[phenixbb] density modification?

[Tom Terwilliger]

Hi John,

Yes, you have several choices for density modification in phenix:

1. Use your experimental Fobs and phases as a starting point for the 
AutoBuild Wizard. After the first cycle, you will have 
density-modified phases. In this example below model-building is 
turned off with maps_only=True to make this go quickly:

phenix.autobuild   my_fobs_exptl_phases.mtz  input_seq_file=seq.dat \
maps_only=True  \
n_cycle_build_max=1   n_cycle_rebuild_max=0

Your density-modified phases will be in 
AutoBuild_run_1_/overall_best_denmod_map_coeffs.mtz
after this run.

2. You can also use resolve directly in phenix with a command like this

phenix.resolve<<EOD
hklin my_fobs_exptl_phases.mtz
labin FP=FP PHIB=PHIB FOM=FOM HLA=HLA HLB=HLB HLC=HLC HLD=HLD
no_build
solvent_content 0.45
EOD

Either of these will do solvent flattening and histogram matching. If 
you have ncs you can specify it with a set of matrices or with a set 
of heavy-atom positions in a PDB file that show the NCS with:

ha_file heavy_atoms_with_ncs.pdb


All the best,
Tom T



. 03:26 PM 8/22/2007, you wrote:
>Is there a way to do density modification in Phenix (solvent and or
>histogram)?  If so how?
>
>Thanks,
>John Bruning
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
>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: 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