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Hi, Just one correction to this. Phaser doesn't substitute values with the same name in an output MTZ file. To get the anisotropy corrected F and SIGF values, you have to run phaser in the separate anisotropy correction mode, and even then it appends the string "_ISO" to the column names and leaves the original columns as they were. We make it hard to get the corrected values, because we think that downstream programs should be able to do a better job once they have more information (e.g. a well-refined structure), but we make it possible to get them because not all potential downstream programs are capable of doing any anisotropy correction at all. Regards, Randy On 29 Feb 2012, at 21:51, Eleanor Dodson wrote: > mtz(1) will contain h k l F SIGF I SIGI and optionally F+ SIGF+ and F- SIGF- This is your master file, providing the space group is correct > > It may NOT have the correct space group however - MR searches may select one space group from several possible ones. If the final SG is different from the one specified after scalepack2mtz just run a jiffy to change it. > > e.g. mtzutils hklin1 scal1.mtz hklout scal2.mtz > symm SGname > end > > then use scal2.mtz as your master.. > > The output from phaser will have the same F but after anisotropic scaling. There will be other columns suitable for input to coot > > the output from REFMAC will also give a scaled F plus extra columns . > > Always start each new refinement with your master mtz as input.. > > coot will automatically select the best output from PHASER or REFMAC to calculate maps. The columns FWT and PHWT are used to generate a 2mFobs-DFcalc map The columns DELFWT and PHDELWT generate a mFobs-DFcalc map > > Eleanor > > On Feb 29 2012, 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 >> > > -- > Professor Eleanor Dodson > YSNL, Dept of Chemistry > University of York > Heslington YO10 5YW > tel: 00 44 1904 328259 > Fax: 00 44 1904 328266 ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [log in to unmask] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk