Re: [modeller_usage] how add sidechains

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

matziast AT 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
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