Re: [phenixbb] low resolution map

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

From: [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 extended set of freeR flags with your hires file most easily with the 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 phenix? 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 To: PHENIX user mailing list Sent: Wednesday, September 2, 2009 6:11:01 PM Subject: Re: [phenixbb] low resolution map

Dear Tom

thanks.

From: Tom Terwilliger To: PHENIX user mailing list Sent: Wednesday, September 2, 2009 9:20:55 AM Subject: Re: [phenixbb] low 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

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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

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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

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