Tell phenix.autosol to find more heavy atoms?
I have a SAD map which is beautiful, but I want to look for more heavy atoms before further refinement... Would the proper procedure be.... SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyss: phenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \ sites_file=deriv_hyss_consensus_model.pdb This will carry out the usual structure solution process, but will read sites from deriv_hyss_consensus_model.pdb, try both hands, and carry on from there. If you know the hand of the substructure, you can fix it with have_hand=True. Would there be a PDS friendly way to do this (not necessary though) ? i.e. phenix.autobuild after_autosol --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis, At 02:11 PM 5/19/2008, Francis E Reyes wrote:
I have a SAD map which is beautiful, but I want to look for more heavy atoms before further refinement...
Would the proper procedure be....
SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyss: phenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \ sites_file=deriv_hyss_consensus_model.pdb This will carry out the usual structure solution process, but will read sites from deriv_hyss_consensus_model.pdb, try both hands, and carry on from there. If you know the hand of the substructure, you can fix it with have_hand=True.
Yes, that is the proper procedure. I should point out however, that Phaser SAD phasing automatically completes the sites (finding more after HYSS) so it is likely that if you feed back in the sites from the previous run (ha_2,pdb_formatted.pdb or something like that) then you probably already have all the sites you are going to get!
Would there be a PDS friendly way to do this (not necessary though) ? i.e. phenix.autobuild after_autosol
Very nice idea...but no, there isn't a nice command like that! All the best, Tom T 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
participants (2)
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Francis E Reyes -
Tom Terwilliger