Re: [phenixbb] low resolution map

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