Author: bugman
Date: Sat Sep 1 10:18:22 2012
New Revision: 17412
URL: http://svn.gna.org/viewcvs/relax?rev=17412&view=rev
Log:
Significant update of the NOE chapter of the user manual.
The sample script used in this chapter was incredibly out of date!
Modified:
trunk/docs/latex/noe.tex
Modified: trunk/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/noe.tex?rev=17412&r1=17411&r2=17412&view=diff
==============================================================================
--- trunk/docs/latex/noe.tex (original)
+++ trunk/docs/latex/noe.tex Sat Sep 1 10:18:22 2012
@@ -47,20 +47,30 @@
pipe.create(`NOE', `noe') \\
\\
\# Load the sequence from a PDB file. \\
-structure.read\_pdb(name, `Ap4Aase\_new\_3.pdb') \\
+structure.read\_pdb(`Ap4Aase\_new\_3.pdb') \\
structure.load\_spins(spin\_id=`@N') \\
+structure.load\_spins(spin\_id=`@NE1') \\
\\
\# Load the reference spectrum and saturated spectrum peak intensities. \\
-noe.read(file=`ref.list', spectrum\_type=`ref') \\
-noe.read(file=`sat.list', spectrum\_type=`sat') \\
+spectrum.read\_intensities(file=`ref.list', spectrum\_id=`ref\_ave',
heteronuc=`N', proton=`HN') \\
+spectrum.read\_intensities(file=`ref.list', spectrum\_id=`ref\_ave',
heteronuc=`NE1', proton=`HE1') \\
+spectrum.read\_intensities(file=`sat.list', spectrum\_id=`sat\_ave',
heteronuc=`N', proton=`HN') \\
+spectrum.read\_intensities(file=`sat.list', spectrum\_id=`sat\_ave',
heteronuc=`NE1', proton=`HE1') \\
+ \\
+\# Set the spectrum types. \\
+noe.spectrum\_type(`ref', `ref\_ave') \\
+noe.spectrum\_type(`sat', `sat\_ave') \\
\\
\# Set the errors. \\
-noe.error(error=3600, spectrum\_type=`ref') \\
-noe.error(error=3000, spectrum\_type=`sat') \\
+spectrum.baseplane\_rmsd(error=3600, spectrum\_id=`ref\_ave') \\
+spectrum.baseplane\_rmsd(error=3000, spectrum\_id=`sat\_ave') \\
\\
\# Individual residue errors. \\
-noe.error(error=122000, spectrum\_type=`ref', res\_num=114) \\
-noe.error(error=8500, spectrum\_type=`sat', res\_num=114) \\
+spectrum.baseplane\_rmsd(error=122000, spectrum\_type=`ref', res\_num=114) \\
+spectrum.baseplane\_rmsd(error=8500, spectrum\_type=`sat', res\_num=114) \\
+ \\
+\# Peak intensity error analysis. \\
+spectrum.error\_analysis() \\
\\
\# Deselect unresolved residues. \\
deselect.read(file=`unresolved', res\_num\_col=1, spin\_name\_col=2) \\
@@ -109,14 +119,17 @@
The first thing which need to be completed prior to any spin specific
command is to generate the molecule, residue and spin data structures for
storing the spin specific data. In the sample script above this is generated
from a PDB file, however a plain text file with the sequence information can
be used instead (see the \texttt{sequence.read} user function on
page~\pageref{uf: sequence.read} for more details). In the case of the
sample script, the command
-\example{structure.read\_pdb(name, `Ap4Aase\_new\_3.pdb')}
+\example{structure.read\_pdb(`Ap4Aase\_new\_3.pdb')}
\index{PDB}
will load the PDB file `Ap4Aase\_new\_3.pdb' into relax. Then
-\example{structure.load\_spins(spin\_id=`@N')}
-
-will generate the molecule, residue, and spin sequence for the current data
pipe. In this situation there will be a single spin system per residue
generated corresponding to the backbone amide nitrogens. Although the PDB
coordinates have been loaded into the program, the structural information
serves no purpose when calculating NOE values.
+\begin{exampleenv}
+structure.load\_spins(spin\_id=`@N') \\
+structure.load\_spins(spin\_id=`@NE1')
+\end{exampleenv}
+
+will generate the molecule, residue, and spin sequence for the current data
pipe. In this situation there will be a single spin system per residue
generated corresponding to the backbone amide nitrogens as well as $^{15}$N
spins set up for the tryptophan indole NH. Although the 3D coordinates have
been loaded into the program from the PDB, the structural information serves
no purpose when calculating NOE values.
% Loading the data.
@@ -124,14 +137,18 @@
\subsection{Loading the data}
-The two commands
-
-\begin{exampleenv}
-noe.read(file=`ref.list', spectrum\_type=`ref') \\
-noe.read(file=`sat.list', spectrum\_type=`sat')
-\end{exampleenv}
-
-will load the peak heights\index{peak!height} of the reference and saturated
NOE experiments (although the volume\index{peak!volume} could be used
instead). The keyword argument \texttt{format} has not been specified hence
the default format of a Sparky\index{software!Sparky} peak list (saved after
typing \texttt{`lt'}) is assumed. If the program XEasy\index{software!XEasy}
was used to analyse the spectra the argument \texttt{format=`xeasy'} is
necessary. The first column of the file should be the Sparky assignment
string and it is assumed that the 4$^\textrm{th}$ column contains either the
peak height or peak volume. For example:
+The commands
+
+\begin{exampleenv}
+spectrum.read\_intensities(file=`ref.list', spectrum\_id=`ref\_ave',
heteronuc=`N', proton=`HN') \\
+spectrum.read\_intensities(file=`ref.list', spectrum\_id=`ref\_ave',
heteronuc=`NE1', proton=`HE1') \\
+spectrum.read\_intensities(file=`sat.list', spectrum\_id=`sat\_ave',
heteronuc=`N', proton=`HN') \\
+spectrum.read\_intensities(file=`sat.list', spectrum\_id=`sat\_ave',
heteronuc=`NE1', proton=`HE1')
+\end{exampleenv}
+
+will load the peak heights\index{peak!height} of the reference and saturated
NOE experiments (although the volume\index{peak!volume} could be used
instead). relax will automatically determine the format of the peak list.
Currently only Sparky\index{software!Sparky}, XEasy\index{software!XEasy},
NMRView\index{software!NMRView} and a generic columnar formatted text file
are supported.
+
+In this case, relax will determine from the file contents that these are
Sparky\index{software!Sparky} peak lists (saved after typing \texttt{`lt'}).
The first column of the file should be the Sparky assignment string and it is
assumed that the 4$^\textrm{th}$ column contains either the peak height or
peak volume. For example:
{\footnotesize \begin{verbatim}
Assignment w1 w2 Data Height
@@ -146,6 +163,8 @@
GLY12N-HN 110.525 9.028 90144
\end{verbatim}}
+For subsequent usage of the data in relax, assuming a 3D structure exists,
it is currently advisable to use the same residue and atom numbering as found
in the PDB file.
+
If you have any other format you would like read by relax please send an
email to the relax development mailing list\index{mailing list!relax-devel}
detailing the software used, the format of the file (specifically where the
residue number and peak intensity\index{peak!intensity} are located), and
possibly attaching an example of the file itself.
@@ -158,17 +177,20 @@
In this example the errors where measured from the base plain noise. The
Sparky\index{software!Sparky} RMSD\index{RMSD} function was used to estimate
the maximal noise levels across the spectrum in regions containing no peaks.
For the reference spectrum the RMSD was approximately 3600 whereas in the
saturated spectrum the RMSD was 3000. These errors are set by the commands
\begin{exampleenv}
-noe.error(error=3600, spectrum\_type=`ref') \\
-noe.error(error=3000, spectrum\_type=`sat')
+spectrum.baseplane\_rmsd(error=3600, spectrum\_id=`ref\_ave') \\
+spectrum.baseplane\_rmsd(error=3000, spectrum\_id=`sat\_ave')
\end{exampleenv}
For the residue G114, the noise levels are significantly increased compared
to the rest of the protein as the peak is located close to the water signal.
The higher errors for this residue are specified by the commands
\begin{exampleenv}
-noe.error(error=122000, spectrum\_type=`ref', res\_num=114) \\
-noe.error(error=8500, spectrum\_type=`sat', res\_num=114)
-\end{exampleenv}
-
+spectrum.baseplane\_rmsd(error=122000, spectrum\_type=`ref', res\_num=114) \\
+spectrum.baseplane\_rmsd(error=8500, spectrum\_type=`sat', res\_num=114)
+\end{exampleenv}
+
+There are many other ways of setting the errors, for example via spectral
duplication, triplication, etc. See the documentation for the
\texttt{spectrum.error\_analysis} user function on page~\pageref{uf:
spectrum.error_analysis} for all possible options. This user function needs
to be executed at this stage to correctly set up the errors for all spin
systems:
+
+\example{spectrum.error\_analysis()}
% Unresolved spins.
@@ -209,22 +231,22 @@
will create a file called \texttt{noe.out} with the NOE values and errors.
The force flag will cause any file with the same name to be overwritten. An
example of the format of \texttt{noe.out} is
-{\footnotesize \begin{verbatim}
-Num Name Value Error
-1 GLY None None
-2 PRO None None
-3 LEU None None
-4 GLY 0.12479588727508535 0.020551827436105764
-5 SER 0.42240815792914105 0.02016346825976852
-6 MET 0.45281703194372114 0.026272719841642134
-7 ASP 0.60727570079478255 0.032369427242382849
-8 SER 0.63871921623680161 0.024695665815261791
-9 PRO None None
-10 PRO None None
-11 GLU None None
-12 GLY 0.92927160307645906 0.059569089743604184
-13 TYR 0.88832516377296256 0.044119641308479306
-14 ARG 0.84945042565860407 0.060533543601110441
+{\scriptsize \begin{verbatim}
+# mol_name res_num res_name spin_num spin_name value
error
+Ap4Aase_new_3_mol1 1 GLY 1 N None
None
+Ap4Aase_new_3_mol1 2 PRO 11 N None
None
+Ap4Aase_new_3_mol1 3 LEU 28 N None
None
+Ap4Aase_new_3_mol1 4 GLY 51 N
-0.038921946984531344 0.019031770246176943
+Ap4Aase_new_3_mol1 5 SER 59 N
-0.312404225679127 0.018596937298386886
+Ap4Aase_new_3_mol1 6 MET 71 N
-0.42850831873249773 0.02525856323041225
+Ap4Aase_new_3_mol1 7 ASP 91 N
-0.5305492810313481 0.027990623144176396
+Ap4Aase_new_3_mol1 8 SER 104 N
-0.5652842977581912 0.021706121467731133
+Ap4Aase_new_3_mol1 9 PRO 116 N None
None
+Ap4Aase_new_3_mol1 10 PRO 133 N None
None
+Ap4Aase_new_3_mol1 11 GLU 150 N None
None
+Ap4Aase_new_3_mol1 12 GLY 167 N
-0.7036626368123614 0.04681370194503697
+Ap4Aase_new_3_mol1 13 TYR 175 N
-0.747464566367261 0.03594640051809186
+Ap4Aase_new_3_mol1 14 ARG 200 N
-0.7524129557634996 0.04957018638401278
\end{verbatim}}
r17412 - /trunk/docs/latex/noe.tex