Re: [modeller_usage] how add sidechains

matziast@med.uth.gr wrote: > I have a problem with the model building. Specifically, I have the coordinates > of the backbone and I want to add its sidechains but I can't find the > appropriate script.

The complete_pdb() script will automatically add in sidechains from internal coordinates. You'll probably then want to optimize the sidechain positions and allow the backbone to relax, with some optimization. One such script to do that is at http://salilab.org/modeller/9v4/manual/node246.html

As Mensur points out, if you don't need the backbone to relax, it could well be more efficient to use SCWRL.

Ben Webb, Modeller Caretaker