Re: [modeller_usage] Weighing the restraints differenlty on the modeller-fly

[Modeller Caretaker <modeller-care@ucsf.edu>]

Mehmet SEN wrote:
>    I am running modeller8v2 to get the model of my protein. In this 
> case, I do have the NMR experimental data (about 400 restraints).  Now, 
> I am able to run my structures with restraints I want to have from the 
> NMR experiments. In this case, I would like to do following. I would 
> like modeller restrains to be applied region for which I do not have any 
> restrains, but for the region where I can define secondary structures 
> via NMR experiment, I want to turn off modeller-derived restrains, or 
> decrease weighing factor of the modeller-derived restraints, that is, I 
> would like my restraints to weigh more then modeller-derived restraints.

You can turn off restraints on selected atoms with the 
model.restraints.unpick() command (follow it with .condense() to remove 
them entirely). See http://salilab.org/modeller/8v2/manual/node166.html

You can make your own restraints weigh more strongly than 
homology-derived restraints by decreasing their standard deviation.

	Ben Webb, Modeller Caretaker
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