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 <ramme29@yahoo.com>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Sent: Wednesday, September 2, 2009 6:11:01 PM
Subject: Re: [phenixbb] low resolution map
Dear Tom
thanks.
From: Tom Terwilliger <terwilliger@lanl.gov>
To: PHENIX user mailing list <phenixbb@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: