On 11/03/2010 05:49 AM, bharat lal wrote:
I want to model the structure of a protein with ser gly tyr but the template structure that I want to use has the reacted form of ser gly tyr ... what i want to model is the position of those 3 residues in my model in place of their reacted form.. so can amybody pls help me out in doing so ??
One easy solution is simply to edit your template PDB file in a text editor, and change each of those modified residues to the corresponding "normal" residue (i.e. replace HETATM with ATOM if necessary, and the modified residue name on the same line with SER, GLY or TYR). Modeller will ignore any "extra" atoms in your modified residues, just using whatever "standard" atoms (e.g. the backbone) it can find to extract distances and angles.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage