Hi Yarrow, you can use GUI or the command line for doing this. 0) It would be best if you update to the latest version, although I believe it might work with the one you have too: http://www.phenix-online.org/download/ 1) GUI: launch PHENIX GUI and go to Maps -> Create Maps. then just add as many maps you want (or use pre-defined ones) and check a box for kick map. 2) From the command line type: phenix.maps and hit Enter (Return). That will create a file called something maps.params. Edit that file to add/remove the maps you need/ don't need and set kicked = True for the one you want to be "kicked", and then run phenix.maps maps.params Let me know if you have any questions or problems. Good luck! Pavel. On 8/2/10 5:38 PM, [email protected] wrote:
Hello,
Disclaimer: I am a newbie to both crystallagraphy and Phenix.
I am running phenix.refine (v1.6-289) in the command line
1. I want to make averaged "kicked-maps" but I keep getting a syntax error. I tried renaming "maps.param" but this file was not recognized.
2. When I enter Phenix.maps into the command line I get a message that syas "not implemented" I am trying to get the latest versiou of phenix installed.
The following is the syntax I put in my custom_params file Thanks
-Yarrow
refinement.main.number_of_macro_cycles = 2 #refinement.main.fix_rotamers = True refinement.refine.strategy = individual_sites+individual_adp refinement.output.prefix = CIN4_refine_omit refinement.output.serial = 12 refinement.output.write_def_file = True refinement.target_weights_wxc.scale = 0.2 refinement.main.max_number_of_interations=15
refinement.electron_density_maps { map { mtz_label_amplitudes = "2FOFCWT_kick" mtz_label_phases = "PH2FOFCWT_kick" likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = True } map { mtz_label_amplitudes = "FOFCWT_kicked" mtz_label_phases = "PHFOFCWT_kicked" likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked = True fill_missing_f_obs_with_weighted_f_model = false }
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