Thank you very much for your inputs and comments. I am getting understand what is going on now.
> If your resolution is high (2.2 A or better?) and you have ARP/wARP Yes, the resolution is about 2A. I have ARP/wARP. Will give a try. One more question about Molecular Replacement. With Phaser, I got tetramer conformation. With autoMR, it gave me dimer conformation. Each molecuale was trucated into two chains. The scores from both methods were high, as expected from 90% sequence identity between template and target. Thank you for advice Ros On 4/18/12, Edward A. Berry <ber...@upstate.edu> wrote: > 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 > >
