Author: bugman
Date: Wed May 14 00:36:39 2014
New Revision: 23163
URL: http://svn.gna.org/viewcvs/relax?rev=23163&view=rev
Log:
Added a new section for the stereochemistry analysis to the N-state model
chapter of the manual.
This is just an initial introduction and an inclusion of the sample script.
Modified:
trunk/docs/latex/n_state.tex
Modified: trunk/docs/latex/n_state.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/n_state.tex?rev=23163&r1=23162&r2=23163&view=diff
==============================================================================
--- trunk/docs/latex/n_state.tex (original)
+++ trunk/docs/latex/n_state.tex Wed May 14 00:36:39 2014
@@ -83,3 +83,171 @@
This is not used in optimisation but rather is used to calculate NOE
constraint violations.
These violations are then compared to evaluate the ensemble.
In the stereochemistry auto-analysis, these violations will also be
converted to Q factors to allow direct comparison with RDC Q factors.
+
+
+
+% Stereochemistry.
+%%%%%%%%%%%%%%%%%%
+
+\section{Determining stereochemistry in dynamic molecules}
+
+A published application of the N-state model in relax is:
+\begin{itemize}
+ \item \bibentry{Sun11}
+\end{itemize}
+
+This analysis of the stereochemistry of a small molecule consists of two
steps.
+The first part is to determine the relative configuration.
+The idea is to use NMR data (consisting of RDCs and NOEs) to find the
relative configuration.
+Ensembles of 10 members are created from molecular dynamics simulations
(MD)\index{molecular dynamics simulation} or simulated annealing
(SA)\index{simulated annealing}.
+These are then ranked by the RDC Q factor and NOE violation.
+By converting the NOE violation into a Q factor:
+\begin{equation}
+ Q_{\textrm{NOE}}^2 = \frac{U}{\sum_i \textrm{NOE}^2},
+\end{equation}
+
+where U is the quadratic flat bottom well potential, i.e.\ the NOE violation
in \AA$^2$, and the denominator is the sum of all squared NOEs.
+A combined Q factor is calculated as:
+\begin{equation}
+ Q_{\textrm{total}}^2 = Q_{\textrm{NOE}}^2 + Q_{\textrm{RDC}}^2.
+\end{equation}
+
+The second step is to distinguish enantiomers.
+As NMR data is symmetric, it cannot distinguish enantiomers.
+Therefore an optical technique such as
\href{http://en.wikipedia.org/wiki/Optical\_rotatory\_dispersion}{optical
rotatory dispersion} can be used.
+For molecules experiencing large amounts of motion, sampling all possible
conformations, calculating the expected dispersion properties, and
calculating an averaged dispersion curve is not feasible.
+The idea is therefore to combine NMR and ORD by taking the best NMR
ensembles from step one to use for ORD spectral prediction.
+
+
+% Auto-analysis.
+%~~~~~~~~~~~~~~~
+
+\subsection{Stereochemistry -- the auto-analysis}
+
+
+Step one of the N-state model is implemented as an auto-analysis.
+This is located in the module
\module{auto\_analysis\pysep{}stereochem\_analysis} (see
\url{http://www.nmr-relax.com/api/3.1/auto_analyses.stereochem_analysis-module.html}).
+The auto-analysis is accessed via the
\module{Stereochem\_\linebreak[0]analysis} class, the details of which can be
seen at
\url{http://www.nmr-relax.com/api/3.1/auto_analyses.stereochem_analysis.Stereochem_analysis-class.html}.
+
+
+% The sample script.
+%~~~~~~~~~~~~~~~~~~~
+
+\subsection{Stereochemistry -- the sample script}
+
+The following script was used for the analysis in \citet{Sun11}.
+It is used to complete the first step of the analysis, the determination of
relative configuration, and for the generation of ensembles for the second
step of the analysis.
+
+
+\begin{lstlisting}
+"""Script for the determination of relative stereochemistry.
+
+The analysis is preformed by using multiple ensembles of structures,
randomly sampled from a given set of structures. The discrimination is
performed by comparing the sets of ensembles using NOE violations and RDC Q
factors.
+
+This script is split into multiple stages:
+
+ 1. The random sampling of the snapshots to generate the N ensembles
(NUM_ENS, usually 10,000 to 100,000) of M members (NUM_MODELS, usually ~10).
The original snapshot files are expected to be named the SNAPSHOT_DIR +
CONFIG + a number from SNAPSHOT_MIN to SNAPSHOT_MAX + ".pdb", e.g.
"snapshots/R647.pdb". The ensembles will be placed into the "ensembles"
directory.
+
+ 2. The NOE violation analysis.
+
+ 3. The superimposition of ensembles. For each ensemble, Molmol is used
for superimposition using the fit to first algorithm. The superimposed
ensembles will be placed into the "ensembles_superimposed" directory. This
stage is not necessary for the NOE analysis.
+
+ 4. The RDC Q factor analysis.
+
+ 5. Generation of Grace graphs.
+
+ 6. Final ordering of ensembles using the combined RDC and NOE Q
factors, whereby the NOE Q factor is defined as::
+
+ Q^2 = U / sum(NOE_i^2),
+
+ where U is the quadratic flat bottom well potential - the NOE violation
in Angstrom^2. The denominator is the sum of all squared NOEs - this must be
given as the value of NOE_NORM. The combined Q is given by::
+
+ Q_total^2 = Q_NOE^2 + Q_RDC^2.
+"""
+
+# relax module imports.
+from auto_analyses.stereochem_analysis import Stereochem_analysis
+
+
+# Stage of analysis (see the docstring above for the options).
+STAGE = 1
+
+# Number of ensembles.
+NUM_ENS = 100000
+
+# Ensemble size.
+NUM_MODELS = 10
+
+# Configurations.
+CONFIGS = ["R", "S"]
+
+# Snapshot directories (corresponding to CONFIGS).
+SNAPSHOT_DIR = ["snapshots", "snapshots"]
+
+# Min and max number of the snapshots (corresponding to CONFIGS).
+SNAPSHOT_MIN = [0, 0]
+SNAPSHOT_MAX = [76, 71]
+
+# Pseudo-atoms.
+PSEUDO = [
+ ["Q7", ["@H16", "@H17", "@H18"]],
+ ["Q9", ["@H20", "@H21", "@H22"]],
+ ["Q10", ["@H23", "@H24", "@H25"]]
+]
+
+# NOE info.
+NOE_FILE = "noes"
+NOE_NORM = 50 * 4**2 # The NOE normalisation factor (sum of all NOEs
squared).
+
+# RDC file info.
+RDC_NAME = "PAN"
+RDC_FILE = "pan_rdcs"
+RDC_SPIN_ID1_COL = 1
+RDC_SPIN_ID2_COL = 2
+RDC_DATA_COL = 2
+RDC_ERROR_COL = None
+
+# Bond length.
+BOND_LENGTH = 1.117 * 1e-10
+
+# Log file output (only for certain stages).
+LOG = True
+
+# Number of buckets for the distribution plots.
+BUCKET_NUM = 200
+
+# Distribution plot limits.
+LOWER_LIM_NOE = 0.0
+UPPER_LIM_NOE = 600.0
+LOWER_LIM_RDC = 0.0
+UPPER_LIM_RDC = 1.0
+
+
+# Set up and code execution.
+analysis = Stereochem_analysis(
+ stage=STAGE,
+ num_ens=NUM_ENS,
+ num_models=NUM_MODELS,
+ configs=CONFIGS,
+ snapshot_dir=SNAPSHOT_DIR,
+ snapshot_min=SNAPSHOT_MIN,
+ snapshot_max=SNAPSHOT_MAX,
+ pseudo=PSEUDO,
+ noe_file=NOE_FILE,
+ noe_norm=NOE_NORM,
+ rdc_name=RDC_NAME,
+ rdc_file=RDC_FILE,
+ rdc_spin_id1_col=RDC_SPIN_ID1_COL,
+ rdc_spin_id2_col=RDC_SPIN_ID2_COL,
+ rdc_data_col=RDC_DATA_COL,
+ rdc_error_col=RDC_ERROR_COL,
+ bond_length=BOND_LENGTH,
+ log=LOG,
+ bucket_num=BUCKET_NUM,
+ lower_lim_noe=LOWER_LIM_NOE,
+ upper_lim_noe=UPPER_LIM_NOE,
+ lower_lim_rdc=LOWER_LIM_RDC,
+ upper_lim_rdc=UPPER_LIM_RDC
+)
+analysis.run()
+\end{lstlisting}
r23163 - /trunk/docs/latex/n_state.tex