DPL94 - Revision history

Bugman: /* Parameter name space in relax */ Included a number of code tags.

2015-11-18T15:01:12Z

Parameter name space in relax: Included a number of code tags.

Bugman: /* See also */ Added more categories.

2015-11-06T16:44:34Z

Bugman: /* Equation - re-written forms */ Switched to labelled section transclusions of Citations for the references.

2015-11-04T09:54:40Z

Equation - re-written forms: Switched to labelled section transclusions of Citations for the references.

Bugman: /* Reference */ Switched to a labelled section transclusion for the citations.

2015-11-04T09:36:09Z

Reference: Switched to a labelled section transclusion for the citations.

Bugman: /* The {{:R1rho}}: {{:R2}} or {{:R2eff}} as function of effective field in rotating frame: {{:weff}} */ Fix for the w_eff parameter template use.

2015-11-03T11:49:07Z

The {{:R1rho}}: {{:R2}} or {{:R2eff}} as function of effective field in rotating frame: {{:weff}}: Fix for the w_eff parameter template use.

Bugman: Switched to parameter templates in the section title.

2015-11-03T11:45:06Z

Switched to parameter templates in the section title.

Bugman: Grammar fixes.

2015-11-03T11:35:17Z

Grammar fixes.

Bugman: Section depth fix.

2015-11-03T11:26:40Z

Section depth fix.

Bugman: /* Parameter name space in relax */ Using {{collapsible script}} to de-clutter the article.

2015-10-22T09:41:08Z

Parameter name space in relax: Using {{collapsible script}} to de-clutter the article.

Bugman at 18:44, 21 October 2015

2015-10-21T18:44:00Z

@@ Line 71: / Line 71: @@
 Which means:
-# {{:R1rhoprime}} = spin.r2 (Fitted)
+# {{:R1rhoprime}} = <code>spin.r2</code> (Fitted)
-# {{:R1rho}} = spin.r2eff (Back calculated)
+# {{:R1rho}} = <code>spin.r2eff</code> (Back calculated)
-# {{:Phiex}} = spin.phi_ex (Fitted)
+# {{:Phiex}} = <code>spin.phi_ex</code> (Fitted)
-# {{:kex}} = spin.kex (Fitted)
+# {{:kex}} = <code>spin.kex</code> (Fitted)
-# {{:R1}} = spin.ri_data['R1'] (Loaded)
+# {{:R1}} = <code>spin.ri_data['R1']</code> (Loaded)
 Please also see this thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5164

← Older revision		Revision as of 16:44, 6 November 2015
Line 128:		Line 128:

	== See also ==		== See also ==
		+	[[Category:Models]]
		+	[[Category:Dispersion models]]
	[[Category:Relaxation dispersion analysis]]		[[Category:Relaxation dispersion analysis]]

@@ Line 82: / Line 82: @@
 Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207
-# Evenäs, J., Malmendal, A. & Akke, M. (2001). Dynamics of the transition between open and closed conformations in a calmodulin C-terminal domain mutant. Structure 9, 185–195 http://dx.doi.org/10.1016/S0969-2126(01)00575-5
+* {{#lst:Citations|Evenäs01}}
-# Kempf, J.G. & Loria, J.P. (2004). Measurement of intermediate exchange phenomena. Methods Mol. Biol. 278, 185–231 http://dx.doi.org/10.1385/1-59259-809-9:185
+* {{#lst:Citations|KempfLoria04}}
-# Palmer, A.G. & Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 http://dx.doi.org/10.1021/cr0404287
+* {{#lst:Citations|Massi05}}
-# Palmer, A.G., Kroenke, C.D. & Loria, J.P. (2001). Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Meth. Enzymol. 339 http://dx.doi.org/10.1016/S0076-6879(01)39315-1
+* {{#lst:Citations|Palmer01}}
-# Francesca Massi, Michael J. Grey, Arthur G. Palmer III* (2005). Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1ρ relaxation experiments, Protein science http://dx.doi.org/10.1110/ps.041139505
+* {{#lst:Citations|PalmerMassi06}}
-# Trott, O. and Palmer, 3rd, A. G. (2002). R1rho relaxation outside of the fast-exchange limit. J. Magn. Reson., 154(1), 157–160. (http://dx.doi.org/10.1006/jmre.2001.2466).
+* {{#lst:Citations|TrottPalmer02}}
 Different graphs.

@@ Line 114: / Line 114: @@
 The reference for the DPL94 model is:
-* Davis, D., Perlman, M., and London, R. (1994). Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1rho and T2 (CPMG) methods. ''J. Magn. Reson.'', '''104'''(3), 266–275. ([http://dx.doi.org/10.1006/jmrb.1994.1084 10.1006/jmrb.1994.1084])
+* {{#lst:Citations|Davis94}}
 == Related models ==

@@ Line 91: / Line 91: @@
 Different graphs.
-== The {{:R1rho}}: {{:R2}} or {{:R2eff}} as function of effective field in rotating frame: {{:weff}} ==
+== The {{:R1rho}}: {{:R2}} or {{:R2eff}} as function of effective field in rotating frame: {{:omegaeff}} ==
 === Discussion ===

@@ Line 31: / Line 31: @@
 {{collapsible script
 | type   = relax script
-| title  = At time of writing (March 2014) the parameters in relax was stored as follows.
+| title  = At time of writing (March 2014) the parameters in relax were stored as demonstrated in this script.
 | lang   = python
 | script =
@@ Line 79: / Line 79: @@
 Please also see this thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5164
-== Equation - re-writed forms ==
+== Equation - re-written forms ==
 Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207

@@ Line 10: / Line 10: @@
 The DPL94 model has the parameters {{{:R1rhoprime}}, ..., {{:Phiex}}, {{:kex}}}.
-=== Essentials ===
+== Essentials ==
 {{note|{{:R1}} should be provided in rad/s, the SI default unit for this relaxation rate.}}
@@ Line 79: / Line 79: @@
 Please also see this thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5164
-=== Equation - re-writed forms ===
+== Equation - re-writed forms ==
 Discussed in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5207
@@ Line 91: / Line 91: @@
 Different graphs.
-==== The R1rho: R2 or R2eff as function of effective field in rotating frame: w_eff ====
+== The R1rho: R2 or R2eff as function of effective field in rotating frame: w_eff ==
-'''Discussion:''' <br>
 It is clear that there is no real name for the pseudo-parameter.  It looks like that {{:Reff}} was Art's original way of denoting this and that he has now changed to {{:R2}} instead. <br>
 But if one look at the reference for the [[TP02|TP02 dispersion model]], one will see yet another notation:

@@ Line 28: / Line 28: @@
 == Parameter name space in relax ==
-At time of writing (March 2014) the parameters in relax was stored as:
-<source lang="python">
+{{collapsible script
 # Load the outcome from an analysis
 state.load(state="results.bz2", dir="results/final")
@@ Line 62: / Line 66: @@
      else:
          print(mol_name, res_num, res_name, spin_id, curspin.r2, curspin.phi_ex, curspin.kex)
 [http://www.nmr-relax.com/manual/Dispersion_model_summary.html Please see the summary of the model parameters here.]

← Older revision		Revision as of 18:44, 21 October 2015
Line 123:		Line 123:

	== See also ==		== See also ==
−	[[Category:~~Relaxation_dispersion~~ analysis]]	+	[[Category:Relaxation dispersion analysis]]