The easiest way to model in the missing loops is to make a homology model of the full sequence using the incomplete structure as a template. (http://swissmodel.expasy.org or I-TASSER)

Alternatively, you can use Modeller to model in the loop and refine it.



2011/10/14 ahmet yıldırım <ahmedo047@gmail.com>
Dear users,

There are 7 missing residues in xxx.pdb file. xxx.pdb consist of chain a and chain b. In chain b there are only 7 missing residues. chain a is complete.
I fitted the complete chain onto the one with missing residues, wrote the new coordinates for the fitted chain and put them in the broken chain using a text editor.
I think the chain a and chain b do not fit/overlap
As result, in chain b alpha is incomplete (see result image). what should I do?

1.way:
pymol-file-open-protein.pdb

PyMOL>create chaina, chain a
PyMOL>align chaina and resi 2-230, chain b and resi 2-230
PyMOL>save chaina.pdb, chaina

2.way:
pymol-file-open-protein.pdb

PyMOL>create chaina, chain a
PyMOL>create chainb, chain b
PyMOL>align chaina and resi 2-230, chainb and resi 2-230
PyMOL>save chaina.pdb, chaina


Again the result didnt change :(
--
Ahmet YILDIRIM

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Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University