Author: bugman
Date: Thu Nov 19 10:38:01 2009
New Revision: 9877
URL: http://svn.gna.org/viewcvs/relax?rev=9877&view=rev
Log:
Merged revisions 9871-9875 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9871 | semor | 2009-11-18 15:20:42 +0100 (Wed, 18 Nov 2009) | 6 lines
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.
........
r9872 | semor | 2009-11-18 16:58:50 +0100 (Wed, 18 Nov 2009) | 7 lines
Added references and instructions in the sample script for consistency
testing.
This is as proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2009-11/msg00034.html
(Message-id: <7f080ed10911180653w6b59b40dn1e8f715d9b718fd5@xxxxxxxxxxxxxx>)
........
r9873 | semor | 2009-11-18 17:58:39 +0100 (Wed, 18 Nov 2009) | 5 lines
Added DOI links to the citations and corrected a fused f and i character.
This was proposed by Edward.
........
r9874 | semor | 2009-11-18 18:29:02 +0100 (Wed, 18 Nov 2009) | 3 lines
Corrected other strange characters causing failures...
........
r9875 | bugman | 2009-11-19 10:37:23 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted the 'Branches' subsection of the development chapter into a
proper section.
........
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/docs/latex/develop.tex
branches/bieri_gui/maths_fns/consistency_tests.py
branches/bieri_gui/sample_scripts/consistency_tests.py
branches/bieri_gui/specific_fns/consistency_tests.py
Propchange: branches/bieri_gui/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Nov 19 10:38:01 2009
@@ -1,1 +1,1 @@
-/1.3:1-9869
+/1.3:1-9876
Modified: branches/bieri_gui/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/docs/latex/develop.tex?rev=9877&r1=9876&r2=9877&view=diff
==============================================================================
--- branches/bieri_gui/docs/latex/develop.tex (original)
+++ branches/bieri_gui/docs/latex/develop.tex Thu Nov 19 10:38:01 2009
@@ -404,12 +404,12 @@
% Branches.
-\subsection{Branches}
+\section{Branches}
\index{branches|textbf}
\index{repository!branches|textbf}
-\subsubsection{Branch creation}
+\subsection{Branch creation}
\index{repository!branch creation}
If a change is likely to be disruptive or cause breakages in the program,
the use of your own temporary branch is recommended. This private branch is
a complete copy of one of the main development lines wherein you can make
changes without disrupting the other developers. Although called a private
branch every change is visible to all other developers and each commit will
result in an automatic email to the relax-commits mailing list\index{mailing
list!relax-commits}. Other developers are even able to check out your branch
and make modifications to it. Private branches can also be used for testing
ideas. If the idea does not work the branch can be deleted from the
repository (in reality the branch will always exist between the revision
numbers of its creation and deletion and can always be resurrected). For
example to create a branch from the main 1.3 development line called
\texttt{molmol\_macros} whereby new Molmol macros are to be written, type
@@ -426,7 +426,7 @@
which will create a directory called \texttt{molmol\_macros} containing all
the relax source files. To have the files placed into a different directory,
type the name of that directory at the end of the last command.
Modifications can be made to this copy while normal development continues on
the main line.
-\subsubsection{Keeping the branch up to date using \texttt{svnmerge.py}}
+\subsection{Keeping the branch up to date using \texttt{svnmerge.py}}
\index{svnmerge.py}
\index{repository!keeping up to date}
\index{repository!svnmerge.py}
@@ -453,7 +453,7 @@
\index{Subversion!commit}
-\subsubsection{Merging the branch back into the main line}
+\subsection{Merging the branch back into the main line}
\index{repository!merging branch back}
Once you have completed the modifications desired for your branch, all
changes which have occurred in the main line have been merged using
\texttt{svnmerge.py}, and the changes have been approved for merging back
into the main line -- then your branch can be merged. First check out a copy
of the main line,
Modified: branches/bieri_gui/maths_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/consistency_tests.py?rev=9877&r1=9876&r2=9877&view=diff
==============================================================================
--- branches/bieri_gui/maths_fns/consistency_tests.py (original)
+++ branches/bieri_gui/maths_fns/consistency_tests.py Thu Nov 19 10:38:01 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: branches/bieri_gui/sample_scripts/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/sample_scripts/consistency_tests.py?rev=9877&r1=9876&r2=9877&view=diff
==============================================================================
--- branches/bieri_gui/sample_scripts/consistency_tests.py (original)
+++ branches/bieri_gui/sample_scripts/consistency_tests.py Thu Nov 19
10:38:01 2009
@@ -20,8 +20,35 @@
#
#
###############################################################################
-# Script for consistency testing.
-#######################################################################
+""" Script for consistency testing.
+
+Severe artifacts can be introduced if model-free analysis is performed from
inconsistent multiple magnetic field datasets. The use of simple tests as
validation tools for the consistency assessment can help avoid such problems
in order to extract more reliable information from spin relaxation
experiments. In particular, these tests are useful for detecting
inconsistencies arising from R2 data. Since such inconsistencies can yield
artifactual Rex parameters within model-free analysis, these tests should be
use routinely prior to any analysis such as model-free calculations.
+
+This script will allow one to calculate values for the three consistency
tests J(0), F_eta and F_R2. Once this is done, qualitative analysis can be
performed by comparing values obtained at different magnetic fields.
Correlation plots and histograms are useful tools for such comparison, such
as presented in Morin & Gagne (2009a) J. Biomol. NMR, 45: 361-372.
+
+
+References
+==========
+
+The description of the consistency testing approach:
+
+ Morin & Gagne (2009a) Simple tests for the validation of multiple field
spin relaxation data. J. Biomol. NMR, 45: 361-372.
http://dx.doi.org/10.1007/s10858-009-9381-4
+
+The origins of the equations used in the approach:
+
+ J(0):
+ Farrow et al. (1995) Spectral density function mapping using 15N
relaxation data exclusively. J. Biomol. NMR, 6: 153-162.
http://dx.doi.org/10.1007/BF00211779
+
+ F_eta:
+ Fushman et al. (1998) Direct measurement of 15N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
http://dx.doi.org/10.1021/ja981686m
+
+ F_R2:
+ Fushman et al. (1998) Direct measurement of 15N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
http://dx.doi.org/10.1021/ja981686m
+
+A study where consistency tests were used:
+
+ Morin & Gagne (2009) NMR dynamics of PSE-4 beta-lactamase: An interplay
of ps-ns order and us-ms motions in the active site. Biophys. J., 96:
4681-4691. http://dx.doi.org/10.1016/j.bpj.2009.02.068
+"""
# Create the run.
name = 'consistency'
Modified: branches/bieri_gui/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/consistency_tests.py?rev=9877&r1=9876&r2=9877&view=diff
==============================================================================
--- branches/bieri_gui/specific_fns/consistency_tests.py (original)
+++ branches/bieri_gui/specific_fns/consistency_tests.py Thu Nov 19 10:38:01
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.
r9877 - in /branches/bieri_gui: ./ docs/latex/ maths_fns/ sample_scripts/ specific_fns/