Author: bugman
Date: Tue Sep 4 16:52:00 2012
New Revision: 17446
URL: http://svn.gna.org/viewcvs/relax?rev=17446&view=rev
Log:
Editing of the relax data model chapter of the user manual.
Modified:
trunk/docs/latex/data_model.tex
Modified: trunk/docs/latex/data_model.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/data_model.tex?rev=17446&r1=17445&r2=17446&view=diff
==============================================================================
--- trunk/docs/latex/data_model.tex (original)
+++ trunk/docs/latex/data_model.tex Tue Sep 4 16:52:00 2012
@@ -190,7 +190,7 @@
structure.load\_spins(`@NE1', ave\_pos=True) \\
structure.load\_spins(`@HE1', ave\_pos=True) \\
\\
-\# Define the spin isotopes.
+\# Define the spin isotopes. \\
spin.isotope(`15N', spin\_id=`@N*') \\
spin.isotope(`1H', spin\_id=`@H*')
\end{exampleenv}
@@ -217,15 +217,29 @@
pipe.create(pipe\_name=`R1 1200', pipe\_type=`relax\_fit') \\
\\
\# Set up the 15N spins. \\
-sequence.read(file=`noe.500.out', mol\_name\_col=None, res\_num\_col=1,
res\_name\_col=2, spin\_num\_col=None, spin\_name\_col=None) \\
-spin.name(`N') \\
-spin.element(element=`N', spin\_id=`@N') \\
+sequence.read(file=`noe.500.out', mol\_name\_col=1, res\_num\_col=2,
res\_name\_col=3, spin\_num\_col=4, spin\_name\_col=5) \\
+spin.element(element=`N', spin\_id=`@N*') \\
spin.isotope(`15N', spin\_id=`@N')
\end{exampleenv}
-Here the molecule, residue, and spin information is extracted from the
\promptstring{noe.500.out} file. The \uf{sequence.read} user function call
assumes that only residue information is present in the file, with the
residue number and name in the first and second columns respectively. The
file can contain columns for the molecule name, the residue name and number,
and the spin name and number in any order. The subsequent user functions in
the above example are used to set up the spin containers appropriately for a
model-free analysis. These are not required in the automatic analysis of GUI
as these user functions will be presented to you when adding relaxation data,
or when clicking on the heteronucleus and proton buttons (\guibutton{X
isotope} and \guibutton{H isotope}).
-
-If 3D structures are to be used later on in the analysis, then the residue
and spin names and numbers must either be blank or match the notation used in
the 3D structure file.
+Here the molecule, residue, and spin information is extracted from the
\promptstring{noe.500.out} file which could look like:
+
+{\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 0.03892194698453
0.01903177024613
+Ap4Aase_new_3_mol1 5 SER 59 N 0.31240422567912
0.01859693729836
+Ap4Aase_new_3_mol1 6 MET 71 N 0.42850831873249
0.0252585632304
+Ap4Aase_new_3_mol1 7 ASP 91 N 0.53054928103134
0.02799062314416
+Ap4Aase_new_3_mol1 8 SER 104 N 0.56528429775819
0.02170612146773
+Ap4Aase_new_3_mol1 9 PRO 116 N None
None
+Ap4Aase_new_3_mol1 40 TRP 685 N 0.65394813490548
0.03830061886537
+Ap4Aase_new_3_mol1 40 TRP 698 NE1 0.67073879732046
0.01426066343831
+\end{verbatim}} \label{verb: noe.500.out}
+
+The file can contain columns for the molecule name, the residue name and
number, and the spin name and number in any order though not all are needed.
For example for a single protein system, the molecule name, residue name and
spin number are nonessential. Or for an organic molecule, the molecule name,
residue name and number and spin number could be nonessential. The
subsequent user functions in the above example are used to set up the spin
containers appropriately for a model-free analysis. These are not required
in the automatic analysis of GUI as these user functions will be presented to
you when adding relaxation data, or when clicking on the heteronucleus and
proton buttons (\guibutton{X isotope} and \guibutton{H isotope}).
In the GUI, the creation of molecule, residue, and spin containers from a
sequence file is also available via the \gui{Load spins} wizard within the
spin viewer window (\textit{vide supra}).
@@ -235,7 +249,7 @@
\subsection{Manual construction} \label{sect: script - manual construction}
-For the masochist, the full molecule, residue and spin data structure can be
manually constructed. For example:
+For the masochists out there, the full molecule, residue and spin data
structure can be manually constructed. For example:
\begin{exampleenv}
\# Manually create the molecule, residue, and spin containers. \\
@@ -341,7 +355,7 @@
\centerline{\includegraphics[width=0.8\textwidth, bb=14 14 1415
1019]{graphics/screenshots/spin_viewer/wizard_sequence.eps.gz}}
\end{minipage}
-Change the \gui{Free format file settings} as needed. Click on
\guibutton{Next} to reach the wizard ending page (see~\pageref{figure: spin
viewer end}). Finally click on \guibutton{Finish} to exit the wizard.
+Select the file to load and change the \gui{Free format file settings} as
needed. An example of a suitable format is given on page~\pageref{verb:
noe.500.out}. Click on \guibutton{Next} to reach the wizard ending page
(see~\pageref{figure: spin viewer end}). Finally click on \guibutton{Finish}
to exit the wizard.
% Manual construction.
r17446 - /trunk/docs/latex/data_model.tex