Hello,
When I am defining a distance restraint between heavy atoms through an open spline restraint (open=True) and using restraints.add(), MODELLER writes to console the following message:
"_modeller.ModellerError: mod_res_688E> Incorrect range for open cubic spline 2085, dimension 1: xlow ( 0.0500) should be less than xhigh ( 5.0500), and the range should be equal to the delta ( 0.1200) times the modality ( 50) minus 1"
the code line that generates this error is the following:
rsr.add(forms.spline(physical.lennard_jones, features.distance(*atoms), open=True, low=first_step, high=last_step, delta=0.12, lowderiv=0, highderiv=0, values=values, use_array=True))
low = 0.5 high = 5.05 len(values) = 50
I guess that range was calculated internally as xhigh - xmin (5). Given that delta*modality - 1 = 5, I can't guess if the message is an error or not.
Thanks for any advice
Regards, Ignacio Ibarra
My mistake,
Low is defined as "0.05", and not as "0.5"
Regards, Ignacio
On Fri, Mar 22, 2013 at 5:45 PM, Ignacio Ibarra ibarra.ignacio@gmail.comwrote:
> Hello, > > When I am defining a distance restraint between heavy atoms through an > open spline restraint (open=True) and using restraints.add(), MODELLER > writes to console the following message: > > "_modeller.ModellerError: mod_res_688E> Incorrect range for open cubic > spline 2085, > dimension 1: xlow ( 0.0500) should be less than > xhigh ( 5.0500), and the range should be equal to the > delta ( 0.1200) times the modality ( 50) minus 1" > > the code line that generates this error is the following: > > rsr.add(forms.spline(physical.lennard_jones, features.distance(*atoms), > open=True, low=first_step, high=last_step, delta=0.12, lowderiv=0, > highderiv=0, values=values, use_array=True)) > > low = 0.5 > high = 5.05 > len(values) = 50 > > I guess that range was calculated internally as xhigh - xmin (5). Given > that delta*modality - 1 = 5, I can't guess if the message is an error or > not. > > Thanks for any advice > > Regards, > Ignacio Ibarra >
After some trial and error, I got that a valid parameters set is the following:
low -> 0.05 high -> 4.95 delta -> 0.1 len(values) -> 50
The equations that I thought reading from the error log were not the real interpretation of what it meant to be. Now I got it right.
Thanks anyway.
Regards, Ignacio
"_modeller.ModellerError: mod_res_688E> Incorrect range for open cubic spline 2085, dimension 1: xlow ( 0.0500) should be less than xhigh ( 5.0500), and the range should be equal to the delta ( 0.1200) times the modality ( 50) minus 1"
On Fri, Mar 22, 2013 at 5:54 PM, Ignacio Ibarra ibarra.ignacio@gmail.comwrote:
> My mistake, > > Low is defined as "0.05", and not as "0.5" > > Regards, > Ignacio > > > On Fri, Mar 22, 2013 at 5:45 PM, Ignacio Ibarra ibarra.ignacio@gmail.comwrote: > >> Hello, >> >> When I am defining a distance restraint between heavy atoms through an >> open spline restraint (open=True) and using restraints.add(), MODELLER >> writes to console the following message: >> >> "_modeller.ModellerError: mod_res_688E> Incorrect range for open cubic >> spline 2085, >> dimension 1: xlow ( 0.0500) should be less than >> xhigh ( 5.0500), and the range should be equal to the >> delta ( 0.1200) times the modality ( 50) minus 1" >> >> the code line that generates this error is the following: >> >> rsr.add(forms.spline(physical.lennard_jones, features.distance(*atoms), >> open=True, low=first_step, high=last_step, delta=0.12, lowderiv=0, >> highderiv=0, values=values, use_array=True)) >> >> low = 0.5 >> high = 5.05 >> len(values) = 50 >> >> I guess that range was calculated internally as xhigh - xmin (5). Given >> that delta*modality - 1 = 5, I can't guess if the message is an error or >> not. >> >> Thanks for any advice >> >> Regards, >> Ignacio Ibarra >> > >
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Ignacio Ibarra