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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
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage