Hello Lukas--
>
> I'm trying to calculate a ensemble of the terminal intrinsically disordered
> part of a protein using PRE restrains.
> I'm having some problems (or I'm misunderstanding something) with the
> averaging of the PRE term in the ensemble.
>
> My setup for the PRE module is as follows:
>
> pot = create_PREPot( file='pre.comb.tbl',
> esim = esim,
> frequency = 700,
> eSpinQuantumNumber=0.5,
> rlxType='r2dd',
> tauc = 140.,
> fixTau = 'False',
> sumWeights=0
> )
> pot.setScale(1)
> pot.setAveType("r-6")
> pot.setEquType("sbmf")
> pot.setEnsInterconvert("fast")
>
> When I do a calculation with 5 ensemble members I get in the violation
> analysis (as example):
>
> V id atoms in set i atoms in set j obs calc diff
> weight S^2 S^2ang S^2rad
> ------------------------------------------------------------------
> 0 ( A 3 THR HN)( A 36 CYSP OS1) 51.5 51.57 0.0697
> 0.016 0.306 1 0.306
> [contrib. from ensemble member 0]
> 164.1 1 1 1
> [contrib. from ensemble member 1]
> 1.283 1 1 1
> [contrib. from ensemble member 2]
> 0.0836 1 1 1
> [contrib. from ensemble member 3]
> 0.5639 1 1 1
> [contrib. from ensemble member 4]
> 1.005 1 1 1
> 1 ( E 3 THR HN)( E 36 CYSP OS1) 51.5 51.49 0.0081
> 0.016 0.683 1 0.683
> [contrib. from ensemble member 0]
> 31.55 1 1 1
> [contrib. from ensemble member 1]
> 36.73 1 1 1
> [contrib. from ensemble member 2]
> 4.478 1 1 1
> [contrib. from ensemble member 3]
> 1.28 1 1 1
> [contrib. from ensemble member 4]
> 1.223 1 1 1
>
> Now, I don't really understand how the averaging is done, since I don't see
> how these values averaged are the calculated PRE.
When using sbmf and fast ensInterconvert, there isn't a straight
averaging over pre contribution, but rather averaging over order
parameter and distance is done all in one go. Please see
http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/prePot.html
> When i use sb mode, I always get the sum of the PRE and I couldn't
> figure out how to change the aveType like in the NOE potential.
Only 1/r^6 distance averaging is supported in the current
releases. What sort of averaging would you like? Perhaps confusingly,
the ensemble weight is already included in the printed contribution,
so the value on the first line should be a simple sum of the
contributions for sb mode.
>
> Am I doing something wrong? How should I set up the averaging?
>
I hope to have started to answer your questions. Looking at the
documentation page, I see that some work is needed... Please continue
to pester me.
best regards--
Charles
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