[phenixbb] maps and autobuild

Tom Terwilliger terwilliger at lanl.gov
Mon Apr 6 09:20:37 PDT 2009

Hi Charlie,

> I am a first time user to phenix , and I have just completed the  
> autobuild function,.
> My question may have been asked many times before, but..
> The output after the cycles of autobuild/refinement gave me a  
> refined file for a 2.2 Angstrom data set with an R/Rfree of .28/.32.
> I want to take a look at the density modified maps and see what I  
> can adjust further,  but am having trouble loading it in coot.
> Am I correct in understanding that Coot can load and construct 2f0- 
> fc maps? if so How? :
> exptl_fobs_phases_freeR_flags.
> mtz
> overall_best_denmod_map_coeffs.mtz;  
> overall_best_refine_map_coeffs.mtz;

You can read in overall_best_refine_map_coeffs.mtz to coot (not auto- 
load) and then select the columns 2FOFCWT and PH2FOFCWT and coot  
should make your map.

> Also from reading the manual, as I understand it, the phenix.refine  
> command will automatically generate Coot compatible maps.
> But if I take my autobuild.pdb file and the original mtz data file,  
> how can I quickly obtain the same R/Rfree, what commands would I  
> have to imput other than phenix.refine mtz pbd?

phenix.refine exptl_fobs_phases_freeR_flags.mtz overall_best.pdb \
   main.number_of_macro_cycles=1 strategy=none

should do it
> Also, is it possible to make 3Fo-2Fc maps?

I'm not certain on that one..
-Tom T

> Thanks
> Charlie
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