Hi Kyle, here it is, step-by-step: 1) make sure you are running a recent PHENIX version: http://www.phenix-online.org/download/ 2) type phenix.maps 3) edit 'maps.params' file by adding/removing maps and switching from "kicked = False" to "kicked = True" for those maps that you want to be kicked 4) run phenix.maps maps.params and you should get your maps. If this does not work, please let me know and send the maps.params file. Also, an easier way is to use PHENIX GUI: PHENIX GUI -> Maps -> Create Maps Let me know if you need any help with this. Pavel. On 8/6/10 2:08 PM, Kyle Dolan wrote:

Hi Pavel,

I am also trying to make kicked maps for the first time in order to improve density for a terminal helix and short loop that have been giving me problems in model building for an MR structure. On a similar note to Yarrow, I tried using his syntax in a maps.params file, like this:

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 = False } 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 }

But when I ran phenix.maps I received this message:

Unused parameter definitions: maps.map.mtz_label_amplitudes (file "maps.params", line 29) maps.map.mtz_label_phases (file "maps.params", line 30) maps.map.likelihood_weighted (file "maps.params", line 31) maps.map.obs_factor (file "maps.params", line 32) maps.map.calc_factor (file "maps.params", line 33) maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params", line 35) maps.map.mtz_label_amplitudes (file "maps.params", line 38) maps.map.mtz_label_phases (file "maps.params", line 39) maps.map.likelihood_weighted (file "maps.params", line 40) maps.map.obs_factor (file "maps.params", line 41) maps.map.calc_factor (file "maps.params", line 42) maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params", line 44) *******************************************************************************

Sorry: Unused parameter definitions.

Next I tried using this in my .params file for phenix.refine:

refinement.electron_density_maps { map { map_type = "2mFo-DFc" format = *xplor ccp4 file_name = None kicked = True fill_missing_f_obs = False grid_resolution_factor = 0.25 scale = *sigma volume region = *selection cell atom_selection = None atom_selection_buffer = 3 acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None } map { map_type = "mFo-DFc" format = *xplor ccp4 file_name = None kicked = True fill_missing_f_obs = False grid_resolution_factor = 0.25 scale = *sigma volume region = *selection cell atom_selection = None atom_selection_buffer = 3 acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None }

When I opened the map_coeffs.mtz output file, it contains these columns 2FOFCWT_no_fill PH2FOFCWT_no_fill FOFCWT PHFOFCWT

Are these the coefficients for the kicked maps?

Cheers, Kyle

Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago [email protected] mailto:[email protected]

On Mon, Aug 2, 2010 at 7:48 PM, Pavel Afonine mailto:[email protected]> wrote:

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] mailto:[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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