Anyone have a phenix.resolve script for after Phaser ?
Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at: phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD This runs, but I could not tell from delving into the documentation if this was ideal or not. Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton
Hi Phil, That script looks fine. If you have NCS, then it is good to add ha_file my-ha-sites.pdb so that it can find the NCS. Also your script will build a model...to skip that say no_build If you are building a model I'd recommend also trying phenix.autobuild which will generally do much better than the resolve run in your script. If you are wanting to run HYSS -> PHASER -> RESOLVE then you can also just run phenix.autosol which will do that for you. All the best, Tom T On Jul 13, 2009, at 11:35 AM, Phil Jeffrey wrote:
Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at:
phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD
This runs, but I could not tell from delving into the documentation if this was ideal or not.
Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton _______________________________________________ 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 CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
Thanks Tom, The Resolve build on a relatively crummy 2.6 (nominal) Angstrom map, although possibly not the best possible, actually tipped the balance on getting Arp to autobuild the structure in a higher resolution different crystal form after I combined it with my SHARP map manual build, so I went from hitting my head against a brick wall to building the structure at 1.7 A in the space of one very good day. I'll take a look at phenix.autosol but I was playing with multiple MAD and SAD datasets, 3 xtal forms, and I didn't have too much confidence that I could bend autosol to my will. Cheers Phil Jeffrey Tom Terwilliger wrote:
Hi Phil, That script looks fine. If you have NCS, then it is good to add
ha_file my-ha-sites.pdb
so that it can find the NCS. Also your script will build a model...to skip that say
no_build
If you are building a model I'd recommend also trying phenix.autobuild which will generally do much better than the resolve run in your script.
If you are wanting to run HYSS -> PHASER -> RESOLVE then you can also just run phenix.autosol which will do that for you.
All the best, Tom T
On Jul 13, 2009, at 11:35 AM, Phil Jeffrey wrote:
Although my usual m.o. is SHELX -> SHARP I'm exploring HYSS -> PHASER -> RESOLVE to see if the maps are any more interpretable. I think I've got good scripts for the first two steps but I'm not sure about my resolve script which stands at:
phenix.resolve << EOD hklin myp3_auto.mtz LABIN FP=F SIGFP=SIGF PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD hklout resolve.mtz solvent_content 0.45 seq_file myp3.pir EOD
This runs, but I could not tell from delving into the documentation if this was ideal or not.
Thanks Phil Jeffrey (a Luddite and not using the GUI) Princeton _______________________________________________ phenixbb mailing list [email protected] mailto:[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] mailto:[email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org 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 CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
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