Hello Qi--
>
> I have a question about the NOE scale factor. In the script newReine.py in the
> eginput/pre, scale factors of 2 and 30 were used, as shown below. Would you
> have
> some explanation how to set these values? Thank you very much.
>
> pot = create_NOEPot("noe_"+name,file)
> # pot.setPotType("soft") # if you think there may be bad NOEs
> pot.setScale(scale)
> noe.append(pot)
> rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )
>
You generally leave force constants alone unless your restraints are
not fitting, or there is evidence of overfitting, the latter usually
indicated by unexpected violations in other terms. For the NOE term in
particular I wouldn't mess with the values unless you have very many
restraints (maybe >7 per residue) or very few (say < 1/3 per
residue). If you have very many, you might try decreasing both values
(the 2 and the 30) by a factor of 5, and similarly increase the values
if you have very few restraints.
best regards--
Charles
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