Heteronuclear NMR simulations - Revision history

Kuprov: sync with Spinach main 3975f139: renamed basis field

2026-09-18T10:00:29Z

sync with Spinach main 3975f139: renamed basis field

Kuprov: /* Exercises */

2026-06-18T16:09:30Z

‎Exercises

Kuprov: /* Exercises */

2026-06-18T16:09:13Z

‎Exercises

Kuprov: /* Exercises */

2026-06-18T16:07:54Z

‎Exercises

Kuprov: /* Exercises */

2026-06-18T16:07:33Z

‎Exercises

Kuprov: /* Exercises */

2026-06-18T16:07:06Z

‎Exercises

Kuprov: /* Camphor CLIP-HSQC simulation */

2026-06-18T16:04:31Z

‎Camphor CLIP-HSQC simulation

Kuprov: /* Camphor spin system import */

2026-06-18T16:01:39Z

‎Camphor spin system import

Kuprov: /* Camphor CLIP-HSQC simulation */

2026-06-18T15:54:41Z

‎Camphor CLIP-HSQC simulation

Kuprov: /* Camphor spin system import */

2026-06-18T15:47:20Z

‎Camphor spin system import

@@ Line 27: / Line 27: @@
       [[bas]].approximation='IK-2';
       [[bas]].connectivity='scalar_couplings';
-      [[bas]].space_level=1;
+      [[bas]].prox_level=1;
-The IK-2 approximation builds a restricted state space rather than the complete Liouville space, and <code>scalar_couplings</code> instructs the basis generator to use the scalar-coupling graph for connectivity. The <code>space_level</code> setting controls how far spatially local correlations are allowed into the basis: since HSQC does not rely on spatial proximity, this parameter is set to 1.
+The IK-2 approximation builds a restricted state space rather than the complete Liouville space, and <code>scalar_couplings</code> instructs the basis generator to use the scalar-coupling graph for connectivity. The <code>prox_level</code> setting controls how far spatially local correlations are allowed into the basis: since HSQC does not rely on spatial proximity, this parameter is set to 1.
 ==HSQC sequence parameters==

@@ Line 141: / Line 141: @@
 # Increase and decrease the number of acquired points in <code>parameters.npoints</code> parameter.
 # Turn the decoupling off in one or both dimensions and observe the changes in the simulated spectrum.
-# Decrease the ''J''-coupling drop threshold and observe the effect on the simulation time.
+# Decrease the ''J''-coupling drop threshold in the spin system import command and observe the effect on the simulation time.
 ''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 141: / Line 141: @@
 # Increase and decrease the number of acquired points in <code>parameters.npoints</code> parameter.
 # Turn the decoupling off in one or both dimensions and observe the changes in the simulated spectrum.
 ''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 140: / Line 140: @@
 # Set the working ''J''-coupling to a deliberately incorrect value and observe the effect.
 # Increase and decrease the number of acquired points in <code>parameters.npoints</code> parameter.
-# Turn the decoupling off in one or both dimensions.
+# Turn the decoupling off in one or both dimensions and observe the changes in the simulated spectrum.
 ''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 140: / Line 140: @@
 # Set the working ''J''-coupling to a deliberately incorrect value and observe the effect.
 # Increase and decrease the number of acquired points in <code>parameters.npoints</code> parameter.
 ''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 136: / Line 136: @@
 ==Exercises==
-These are open-ended exploration tasks, see the built-in pulse sequence list for what is available. Suggestions:
+These are open-ended exploration tasks, see the [[Built-in_experiments|built-in pulse sequence list]] for what is available. Suggestions:
 ''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 134: / Line 134: @@
       [[plot_2d.m|plot_2d]]([[Appendix_D:_kernel_data_structures|spin_system]],real(spectrum),[[Appendix_E:_experiment_parameters|parameters]],...
 ,[0.05 0.5 0.05 0.5],2,256,6,'negative');
 ''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 103: / Line 103: @@
 ==Camphor spin system import==
-[[File:camphor.png|thumb|300px|right|Chemical structure of camphor.]] Create a new function file. The difference with the previous example is that here we will import spin system information from a Gaussian log file:
+[[File:camphor.jpg|thumb|200px|right|Chemical structure of camphor.]] Create a new function file. The difference with the previous example is that here we will import spin system information from a Gaussian log file:
       options.min_j=3.0; options.no_xyz=0;

← Older revision		Revision as of 15:54, 18 June 2026
Line 136:		Line 136:


−	''Version 2.12, authors: [[Ilya Kuprov~~]], [[Luke Edwards~~]]''	+	''Version 2.12, authors: [[Ilya Kuprov]]''

@@ Line 103: / Line 103: @@
 ==Camphor spin system import==
-[[File:camphor_clip_hsqc.png|thumb|400px|right|CLIP-HSQC simulation for camphor.]] Create a new function file. The difference with the previous example is that here we will import spin system information from a Gaussian log file:
+[[File:camphor.png|thumb|300px|right|Chemical structure of camphor.]] Create a new function file. The difference with the previous example is that here we will import spin system information from a Gaussian log file:
       options.min_j=3.0; options.no_xyz=0;
@@ Line 109: / Line 109: @@
                        {{'H','1H'},{'C','13C'}},[31.8 182.1],options);
-The [[gparse.m|gparse]] function reads the Gaussian output file. The [[g2spinach.m|g2spinach]] function converts the parsed electronic-structure data into Spinach input structures. The particle list imports hydrogen atoms as <sup>1</sup>H and carbon atoms as <sup>13</sup>C. The reference vector <code>[31.8 182.1]</code> supplies the absolute shielding references used by the conversion to chemical shifts. The <code>options.min_j=3.0</code> setting discards scalar couplings smaller than 3 Hz, and <code>options.no_xyz=0</code> keeps the coordinate information. We then specify the magnetic field:
+[[File:camphor_clip_hsqc.png|thumb|400px|right|CLIP-HSQC simulation for camphor.]] The [[gparse.m|gparse]] function reads the Gaussian output file. The [[g2spinach.m|g2spinach]] function converts the parsed electronic-structure data into Spinach input structures. The particle list imports hydrogen atoms as <sup>1</sup>H and carbon atoms as <sup>13</sup>C. The reference vector <code>[31.8 182.1]</code> supplies the absolute shielding references used by the conversion to chemical shifts. The <code>options.min_j=3.0</code> setting discards scalar couplings smaller than 3 Hz, and <code>options.no_xyz=0</code> keeps the coordinate information. We then specify the magnetic field:
       [[sys]].magnet=14.1;