Re: [modeller_usage] PDBs missing chains

You should go through the tutorial ;-)

You'll need to perform a homology search using the PIR database which is prepared for you already -- see the Data sets section for pir_95. You'll need to format your pdb into modeller's alignment format -- see the format section.

After this homology search, sift through the top hits and then build an alignment from those and your target. You can align with however many templates you see fit.

Modeller has an automodel method which you can use that actually builds models between your template(s) and your target.

Checkout: http://salilab.org/modeller/tutorial/basic.html

Cheers,

Paul

On Fri, Apr 2, 2010 at 9:33 AM, Daniel Fernandez <">> wrote:

Hi,

I am trying to use modeller to fill in missing side chain or backbone atoms in the 1ahoa protein. Do you have any suggestion on how to do that using modeller, i.e., which one I should use as a template and as a target protein for that problem. I am relatively new to the software and protein modelling literature. Any help would be strongly appreciated.

Best,

Daniel

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Paul Rigor
Pre-doctoral BIT Fellow and Graduate Student
Institute for Genomics and Bioinformatics
Donald Bren School of Information and Computer Sciences
University of California, Irvine
http://www.ics.uci.edu/~prigor