I would say yes. In any case you need to examine each mutated residue to be sure the correct conformation is chosen, so you might as well do the mutagenesis in coot or O. The ccp4 "chainsaw" program is sometimes used to prepare models for MR, but it truncates the mutated residues to variable extent rather than mutating- the purpose is to improve chances of success, not to arrive at a model with the correct sequence.
If your resolution is high (2.2 A or better?) and you have ARP/wARP installed, run A/W in the mode "to improve an existing model", giving it your current model and the correct sequence. Not only will it build most of the mutated residues correctly, but in its role as a "model bias remover" it will fix or remove incorrect parts of the structure that may not be obvious in the initial maps. Uma Ratu wrote:
Hello, I have a question about molecular replacement. I use "Phaser" or "AutoMR" to generate models of my target protein. Input .mtz is from X-ray diffraction. Template is from a known structure. I also set up seq file using my target protein. The sequence identity between template and my target protein is quite high, over 90%. When I exam the ouputs, I found the sequence of the output .pdb is exactly same as the template. Is this normal for Molecular replacement? In order to have my target .pdb, I need to mutate the residues using coot? Thank you for advice Ros
