I always start MR by running chainsaw - you need a pit file or fast or blast output with the sequence alignment of the template and your new protein. chainsaw will edit the template to a) renumber residues taking account of any insertions and deletions b) prune and rename residues to the given sequence. e.g. if you have PHE and template has TYR the OH atom will be removed and the rest kept. This will actually help your MR search - there should be fewer clashes.. And it most certainly helps during rebuilding.. Eleanor
On 18 April 2012 00:34, Uma Ratu <[email protected]> wrote: > > Does that mean a different number of molecules in the asymmetric was > found, > > With Phaser, 4 monomers. With AutoMR, 2 monomers. > > >did you divide the molecule and find each part separately? > > Each monomer (by AutoMR) is composed of two chains. One chain is part > of my target. The other chain matchs to the rest of my target. > > The original template .pdb is a tetramer with four monomers. I used > one of the monomer as the template for the molecualr replacement in > both Phaser and AutoMR. The seq file is the whole of my target. > > >Provide more details like space group > > Space group is P21. > > > whether the tetramer is crystallograhic or all in the asymmetric unit, > > The tetramer is crystallograhic > > Thank you > > Ros > > On 4/18/12, Edward A. Berry <[email protected]> wrote: > > > 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 > > > > Does that mean a different number of molecules in the asymmetric > > was found, or just that they were arranged differently? If the latter, > > try generating symmetry-mates around one dimer and see if the tetramer > > is created. Ideally if the solutions are right they should be the > > same, within an arbitrary choice of asymmetric unit and origin. > > > > What does it mean, each molecule was . . two chains? did you > > divide the molecule and find each part separately? Is you > > dimer a heterodimer? Provide more details like space group and > > whether the tetramer is crystallograhic or all in the asymmetric > > unit, and some expert may be able to provide suggestions. > > > > > > Uma Ratu wrote: > >> 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<[email protected]> 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 > >>> > >>> > >> > > > > >
