[phenixbb] syntax for Averaged Kicked maps and maps.param

Pavel Afonine pafonine at lbl.gov
Mon Aug 2 17:48:45 PDT 2010


  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, amadrona at uci.edu 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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