Thank you very much! It is clear for me now.
Cheers Ros On Wed, Feb 29, 2012 at 9:18 AM, Vellieux Frederic <frederic.velli...@ibs.fr > wrote: > Hi, > > The refinement program generates an mtz file with map coefficients > (including difference Fourier coefficients) so you should use that one for > model rebuilding in coot; > for the next refinement rounds, at the beginning of each round you should > provide the initial mtz file coming from data processing and post > processing (1 in your terminology I suppose). This is because several > refinement programs scale the Fobs (and sigmaFobs). Refmac is one of them I > think; > for data deposition, you deposit the same mtz file (1), and if you also > wish to deposit map coefficients you can also extract the map coefficients > from the "final" refinement and map calculation round mtz (using, say, > sftools) and deposit those. > > Phaser does not carry out model refinement per se (adjusting atom > positions and temperature factors). But the map coefficients present in the > mtz file are generated in the same way (Sigmaa coefficients) with Phaser > and with Refmac. There might be small difference in terms of the program > code used internally but that shouldn't make much of a difference. > > Since a model that has "seen" refmac is (normally) improved, the electron > density maps generated using the refmac mtz should be improved wrt the maps > coming directly from Phaser (molecular replacement). Normally, the model > you refine will have had the differences in the sequence between molecular > replacement search model and 'your' structure corrected (gradually?), the > solvent model is introduced and improved, ligands, ions etc are being > introduced... Thus the maps improve seen that your model should reflect > more and more what is present in the crystal as you build and refine. > > HTH, > > Fred. > > > Uma Ratu wrote: > >> Hello, >> I have a question about .mtz files used in model building. >> Here is how I did: >> Diffraction data - HKL 2000: .sca >> CCp4i: scalepack2mtz: .mtz (1) >> Phaser: In: template pdb & .mtz(1) >> Out: model .pdb(1) & .mtz(2) >> Refmac5: model .pdb(2) & .mtz(3) >> Here is the question: >> 1. Coot check and refinment: which mtz file shoudl I use? >> 2. With further refinemnt by refmac5, which mtz file should I use? >> 3. When I deposit data, which mtz file to use? >> 4. What is the difference between .mtz(1) and the .mtz files generated >> from "phaser" and "refmac"? >> Thank you for advice >> Ros >> >
