Dear All, I got a Se-crystal diffracted to 3.3A. The protein is predicted to be a coiled coil. After I got the heavy atom positions from a shelxd based programs from AutoRickShaw, I run phaser and phenix.autobuild to get a initial phase shown in the attachment. I fit a "standard helix" into the density maps. After that, I did a two step iteration to improve my phases similar to the methods mentioned in Roversi's paper "With phases: how two wrongs can sometimes make a right". Step 1: Run DM with current model, heavy atom positions, the initial density maps to get a new DM map. Step 2: In the new DM map, some new density appears. Fit new helixes in this new map. The iteration ends when I found no obvious helix densities. However, when I run refinement, I still got very bad R/Rfree values. It seemed I got a lot of model bias during the process above.
Now, I have some questions that puzzled me a lot. 1. Is there any programs that could help to compare and check the heavy atom positions in shelxd solutions? Especially in cases when the solutions are not obvious. SitCOM seemed very good, is there a 32-bit distribution of this programs? Or any others have similar functions? 2. How to reduce the model bias and phase errors in my situations? any suggestions? 3. Should I collect a MAD data instead of SAD data? How much would that could help? Best regards & Many thanks! Yuan
