[phenixbb] Anyone have a phenix.resolve script for after Phaser ?
pjeffrey at Princeton.EDU
Tue Jul 14 17:00:18 PDT 2009
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.
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
> 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
>> This runs, but I could not tell from delving into the documentation if
>> this was ideal or not.
>> Phil Jeffrey (a Luddite and not using the GUI)
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> Thomas C. Terwilliger
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