Weighing the restraints differenlty on the modeller-fly
Hello 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. If you need make any comments on this subject, I would be so much pleased. If you have performed anything like that, and have any script available, I really want to get it. Mehmet Sen
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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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Mehmet SEN -
Modeller Caretaker