[phenixbb] Anyone have a phenix.resolve script for after Phaser ?

Phil Jeffrey pjeffrey at Princeton.EDU
Tue Jul 14 17:00:18 PDT 2009


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
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> 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: terwilliger at LANL.gov 
> <mailto:terwilliger at LANL.gov>
> 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
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb




More information about the phenixbb mailing list