I have a dataset from a Cs-soaked crystal, and the protein has a domain solved in the PDB. The problem is that the map obtained just with the experimental phasing is not so easily interpreted, and the domain is just about 25% of the whole protein. Inspection of the map generated by MR suggests that it's a good solution, with residues fitting reasonably well on the density. Given the new features on Phaser 2.0, which I suppose is included in Phenix 1.3b, can anyone suggest a protocol to profit from both things (anomalous scattering + good search model)? Thanks in advance, Lucas ____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso
Hi Lucas, Yes, here is one thing you can do: (#1 will be by hand for the version that you have unfortunately): 1. Use the MR solution to calculate phases; get an anomalous difference Fourier, and pick the top peaks as your heavy-atom sites. 2. Read in the anomalous data and sites to AutoSol and get experimental phases. 3. Read in the experimental phases and the MR model to AutoBuild, with rebuild_in_place=False (build model from scratch) and include_input_model=True (default) and let it try to density modify and continue on with model rebuilding starting from the 25% model. Good luck! -Tom T At 08:13 AM 6/16/2007, Lucas Bleicher wrote:
I have a dataset from a Cs-soaked crystal, and the protein has a domain solved in the PDB. The problem is that the map obtained just with the experimental phasing is not so easily interpreted, and the domain is just about 25% of the whole protein. Inspection of the map generated by MR suggests that it's a good solution, with residues fitting reasonably well on the density.
Given the new features on Phaser 2.0, which I suppose is included in Phenix 1.3b, can anyone suggest a protocol to profit from both things (anomalous scattering + good search model)?
Thanks in advance, Lucas
____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
Dear Lucas, You'll need Phaser version 2.1, which will be in the next developer release of Phenix-1.3b. This has a new feature that exactly addresses your problem. You can start the SAD phasing using the molecular replacement model as an initial "substructure". Then log-likelihood-gradient maps are used to add in the anomalous scatterers. We've found that the resulting anomalous scatterer model is usually more accurate and, perhaps more importantly, is more complete. Often the S atoms can be found, even when the wavelength is not optimal for S-SAD. The map that comes out of this phasing process automatically combines the molecular replacement and anomalous scattering information, properly weighted and with a correction for model bias. I'm in Grenoble right now at a phasing workshop, but when I get back I should be able to send you a statically-linked Linux executable of the beta-test version of Phaser-2.1. Randy Read On Jun 16 2007, Lucas Bleicher wrote:
I have a dataset from a Cs-soaked crystal, and the protein has a domain solved in the PDB. The problem is that the map obtained just with the experimental phasing is not so easily interpreted, and the domain is just about 25% of the whole protein. Inspection of the map generated by MR suggests that it's a good solution, with residues fitting reasonably well on the density.
Given the new features on Phaser 2.0, which I suppose is included in Phenix 1.3b, can anyone suggest a protocol to profit from both things (anomalous scattering + good search model)?
Thanks in advance, Lucas
____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Lucas Bleicher -
Randy J. Read -
Tom Terwilliger