Defining heavy atom sites for AutoSol
Hi all, I used AutoSol to generate SAD phases for a protein after completing a partial MR model. My strategy worked, but I noticed there were more heavy atom sites in the solution than I was expecting. Having continued to build and refine the structure, I am fairly certain that I know which sites are the real sites and which ones are noise. I would like to use the real sites to reproduce the experimental phases in AutoSol or another Phenix module to perhaps improve the map quality (essentially running just SOLVE or Phaser without HYSS or model-building). What is the right approach? I am guessing something like this: phenix.autosol data.sca sequence.dat sites_file=sites.pdb build=False Cheers, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago [email protected]
Hi Kyle, Yes, your guess is correct. You could add "have_hand=True" if you know the hand of the solution too. You might also add "phaser_completion=False" if you really don't want any more sites added. On the other hand...usually phaser is pretty good at adding things that are real, even if you might not recognize them as such at first, so you might look carefully at the results that you get each way. We would be interested in which turns out to be better! All the best, Tom T
Hi all,
I used AutoSol to generate SAD phases for a protein after completing a partial MR model. My strategy worked, but I noticed there were more heavy atom sites in the solution than I was expecting. Having continued to build and refine the structure, I am fairly certain that I know which sites are the real sites and which ones are noise. I would like to use the real sites to reproduce the experimental phases in AutoSol or another Phenix module to perhaps improve the map quality (essentially running just SOLVE or Phaser without HYSS or model-building). What is the right approach? I am guessing something like this:
phenix.autosol data.sca sequence.dat sites_file=sites.pdb build=False
Cheers, Kyle
Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear Kyle, Just to amplify what Tom said, usually if Phaser adds sites, they represent something real, e.g. another (perhaps unexpected) anomalous scatterer (S, Cl, metal, depending on the wavelength) or a split site arising from static disorder. If the sites are real, deleting them can degrade your phase quality significantly. However, I've seen a few data sets where there's some noise in the data that leads to false sites, so it wouldn't hurt to do a run on the side where you limit the number of sites. All the best, Randy On Jul 22 2010, Kyle Dolan wrote:
Hi all,
I used AutoSol to generate SAD phases for a protein after completing a partial MR model. My strategy worked, but I noticed there were more heavy atom sites in the solution than I was expecting. Having continued to build and refine the structure, I am fairly certain that I know which sites are the real sites and which ones are noise. I would like to use the real sites to reproduce the experimental phases in AutoSol or another Phenix module to perhaps improve the map quality (essentially running just SOLVE or Phaser without HYSS or model-building). What is the right approach? I am guessing something like this:
phenix.autosol data.sca sequence.dat sites_file=sites.pdb build=False
Cheers, Kyle
Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago [email protected]
participants (3)
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Kyle Dolan -
Randy J. Read -
Thomas C. Terwilliger