Hi Pavel,<br><br>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:<br>
<br>map {<br> mtz_label_amplitudes = 2FOFCWT_kick<br> mtz_label_phases = PH2FOFCWT_kick<br> likelihood_weighted = True<br>
obs_factor = 2<br> calc_factor = 1<br> kicked = True<br> fill_missing_f_obs_with_weighted_f_model = False<br> }<br> map {<br> mtz_label_amplitudes = "FOFCWT_kicked"<br> mtz_label_phases = "PHFOFCWT_kicked"<br>
likelihood_weighted = True<br> obs_factor = 1<br> calc_factor = 1<br> kicked = True<br> fill_missing_f_obs_with_weighted_f_model = False<br> }<br><br>But when I ran phenix.maps I received this message:<br>
<br>Unused parameter definitions:<br>
maps.map.mtz_label_amplitudes (file "maps.params", line 29)<br>
maps.map.mtz_label_phases (file "maps.params", line 30)<br>
maps.map.likelihood_weighted (file "maps.params", line 31)<br>
maps.map.obs_factor (file "maps.params", line 32)<br>
maps.map.calc_factor (file "maps.params", line 33)<br>
maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params", line 35)<br>
maps.map.mtz_label_amplitudes (file "maps.params", line 38)<br>
maps.map.mtz_label_phases (file "maps.params", line 39)<br>
maps.map.likelihood_weighted (file "maps.params", line 40)<br>
maps.map.obs_factor (file "maps.params", line 41)<br>
maps.map.calc_factor (file "maps.params", line 42)<br>
maps.map.fill_missing_f_obs_with_weighted_f_model (file "maps.params", line 44)<br>
*******************************************************************************<br>
<br>
Sorry: Unused parameter definitions.<br><br>Next I tried using this in my .params file for phenix.refine:<br><br>refinement.electron_density_maps {<br> map {<br> map_type = "2mFo-DFc"<br> format = *xplor ccp4<br>
file_name = None<br> kicked = True<br> fill_missing_f_obs = False<br> grid_resolution_factor = 0.25<br> scale = *sigma volume<br> region = *selection cell<br> atom_selection = None<br>
atom_selection_buffer = 3<br>
acentrics_scale = 2<br> centrics_pre_scale = 1<br> sharpening = False<br> sharpening_b_factor = None<br> }<br> map {<br> map_type = "mFo-DFc"<br> format = *xplor ccp4<br> file_name = None<br>
kicked = True<br> fill_missing_f_obs = False<br> grid_resolution_factor = 0.25<br> scale = *sigma volume<br> region = *selection cell<br> atom_selection = None<br> atom_selection_buffer = 3<br>
acentrics_scale = 2<br> centrics_pre_scale = 1<br> sharpening = False<br> sharpening_b_factor = None<br> }<br><br>When I opened the map_coeffs.mtz output file, it contains these columns<br>2FOFCWT_no_fill<br>
PH2FOFCWT_no_fill<br>FOFCWT<br>PHFOFCWT<br><br>Are these the coefficients for the kicked maps? <br><br>Cheers,<br>Kyle<br><br>Kyle T. Dolan<br>Department of Biochemistry and Molecular Biology<br>
The University of Chicago<br><a href="mailto:ktd@uchicago.edu" target="_blank">ktd@uchicago.edu</a><br>
<br><div class="gmail_quote">On Mon, Aug 2, 2010 at 7:48 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Yarrow,<br>
<br>
you can use GUI or the command line for doing this.<br>
<br>
0) It would be best if you update to the latest version, although I believe it might work with the one you have too:<br>
<br>
<a href="http://www.phenix-online.org/download/" target="_blank">http://www.phenix-online.org/download/</a><br>
<br>
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.<br>
<br>
2) From the command line type:<br>
<br>
phenix.maps<br>
<br>
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<br>
<br>
kicked = True<br>
<br>
for the one you want to be "kicked", and then run<br>
<br>
phenix.maps maps.params<br>
<br>
Let me know if you have any questions or problems.<br>
<br>
Good luck!<br><font color="#888888">
Pavel.</font><div><div></div><div><br>
<br>
<br>
On 8/2/10 5:38 PM, <a href="mailto:amadrona@uci.edu" target="_blank">amadrona@uci.edu</a> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br>
<br>
Disclaimer: I am a newbie to both crystallagraphy and Phenix.<br>
<br>
I am running phenix.refine (v1.6-289) in the command line<br>
<br>
1. I want to make averaged "kicked-maps" but I keep getting a syntax<br>
error. I tried renaming "maps.param" but this file was not recognized.<br>
<br>
2. When I enter Phenix.maps into the command line I get a message that<br>
syas "not implemented"<br>
I am trying to get the latest versiou of phenix installed.<br>
<br>
The following is the syntax I put in my custom_params file<br>
Thanks<br>
<br>
-Yarrow<br>
<br>
refinement.main.number_of_macro_cycles = 2<br>
#refinement.main.fix_rotamers = True<br>
refinement.refine.strategy = individual_sites+individual_adp<br>
refinement.output.prefix = CIN4_refine_omit<br>
refinement.output.serial = 12<br>
refinement.output.write_def_file = True<br>
refinement.target_weights_wxc.scale = 0.2<br>
refinement.main.max_number_of_interations=15<br>
<br>
<br>
refinement.electron_density_maps {<br>
map {<br>
mtz_label_amplitudes = "2FOFCWT_kick"<br>
mtz_label_phases = "PH2FOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 2<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = True<br>
}<br>
map {<br>
mtz_label_amplitudes = "FOFCWT_kicked"<br>
mtz_label_phases = "PHFOFCWT_kicked"<br>
likelihood_weighted = True<br>
obs_factor = 1<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = false<br>
}<br>
<br>
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