Dear Charles and other Xplor users,
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 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.
The avetype in the ensemble is average and the weight of all ensemble members
is equal (0.2) at least at the beginning of the script.
Am I doing something wrong? How should I set up the averaging?
Thanks a lot in advance!
bw,
Lukas
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