[phenixbb] low resolution map

r n ramme29 at yahoo.com
Mon Sep 7 20:55:49 PDT 2009

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

From: r n <ramme29 at yahoo.com>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Wednesday, September 2, 2009 6:11:01 PM
Subject: Re: [phenixbb] low resolution map

Dear Tom


From: Tom Terwilliger <terwilliger at lanl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
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:

>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.

>phenixbb mailing list
>phenixbb at phenix-online.org

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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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