Not that Phaser needs my approval, but I recently did exactly what Randy recommended and it really found basically all of the S and Cl sites, with data at resolution 2.2 Ang and wavelength 0.979 Ang, too. I also played a bit with the sigma cutoff for adding new sites so that the stronger sites (Se in my case) are found but the weaker ones not. Also, don't forget to click the "output LLG map coefficients" option to get the right columns in your mtz.
Jacob On Sat, Nov 26, 2011 at 6:13 AM, Randy J. Read <rj...@cam.ac.uk> wrote: > Dear Yuri, > > In addition to the other good options that have been presented, you can use > the log-likelihood gradient maps in Phaser to find anomalous scatterers. We > find this to be very sensitive, and it has the advantage of being iterative > (i.e. when you find some anomalous scatterers, this improves your model and > thus the sensitivity for finding additional sites). > > When you're starting from a refined model, we think it is best to look for > purely imaginary scatterers to add to the real scattering in your model. In > the ccp4i GUI, choose the "SAD with molecular replacement partial structure" > mode, provide the data (with F+ and F-), the wavelength, and the current > model, then turn on LLG-map completion and select the "Complete with purely > anomalous scatterer" option. > > If you want to see the initial LLG map, set the number of completion cycles > to 0 and turn on the option to output log-likelihood-gradient map > coefficients. Open these in coot as a difference map, choosing the columns > FLLG_AX and PHLLG_AX. If you let Phaser complete the sites, then the final > LLG map should be nearly flat and you have to look at the PDB file > containing the sites that it found. > > Best wishes, > > Randy Read > On Nov 26 2011, Yuri Pompeu wrote: > >> Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite >> beautiful at 1.17A and it has a really big peak 18sigma! Is there a utility >> for calculating anomalous maps, or is it simply an option in the refinement >> program? >> > > -- > Randy J. Read > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
