Hi, all

I have a similar question.

I have spent several months working on a MAD data (3.5 Ang) and already build 70% of the model (R/Rfree=30/40).
Recently, I collected two dataset (pk and infl, both 3.1 Ang) from single point mutation, and native data(3.3 Ang).
I first tried to use phenix autosol to generate a new map by using point mutation dataset,
but failed to generate a reasonable map for unknown reason (phenix complained different cell dimensions)

Now I am thinking to combine all data I have (although I don't know if this make sense to you) like this:

phenix.autobuild data=resolve_3.5Ang.mtz
hires_file=3.1Ang_pk.sca
hires_file=3.1Ang_inf.sca
hires_file=3.3Ang_native.sca
model=partial_model.pdb
seq_file=seq.dat


Can I use three hires command? Does this make sense to you all?

Any suggestion will be helpful to me since this my first structure and it is 3.5 Ang!


PC




> Fr! om: [email protected]
> To: [email protected]
> Date: Tue, 8 Sep 2009 08:58:44 -0600
> Subject: Re: [phenixbb] low resolution map
>
> Hi Venkat,
>
> You can combine your low-res phased data with your high-res native
> data in phenix.autobuild using the keyword
>
> hires_file=my_native_data.mtz
>
> This will substitute your native FP and SIGFP, extend the resolution
> to that of your native, and keep your experimental phases.
>
> You should probably add a step to keep and extend your freeR flags:
>
> iotbx.r_free_flags_completion_simple exptl_fobs_freeR_flags.mtz 2.8
>
> where exptl_fobs_freeR_flags.mtz is your refinement data file from
> your previous runs of autobuild (which contains your current set of
> freeR flags). This will produce a file with JUST the extended freeR
> flags. You can then combine this extende! d set of freeR flags with your
> hires file most easily with t he reflection tools in the current PHENIX
> GUI. Then use that hires_file in autobuild.
>
> Let me know if that doesn't help!
> All the best,
> Tom T
>
>
> On Sep 7, 2009, at 9:55 PM, r n wrote:
>
> > Hi all
> >
> > I am working on low resolution structure sad data and build 70% of
> > the molecule and R/Rfree is 25/32%, there are some weak density for
> > remaining 20% of the molecule,.
> >
> > I was trying to improve the map using the both experimental (3.5
> > Ang) and native data (2.8 Ang) using phenix.Gui
> > using two dataset for autobuild, but not successful, Phenix not
> > able to find extra residues other than what I have given as input
> > after5 cycle of autobuild.
> >
> > How can I combine the two data set with low and high resolution
> > extend the phase with phen! ix?
> > Any possibility of identifying the missing parts just even as poly
> > ala trace?
> >
> > Is it possible to achieve phase combination and extension to improve
> > the map ?
> > Possible a fragment or domain using known phases and map by Phenix?
> >
> > Any suggestions will be appreciated
> > Thanks
> > Venkat
> >
> > From: r n <[email protected]>
> > To: PHENIX user mailing list <[email protected]>
> > Sent: Wednesday, September 2, 2009 6:11:01 PM
> > Subject: Re: [phenixbb] low resolution map
> >
> > Dear Tom
> >
> > thanks.
> >
> > From: Tom Terwilliger <[email protected]>
> > To: PHENIX user mailing list <[email protected]>
> > Sent: Wednesday, September 2, 2009 9:20:55 AM
> > Subject: Re: [phenixbb] lo! w resolution map
> >
> > Hi Venkat,
> > Yes , you can use autobuild to create a map including model and
> > experimental phase information:
> >
> > phenix.autobuild data=sad_phase_info.mtz
> > model=partial_mr_solution.pdb \
> > seq_file=seq.dat maps_only=true
> >
> > This will refine the partial model, use it along with the sad phases
> > in density modification, and produce coefficients for a new map for
> > you:
> >
> > --- Density-modified map coefficients FP PHIM FOM ---
> > hklout_denmod: AutoBuild_run_3_/cycle_best_2.mtz
> >
> >
> > All the best,
> > Tom T
> >
> >
> > On Sep 2, 2009, at 8:12 AM, r n wrote:
> >
> >> Hi
> >>
> >> I would like to know for low resolution data with poor phase
> >> information (SAD and partial MR), Is there possibility to
> >> in Phenix ! to improve the phase and map using the partial model at
> >> low resolution (3.5 Ang), similar to TNT/BUSTER.
> >>
> >> Thanks
> >> venkat
> >>
> >>
> >>
> >> _______________________________________________
> >> 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://techcente! r.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
> > [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-Se! curity Science web site: http://www.lanl.gov/cbss
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> [email protected]
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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