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 <ahmedo...@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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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