Dx map - Revision history

Bugman: Switch to the {{gna bug url}} and {{gna bug url}} templates to remove dead Gna! links.

2020-10-16T19:44:55Z

Switch to the {{gna bug url}} and {{gna bug url}} templates to remove dead Gna! links.

Tlinnet: /* Sample data to try dx */

2017-10-17T07:16:50Z

Sample data to try dx

Tlinnet: /* Sample data to try dx */

2017-10-17T07:07:45Z

Sample data to try dx

Tlinnet: /* Code to generate map */

2017-10-17T06:42:13Z

Code to generate map

Bugman: /* Code to generate map */ Using the {{collapsible script}} template to declutter the article.

2015-11-06T18:46:41Z

Code to generate map: Using the {{collapsible script}} template to declutter the article.

Bugman: /* How to use dx */ Formatting using the `tag.`


2015-11-06T18:42:52Z
How to use dx:  Formatting using the <code> tag.

				
				
				
				
				
				← Older revision
				Revision as of 18:42, 6 November 2015
				
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  == How to use dx ==   == How to use dx ==
− * Run 'dx', + Run <code>dx</code>, and then in the '''Data explorer''' or '''DE'''.
− In teh '''Data explorer''' or '''DE'''. + * Click on <code>Edit Visual Programs...</code>.
− * Click on '''Edit Visual Programs...'''. + * Select the <code>map.net</code> program created by relax,
− * Select the map.net program created by relax,  
    
− Now in the '''Visual Program Editor''' or '''VPE'''. + Now in the <code>Visual Program Editor</code> or <code>VPE</code>.
− * Select the menu entry 'Execute->Execute on change'. + * Select the menu entry <code>Execute->Execute on change</code>.
    
  That's it.   That's it.
    
− You now have a 3D frame, but nothing in it.  <br> + You now have a 3D frame, but nothing in it.  Therefore the contour levels must be too low or high. From the map file, the values are in the hundreds of thousands.
− Therefore the contour levels must be too low or high. <br>  
− From the map file, the values are in the hundreds of thousands.  
    
  Then:   Then:
− * In the main program window, double click on the 'Isosurface elements'. + * In the main program window, double click on the <code>Isosurface elements</code>.
  * Change the values until you see surfaces.  In the first the value is 500.  I changed this to 500,000. Multiply all by 1000.   * Change the values until you see surfaces.  In the first the value is 500.  I changed this to 500,000. Multiply all by 1000.
  * In the second, 100 -> 100000.   * In the second, 100 -> 100000.
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  This should maybe be performed by the dx.map user function, determining reasonable contour levels.      This should maybe be performed by the dx.map user function, determining reasonable contour levels.   
    
− With a bit of zooming, clicking on 'File -> Save image' in the "Surface" window, "allowing rendering", and outputting to a large TIFF file, "save current", then "apply". + With a bit of zooming, clicking on <code>File -> Save image</code> in the <code>Surface</code> window, <code>allowing rendering</code>, and outputting to a large TIFF file, <code>save current</code>, then <code>apply</code>.
    
− An example image cropped and converted to PNG in the GIMP at <br> + An example image cropped and converted to PNG in the GIMP at https://gna.org/bugs/download.php?file_id=20641.  
− https://gna.org/bugs/download.php?file_id=20641.    
    
− Note that for a good resolution plot, you will need many more increments. <br> + Note that for a good resolution plot, you will need many more increments.  Using the lower and upper dx.map arguments will be useful to zoom into the space.
− Using the lower and upper dx.map arguments will be useful to zoom into the space.  
    
  == Example images ==   == Example images ==



Bugman: Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.
2015-10-15T13:36:50Z
Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

				
				
				
				
				
				← Older revision
				Revision as of 13:36, 15 October 2015
				
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  + __TOC__
  + 
  == Code to generate map ==   == Code to generate map ==
  <source lang="Python">   <source lang="Python">



Bugman: /* Code to generate map */ Split the code line to shorten the width - this will help in the formatting of the 'Did you know...' section of the main page.
2015-10-15T13:36:30Z
Code to generate map:  Split the code line to shorten the width - this will help in the formatting of the 'Did you know...' section of the main page.

				
				
				
				
				
				← Older revision
				Revision as of 13:36, 15 October 2015
				
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  for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):   for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
       file_name = "map%s" % (cur_spin_id .replace('#', '_').replace(':', '_').replace('@', '_'))        file_name = "map%s" % (cur_spin_id .replace('#', '_').replace(':', '_').replace('@', '_'))
−      dx.map(params=['dw', 'pA', 'kex'], map_type='Iso3D', spin_id=":1@N", inc=70, lower=None, upper=None, axis_incs=5, file_prefix=file_name, dir=ds.resdir, point=None, point_file='point', remap=None) +      dx.map(params=['dw', 'pA', 'kex'], map_type='Iso3D', spin_id=":1@N", inc=70, lower=None, upper=None, axis_incs=5,
  +         file_prefix=file_name, dir=ds.resdir, point=None, point_file='point', remap=None)
       #vp_exec:  A flag specifying whether to execute the visual program automatically at start-up.        #vp_exec:  A flag specifying whether to execute the visual program automatically at start-up.
       dx.execute(file_prefix=file_name, dir=ds.resdir, dx_exe='dx', vp_exec=True)        dx.execute(file_prefix=file_name, dir=ds.resdir, dx_exe='dx', vp_exec=True)



Troels Emtekær Linnet: /* Code */
2014-05-10T11:27:07Z
Code

				
				
				
				
				
				← Older revision
				Revision as of 11:27, 10 May 2014
				
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       # Add more spins here.        # Add more spins here.
       spins = [        spins = [
−              ['Ala', 1, 'N', {'r2': {r20_key_1: 25.0, r20_key_2: 24.0}, 'r2a': {r20_key_1: 25.0, r20_key_2: 24.0}, 'r2b': {r20_key_1: 25.0, r20_key_2: 24.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 3.0} ] +              ['Ala', 1, 'N', {'r2': {r20_key_1: 25.0, r20_key_2: 24.0}, 'r2a': {r20_key_1: 25.0, r20_key_2: 24.0}, 'r2b': {r20_key_1: 25.0, r20_key_2: 24.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 0.5} ]
               #['Ala', 2, 'N', {'r2': {r20_key_1: 15.0, r20_key_2: 14.0}, 'r2a': {r20_key_1: 15.0, r20_key_2: 14.0}, 'r2b': {r20_key_1: 15.0, r20_key_2: 14.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 1.5} ]                #['Ala', 2, 'N', {'r2': {r20_key_1: 15.0, r20_key_2: 14.0}, 'r2a': {r20_key_1: 15.0, r20_key_2: 14.0}, 'r2b': {r20_key_1: 15.0, r20_key_2: 14.0}, 'kex': 2200.0, 'pA': 0.993, 'dw': 1.5} ]
               ]                ]
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  # To map the hypersurface of chi2, when altering kex, dw and pA.   # To map the hypersurface of chi2, when altering kex, dw and pA.
  if not hasattr(ds, 'opendx'):   if not hasattr(ds, 'opendx'):
−      ds.opendx = False +      #ds.opendx = False
−      #ds.opendx = True +      ds.opendx = True
    
  # Which parameters to map on chi2 surface.   # Which parameters to map on chi2 surface.
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           cur_spin_id = ":%i@%s"%(res_num, spin_name)            cur_spin_id = ":%i@%s"%(res_num, spin_name)
           cur_spin = return_spin(cur_spin_id)            cur_spin = return_spin(cur_spin_id)
  + 
  +         # Save all the paramers to loop throgh later.
  +         ds.model_analyse_params = cur_spin.params
    
           par_dic = {}            par_dic = {}
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                   clust_r2 = clust_params[mo_param]                    clust_r2 = clust_params[mo_param]
                   set_r2 = params[mo_param]                    set_r2 = params[mo_param]
−                  for key, val in getattr(cur_spin, mo_param).items(): +                  for key, val in min_r2.items():
                       grid_r2_frq = grid_r2[key]                        grid_r2_frq = grid_r2[key]
                       min_r2_frq = min_r2[key]                        min_r2_frq = min_r2[key]



Troels Emtekær Linnet: /* Code to generate map */
2014-05-10T11:26:52Z
Code to generate map

				
				
				
				
				
				← Older revision
				Revision as of 11:26, 10 May 2014
				
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  relax cpmg_synthetic.py   relax cpmg_synthetic.py
  </source>   </source>
− Here it the code + Here is the synthetic data generator code.
  === Code ===   === Code ===
  <source lang="Python">   <source lang="Python">

@@ Line 79: / Line 79: @@
 == Example images ==
-These images is from [https://gna.org/bugs/index.php?22024 bug 22024.  Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]
+These images is from {{gna bug link|22024|text=bug 22024.  Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.}}
 {|style="margin: 0 auto;"
-| [[File:Bug 22024 R2eff.png|thumb|center|upright=2|https://gna.org/bugs/index.php?22024Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
+| [[File:Bug 22024 R2eff.png|thumb|center|upright=2|{{gna bug url|22024}} Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
-| [[File:Bug 22024 Dw kex.png|thumb|upright=2|https://gna.org/bugs/index.php?22024Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
+| [[File:Bug 22024 Dw kex.png|thumb|upright=2|{{gna bug url|22024}} Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
 |}
 {|style="margin: 0 auto;"
-| [[File:Bug 22024 Dw kex pA.png|thumb|upright=2|https://gna.org/bugs/index.php?22024Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
+| [[File:Bug 22024 Dw kex pA.png|thumb|upright=2|{{gna bug url|22024}} Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
-| [[File:Bug 22024 Dw pA.png|thumb|upright=2|https://gna.org/bugs/index.php?22024Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
+| [[File:Bug 22024 Dw pA.png|thumb|upright=2|{{gna bug url|22024}} Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
-| [[File:Bug 22024 Kex pA.png|thumb|upright=2|https://gna.org/bugs/index.php?22024Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
+| [[File:Bug 22024 Kex pA.png|thumb|upright=2|{{gna bug url|22024}} Bug 22024: Minimisation space for CR72 is catastrophic. The chi2 surface over dw and pA is bounded.]]
 |}

@@ Line 23: / Line 23: @@
 sed -i.bak "s/res_num_col=1, data_col=3, error_col=4)/mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)/g" map_mod.py
 sed -i.bak "s/sequence\.attach_protons/#sequence\.attach_protons/g" map_mod.py
 # Run

@@ Line 15: / Line 15: @@
 cp $HOME/software/relax/test_suite/shared_data/model_free/sphere/*.out .
 cp $HOME/software/relax/test_suite/shared_data/model_free/sphere/*.pdb .
 # Run
-cat map.py
+relax map_mod.py
 </source>
 == Code to generate map ==

← Older revision		Revision as of 06:42, 17 October 2017
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	__TOC__		__TOC__
		+
		+	== Sample data to try dx ==
		+	<source lang="bash">
		+	cd $HOME/Desktop
		+	mkdir test_dx
		+	cd test_dx
		+
		+	# See sample scripts
		+	ls -la $HOME/software/relax/sample_scripts/model_free
		+	cp $HOME/software/relax/sample_scripts/model_free/map.py .
		+
		+	# Get data
		+	ls -la $HOME/software/relax/test_suite/shared_data/model_free/sphere
		+	cp $HOME/software/relax/test_suite/shared_data/model_free/sphere/*.out .
		+	cp $HOME/software/relax/test_suite/shared_data/model_free/sphere/*.pdb .
		+
		+	# Run
		+	cat map.py
		+	relax map.py
		+	</source>
		+

	== Code to generate map ==		== Code to generate map ==

@@ Line 67: / Line 67: @@
 relax cpmg_synthetic.py
 </source>
-Here is the synthetic data generator code.
-=== Code ===
+Here is the synthetic data generator code:
-<source lang="Python">
 ###############################################################################
 #                                                                             #
@@ Line 650: / Line 655: @@
 if ds.opendx:
      print_res(cur_spins=cur_spins, grid_params=ds.grid_results[i][3], min_params=ds.min_results[i][3], clust_params=ds.clust_results[i][3])
-</source>
+}}
 = See also =
 [[Install dx]]
 [[Category:User_functions]]

← Older revision		Revision as of 13:36, 15 October 2015
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		+	__TOC__
		+
	== Code to generate map ==		== Code to generate map ==
	<source lang="Python">		<source lang="Python">

Dx map - Revision history

Bugman: Switch to the {{gna bug url}} and {{gna bug url}} templates to remove dead Gna! links.

Tlinnet: /* Sample data to try dx */

Tlinnet: /* Sample data to try dx */

Tlinnet: /* Code to generate map */

Bugman: /* Code to generate map */ Using the {{collapsible script}} template to declutter the article.

Bugman: /* How to use dx */ Formatting using the tag.

Bugman: Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

Bugman: /* Code to generate map */ Split the code line to shorten the width - this will help in the formatting of the 'Did you know...' section of the main page.

Troels Emtekær Linnet: /* Code */

Troels Emtekær Linnet: /* Code to generate map */

Bugman: /* How to use dx */ Formatting using the `tag.`