<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Kyle,<br>
<br>
here it is, step-by-step:<br>
<br>
1) make sure you are running a recent PHENIX version:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/">http://www.phenix-online.org/download/</a><br>
<br>
2) type<br>
<br>
phenix.maps<br>
<br>
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<br>
<br>
4) run<br>
<br>
phenix.maps maps.params<br>
<br>
and you should get your maps.<br>
<br>
If this does not work, please let me know and send the maps.params
file.<br>
<br>
Also, an easier way is to use PHENIX GUI:<br>
<br>
PHENIX GUI -> Maps -> Create Maps<br>
<br>
Let me know if you need any help with this.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 8/6/10 2:08 PM, Kyle Dolan wrote:
<blockquote
cite="mid:AANLkTin0grGLZjBchmAxnyNsh5g4v1GApuVi9+QTWjFq@mail.gmail.com"
type="cite">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 moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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><br>
<br>
<br>
On 8/2/10 5:38 PM, <a moz-do-not-send="true"
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>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org"
target="_blank">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</blockquote>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
</div>
</div>
</blockquote>
</div>
<br>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>