Author: semor
Date: Wed Nov 18 15:20:42 2009
New Revision: 9871
URL: http://svn.gna.org/viewcvs/relax?rev=9871&view=rev
Log:
Added references to the consistency tests code.
In particular, the reference for this newly published paper was added:
Morin & Gagne (2009) JBNMR, 45: 361-372.
Modified:
1.3/maths_fns/consistency_tests.py
1.3/specific_fns/consistency_tests.py
Modified: 1.3/maths_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/consistency_tests.py?rev=9871&r1=9870&r2=9871&view=diff
==============================================================================
--- 1.3/maths_fns/consistency_tests.py (original)
+++ 1.3/maths_fns/consistency_tests.py Wed Nov 18 15:20:42 2009
@@ -1,7 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2004 Edward d'Auvergne
#
-# Copyright (C) 2007-2008 Sebastien Morin
#
+# Copyright (C) 2007-2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
#
#
@@ -35,18 +35,23 @@
These three tests are used to assess the consistency of datasets
aquired at different
magnetic fields. Inconsistency can affect extracted information from
experimental data and
- can be caused by variations in temperature, concentration, pH, water
suppression, etc.
+ can be caused by variations in temperature, concentration, pH, water
suppression, etc. The
+ approach is described in Morin & Gagne (2009) JBNMR, 45: 361-372.
This code calculates three functions for each residue. When
comparing datasets from
- different magnetic field, the value should be the same for each
function as these are field
+ different magnetic fields, the value should be the same for each
function as these are field
independent. The J(0) function is the spectral density at the zero
frequency and is obtained
- using a reduced spectral density approach. The F_eta and F_R2
functions are the
- consistency functions proposed by Fushman D. et al. (1998) JACS,
120: 10947-10952.
+ using a reduced spectral density approach (Farrow et al. (1995)
JBNMR, 6: 153-162). The
+ F_eta and F_R2 functions are the consistency functions proposed by
Fushman et al. (1998)
+ JACS, 120: 10947-10952.
- To assess the consistency of its datasets, one should first
calculate those values (J(0),
- F_eta and F_R2) for each field. Then, the user should compare values
obtained for different
- magnetic fields. Comparisons could proceed using correlation plots
and histograms, and the
+ To assess the consistency of its datasets, one should first
calculate one of those values
+ (J(0), F_eta and F_R2, preferentially J(0) as discussed in Morin &
Gagne (2009) JBNMR, 45:
+ 361-372) for each field. Then, the user should compare values
obtained for different
+ magnetic fields. Comparisons should proceed using correlation plots
and histograms, and the
user could also calculate correlation, skewness and kurtosis
coefficients.
+
+ For examples, see Morin & Gagne (2009) JBNMR, 45: 361-372.
"""
# Initialise the data container.
@@ -123,7 +128,7 @@
# Calculate eta.
# eta is the cross-correlation rate between 15N CSA and 15N-1H
dipolar interaction. It is
- # expressed here as proposed in Fushman D. & Cowburn D. (1998) JACS,
120: 7109-7110.
+ # expressed here as proposed in Fushman & Cowburn (1998) JACS, 120:
7109-7110.
eta = ((d * c/3.0) ** 0.5) * (4.0 * j0 + 3.0 * jwx) * p_2
# Calculate F_eta.
Modified: 1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=9871&r1=9870&r2=9871&view=diff
==============================================================================
--- 1.3/specific_fns/consistency_tests.py (original)
+++ 1.3/specific_fns/consistency_tests.py Wed Nov 18 15:20:42 2009
@@ -1,7 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2004-2009 Edward d'Auvergne
#
-# Copyright (C) 2007-2008 Sebastien Morin
#
+# Copyright (C) 2007-2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
#
#
@@ -204,9 +204,9 @@
- 'orientation', angle between the 15N-1H vector and the
principal axis of the 15N
chemical shift tensor.
- 'tc', correlation time.
- - 'j0', spectral density value at 0 MHz.
- - 'f_eta', eta-test (from Fushman D. et al. (1998) JACS, 120:
10947-10952).
- - 'f_r2', R2-test (from Fushman D. et al. (1998) JACS, 120:
10947-10952).
+ - 'j0', spectral density value at 0 MHz (from Farrow et al.
(1995) JBNMR, 6: 153-162).
+ - 'f_eta', eta-test (from Fushman et al. (1998) JACS, 120:
10947-10952).
+ - 'f_r2', R2-test (from Fushman et al. (1998) JACS, 120:
10947-10952).
@keyword set: An unused variable.
r9871 - in /1.3: maths_fns/consistency_tests.py specific_fns/consistency_tests.py