Hi everyone.
I asked a similar question earlier, however, I wasn't specific with my system.
I have two proteins that interact with an ultra weak affinity; there is no
stereospecific, high-affinity complex.
To determine whether the PRE Q-factors will decrease as a function of
population percentage, I would like to introduce a "p" factor to the Q-factor
equation (Tang, C. et al. (2008) Visualization of transient ultra-weak
protein self-association in solution using paramagnetic relaxation
enhancement. JACS 130, 4048-4056).
Is this the command in prePotTools.py to determine the Q-factor?
def Qfactor(term):
""" term can be a single potential term, or a list of terms
"""
if term.potName()=='PRE':
q=term.qFactor()
else:
# assume we have a list of terms
from simulationTools import flattenPotList
prelist = flattenPotList(term)
from math import sqrt
snu = 0.0 ; sde = 0.0
for p in prelist:
rn = float(p.numRestraints())
if p.assignType() == "nonstereo" :
rn = float( p.numRestraints()) * 2.0
pass
snu += p.rms() * p.rms() * rn
sde += p.AveSqObs(1) * rn
pass
q = sqrt(snu / sde)
pass
return q
If so, how do I introduce "p" to the above to specify a population?
I'd like to change Gamma2(obs) - Gamma2(calc) to
Gamma2(obs) - pGamma2(calc).
Do I need to write my own subroutine to do this? If so, how I can
access Gamma2(obs) and Gamma2(calc) for each entry in prelist above?
I hope I'm making sense,
Valerie
