Re: [ccp4bb] Methods to reduce the model bias and increase the SAD phase
Dear Yuan. 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? If you use shelxd to search the heavy atom, you can get the value of "CC All/Weak" in shelxd.log. "CC All" should be larger than 35 if you want to solve the structure by SAD. 2. How to reduce the model bias and phase errors in my situations? any suggestions? Try TLS refinement in refmac or phenix.refine after model building. 3. Should I collect a MAD data instead of SAD data? How much would that could help? I don't think the MAD data will be better than SAD data. Maybe you can try to collect data with small oscillation angle (e.g.0.5deg) 。 If you need more help, please send me the log file outputted by HKL2000. Best regards & Many thanks! Yuan Wei
Re: [ccp4bb] Methods to reduce the model bias and increase the SAD phase
I check ha sites by 1) looking at the shelxe plots ( these are displayed in the CCP4 GUI task - prob also in phenix? ) If there is good contrast for one hand rather than the other the sites are likely to be correct - if not - hmmm; there might be a reason but they could be wrong.. Then I check the sites by giving the strongest ones to phaser_ep and seeing if it suggests more which agree with SHELX ones.. Bias is not usually a problem if the initial build is correct but if the Rfactors are not coming down that may not be the case. Can you see sidechains - espec MET near your Se sites? Eleanor On 12 July 2013 04:12, Yuan SHANG wrote: > 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 >
[ccp4bb] Methods to reduce the model bias and increase the SAD phase
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
