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Subhendu I wonder if you approached this issue by molecular replacement using the antigen-binding fragment (Fab) of any antibody (e.g. 1FVD). You can separate the Fab into the two domains; Variable and Constant, delete the loops from each, and use them as models in Molecular replacement. Please let me know if you need more details using this approach Akram Alian UCSF From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of subhendu chakraborti Sent: Tuesday, December 15, 2009 7:13 PM To: [log in to unmask] Subject: [ccp4bb] Rosetta vs Modeller Hi everyone, I am currently in the process of solving some antigen-antibody complex structures. I was wondering if people here have used Modeller and Rosetta for homology modeling and have any recommendations.I would like to build the model of the antigen/antibody to the known structure of the antibody/antigen ( to get a model of the complex while my crystallization/structure solving process continues).I have experience in Modller but I have not tried Rosetta or the newer PyRosetta (which looks interesting). In the event of docking a protein to another are there any great programs that people here have used/recommend? I would really appreciate your suggestions/insights. Subhendu UCSF