
> -likelihoodCutoff 0.9. Upon checking quickly, I right away found one
> peak that has two assignment possibilities with likelihoods between  
> 0.5
> and 0.6 and none larger than that (in the final.peaks file), so I  
> guess
> these should show up in the xplor_noes file if likelihoodCutoff 0.5 is
> used - but the peak is still listed with a "no assignments for this
> peak". Have I missed setting some parameter somewhere else?
>
> Thanks a lot in advance, best greetings,
> --robert.
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