Running Autobuild after Autosol
Hi, how do I specify running Autobuild after Autosol, in the command line mode? I see the "phenix.autobuild after_autosol" option in the manual, but how will Autobuild know which Autosol run to use? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: [email protected]
Dear Katya,
2009/8/14 Katya Heldwein
Hi,
how do I specify running Autobuild after Autosol, in the command line mode? I see the "phenix.autobuild after_autosol" option in the manual, but how will Autobuild know which Autosol run to use?
AutoBuild will choose the best solution from either of the AutoSol runs. Exactly how this is done I do not know. If you want to use the output from an explicit AutoSol run you could simply define the result from that AutoSol run when you start AutoBuild eg: phenix.autobuild data=AutoSol_run_1_/phaser_1.mtz seq_file=yourseq.dat Or solve_1.mtz if you are do not have SAD data. Hope this helps. Best regards, Folmer Fredslund
Hi Katya, AutoBuild will look through all the autosol runs and choose the solution with the highest final score, and use that one. You can see this near the beginning of the AutoBuild run: Appending solution 4060.75360229 1 75.3602294036 exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz Appending solution 59.3469818876 2 59.3469818876 None solve_2.mtz Best solution 4060.75360229 1 75.3602294036 exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz AutoSol_run_2_ In this case it took run 2 with the solution solve_1.mtz with score of 4060.7 over the solution solve_2.mtz with score of 59. If you want to choose a different AutoSol solution, then you will need to explicitly tell AutoBuild all the files that you want to use. All the best, Tom T
Hi,
how do I specify running Autobuild after Autosol, in the command line mode? I see the "phenix.autobuild after_autosol" option in the manual, but how will Autobuild know which Autosol run to use?
Katya
-- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111
phone: 617-636-0858 fax: 617-636-0337 e-mail: [email protected]
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Dear Tom,
2009/8/14 Thomas C. Terwilliger
Hi Katya,
AutoBuild will look through all the autosol runs and choose the solution with the highest final score, and use that one. You can see this near the beginning of the AutoBuild run:
Appending solution 4060.75360229 1 75.3602294036 exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz Appending solution 59.3469818876 2 59.3469818876 None solve_2.mtz Best solution 4060.75360229 1 75.3602294036 exptl_fobs_phases_freeR_flags_1.mtz solve_1.mtz AutoSol_run_2_
If I understand correctly solve_1.mtz and solve_2.mtz both originate from the AutoSol_run_2_ directory? How did AutoBuild choose to go with that solution in the first place? What about the scores for solution from eg AutoSol_run_1_ or AutoSol_run_3_?
In this case it took run 2 with the solution solve_1.mtz with score of 4060.7 over the solution solve_2.mtz with score of 59.
If you want to choose a different AutoSol solution, then you will need to explicitly tell AutoBuild all the files that you want to use.
All the best, Tom T
Best regards, Folmer Fredslund
participants (3)
-
Folmer Fredslund -
Katya Heldwein -
Thomas C. Terwilliger