[phenixbb] syntax for Averaged Kicked maps and maps.param
Pavel Afonine
pafonine at lbl.gov
Fri Aug 6 15:57:52 PDT 2010
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
> ktd at uchicago.edu <mailto:ktd at uchicago.edu>
>
> On Mon, Aug 2, 2010 at 7:48 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto:pafonine at lbl.gov>> 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, amadrona at uci.edu <mailto: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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