hello, 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; 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? Also, is it possible to make 3Fo-2Fc maps? Thanks Charlie
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Charlie,
Also from reading the manual, as I understand it, the phenix.refine command will automatically generate Coot compatible maps.
phenix.refine always outputs maps ready to visualize in Coot. The files is called xxx_map_coeffs.mtz and it contains various columns with Fourier map coefficients. When loading this file into Coot you need to choose which map to display (which map coefficients to use).
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?
In addition to what Tom wrote, there is a specific command to do this: phenix.model_vs_data model.pdb data.mtz and it will give you complete model and data statistics, including R-factors.
Also, is it possible to make 3Fo-2Fc maps?
phenix.refine can create a map i*mFo-j*DFc or i*Fo-j*Fc, where i and j are any user provided numbers. Example: phenix.refine model.pdb data.hkl params.txt where params.txt file contains these lines: refinement.electron_density_maps { map { mtz_label_amplitudes = 3FO2FCWT mtz_label_phases = PH3FO2FCWT likelihood_weighted = True obs_factor = 3 calc_factor = 2 kicked = False fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = 1.5FO1.2FCWT mtz_label_phases = PH1.5FO1.2FCWT likelihood_weighted = False obs_factor = 1.5 calc_factor = 1.2 kicked = False fill_missing_f_obs_with_weighted_f_model = True } } Pavel.
participants (3)
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chandra bose -
Pavel Afonine -
Tom Terwilliger