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Dear all, I have a protein that has a homolog with known crystal structure. I aligned them manually and very carefully to make sure that we get what we have known right. I want to now replace the conserved residues in the model into those of my protein of interest and hopefully also do some sort of positional minimization so that I could have a rough idea about the surface of my protein of interest. Would there be any program doing this for me - that is, take the model pdb and my alignment file and generate a model for my protein of interest? If not, would you be kind enough to share your protocol with me if you have done this by hand. Happy Holidays! Thanks! -yong
