Author: bugman
Date: Fri Jun 14 21:51:33 2013
New Revision: 20138
URL: http://svn.gna.org/viewcvs/relax?rev=20138&view=rev
Log:
Added the CPMG dispersion analysis sample script to the relax manual.
Modified:
branches/relax_disp/docs/latex/relax_disp.tex
Modified: branches/relax_disp/docs/latex/relax_disp.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax_disp.tex?rev=20138&r1=20137&r2=20138&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax_disp.tex (original)
+++ branches/relax_disp/docs/latex/relax_disp.tex Fri Jun 14 21:51:33 2013
@@ -256,6 +256,136 @@
\subsection{Dispersion script mode -- the sample script}
+The following is a verbatim copy of the contents of the
\file{sample\_scripts/relax\_disp/\linebreak[0]{}cpmg\_analysis.py} file.
+You will need to first copy this script to a dedicated analysis directory
containing peak lists, a sequence or PDB file and a file listing unresolved
spin systems, and then modify its contents to suit your specific analysis.
+The script contents are:
+
+\begin{exampleenv}
+"""Script for performing a full relaxation dispersion analysis using
CPMG-type data.""" \\
+ \\
+ \\
+\# Python module imports. \\
+from os import sep \\
+ \\
+\# relax module imports. \\
+from auto\_analyses.relax\_disp import Relax\_disp \\
+ \\
+ \\
+\# Analysis variables. \\
+\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# \\
+ \\
+\# The dispersion models. \\
+MODELS = [`R2eff', `No Rex', `LM63', `CR72', `IT99'] \\
+ \\
+\# The grid search size (the number of increments per dimension). \\
+GRID\_INC = 21 \\
+ \\
+\# The number of Monte Carlo simulations to be used for error analysis at
the end of the analysis. \\
+MC\_NUM = 500 \\
+ \\
+\# The model selection technique to use. \\
+MODSEL = `AIC' \\
+ \\
+ \\
+\# Set up the data pipe. \\
+\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# \\
+ \\
+\# Create the data pipe. \\
+pipe\_name = `base pipe' \\
+pipe\_bundle = `relax\_disp' \\
+pipe.create(pipe\_name=pipe\_name, bundle=pipe\_bundle,
pipe\_type=`relax\_disp') \\
+ \\
+\# Load the sequence. \\
+sequence.read(`fake\_sequence.in', res\_num\_col=1, res\_name\_col=2) \\
+ \\
+\# Name the spins so they can be matched to the assignments, and the isotope
for field strength scaling. \\
+spin.name(name=`N') \\
+spin.isotope(isotope=`15N') \\
+ \\
+\# Set the relaxation dispersion experiment type. \\
+relax\_disp.exp\_type(`cpmg fixed') \\
+ \\
+\# The spectral data - spectrum ID, peak list file name, CPMG frequency
(Hz), spectrometer frequency in Hertz. \\
+data = [ \\
+\hspace*{4ex} [`500\_reference.in',
`500\_MHz'+sep+`reference.in\_sparky', None, 500e6], \\
+\hspace*{4ex} [`500\_66.667.in', `500\_MHz'+sep+`66.667.in\_sparky',
66.6666, 500e6], \\
+\hspace*{4ex} [`500\_133.33.in', `500\_MHz'+sep+`133.33.in\_sparky',
133.3333, 500e6], \\
+\hspace*{4ex} [`500\_133.33.in.bis',
`500\_MHz'+sep+`133.33.in.bis\_sparky', 133.3333, 500e6], \\
+\hspace*{4ex} [`500\_200.in', `500\_MHz'+sep+`200.in\_sparky',
200.0000, 500e6], \\
+\hspace*{4ex} [`500\_266.67.in', `500\_MHz'+sep+`266.67.in\_sparky',
266.6666, 500e6], \\
+\hspace*{4ex} [`500\_333.33.in', `500\_MHz'+sep+`333.33.in\_sparky',
333.3333, 500e6], \\
+\hspace*{4ex} [`500\_400.in', `500\_MHz'+sep+`400.in\_sparky',
400.0000, 500e6], \\
+\hspace*{4ex} [`500\_466.67.in', `500\_MHz'+sep+`466.67.in\_sparky',
466.6666, 500e6], \\
+\hspace*{4ex} [`500\_533.33.in', `500\_MHz'+sep+`533.33.in\_sparky',
533.3333, 500e6], \\
+\hspace*{4ex} [`500\_533.33.in.bis',
`500\_MHz'+sep+`533.33.in.bis\_sparky', 533.3333, 500e6], \\
+\hspace*{4ex} [`500\_600.in', `500\_MHz'+sep+`600.in\_sparky',
600.0000, 500e6], \\
+\hspace*{4ex} [`500\_666.67.in', `500\_MHz'+sep+`666.67.in\_sparky',
666.6666, 500e6], \\
+\hspace*{4ex} [`500\_733.33.in', `500\_MHz'+sep+`733.33.in\_sparky',
733.3333, 500e6], \\
+\hspace*{4ex} [`500\_800.in', `500\_MHz'+sep+`800.in\_sparky',
800.0000, 500e6], \\
+\hspace*{4ex} [`500\_866.67.in', `500\_MHz'+sep+`866.67.in\_sparky',
866.6666, 500e6], \\
+\hspace*{4ex} [`500\_933.33.in', `500\_MHz'+sep+`933.33.in\_sparky',
933.3333, 500e6], \\
+\hspace*{4ex} [`500\_933.33.in.bis',
`500\_MHz'+sep+`933.33.in.bis\_sparky', 933.3333, 500e6], \\
+\hspace*{4ex} [`500\_1000.in', `500\_MHz'+sep+`1000.in\_sparky',
1000.0000, 500e6], \\
+\hspace*{4ex} [`800\_reference.in',
`800\_MHz'+sep+`reference.in\_sparky', None, 800e6], \\
+\hspace*{4ex} [`800\_66.667.in', `800\_MHz'+sep+`66.667.in\_sparky',
66.6666, 800e6], \\
+\hspace*{4ex} [`800\_133.33.in', `800\_MHz'+sep+`133.33.in\_sparky',
133.3333, 800e6], \\
+\hspace*{4ex} [`800\_133.33.in.bis',
`800\_MHz'+sep+`133.33.in.bis\_sparky', 133.3333, 800e6], \\
+\hspace*{4ex} [`800\_200.in', `800\_MHz'+sep+`200.in\_sparky',
200.0000, 800e6], \\
+\hspace*{4ex} [`800\_266.67.in', `800\_MHz'+sep+`266.67.in\_sparky',
266.6666, 800e6], \\
+\hspace*{4ex} [`800\_333.33.in', `800\_MHz'+sep+`333.33.in\_sparky',
333.3333, 800e6], \\
+\hspace*{4ex} [`800\_400.in', `800\_MHz'+sep+`400.in\_sparky',
400.0000, 800e6], \\
+\hspace*{4ex} [`800\_466.67.in', `800\_MHz'+sep+`466.67.in\_sparky',
466.6666, 800e6], \\
+\hspace*{4ex} [`800\_533.33.in', `800\_MHz'+sep+`533.33.in\_sparky',
533.3333, 800e6], \\
+\hspace*{4ex} [`800\_533.33.in.bis',
`800\_MHz'+sep+`533.33.in.bis\_sparky', 533.3333, 800e6], \\
+\hspace*{4ex} [`800\_600.in', `800\_MHz'+sep+`600.in\_sparky',
600.0000, 800e6], \\
+\hspace*{4ex} [`800\_666.67.in', `800\_MHz'+sep+`666.67.in\_sparky',
666.6666, 800e6], \\
+\hspace*{4ex} [`800\_733.33.in', `800\_MHz'+sep+`733.33.in\_sparky',
733.3333, 800e6], \\
+\hspace*{4ex} [`800\_800.in', `800\_MHz'+sep+`800.in\_sparky',
800.0000, 800e6], \\
+\hspace*{4ex} [`800\_866.67.in', `800\_MHz'+sep+`866.67.in\_sparky',
866.6666, 800e6], \\
+\hspace*{4ex} [`800\_933.33.in', `800\_MHz'+sep+`933.33.in\_sparky',
933.3333, 800e6], \\
+\hspace*{4ex} [`800\_933.33.in.bis',
`800\_MHz'+sep+`933.33.in.bis\_sparky', 933.3333, 800e6], \\
+\hspace*{4ex} [`800\_1000.in', `800\_MHz'+sep+`1000.in\_sparky',
1000.0000, 800e6] \\
+] \\
+ \\
+\# Loop over the spectra. \\
+for id, file, cpmg\_frq, H\_frq in data: \\
+\hspace*{4ex} \# Load the peak intensities. \\
+\hspace*{4ex} spectrum.read\_intensities(file=file, spectrum\_id=id,
int\_method=`height') \\
+ \\
+\hspace*{4ex} \# Set the relaxation dispersion CPMG frequencies. \\
+\hspace*{4ex} relax\_disp.cpmg\_frq(spectrum\_id=id, cpmg\_frq=cpmg\_frq) \\
+ \\
+\hspace*{4ex} \# Set the NMR field strength of the spectrum. \\
+\hspace*{4ex} spectrometer.frequency(id=id, frq=H\_frq) \\
+ \\
+\hspace*{4ex} \# Relaxation dispersion CPMG constant time delay T (in s). \\
+\hspace*{4ex} relax\_disp.relax\_time(spectrum\_id=id, time=0.030) \\
+ \\
+\# Specify the duplicated spectra. \\
+spectrum.replicated(spectrum\_ids=[`500\_133.33.in', `500\_133.33.in.bis'])
\\
+spectrum.replicated(spectrum\_ids=[`500\_533.33.in', `500\_533.33.in.bis'])
\\
+spectrum.replicated(spectrum\_ids=[`500\_933.33.in', `500\_933.33.in.bis'])
\\
+spectrum.replicated(spectrum\_ids=[`800\_133.33.in', `800\_133.33.in.bis'])
\\
+spectrum.replicated(spectrum\_ids=[`800\_533.33.in', `800\_533.33.in.bis'])
\\
+spectrum.replicated(spectrum\_ids=[`800\_933.33.in', `800\_933.33.in.bis'])
\\
+ \\
+\# Peak intensity error analysis. \\
+spectrum.error\_analysis(subset=[`500\_reference.in', `500\_66.667.in',
`500\_133.33.in', `500\_133.33\linebreak[0]{}.in.bis', `500\_200.in',
`500\_266.67.in', `500\_333.33.in', `500\_400.in', `500\_466.67.in',
`500\_533\linebreak[0]{}.33.in', `500\_533.33.in.bis', `500\_600.in',
`500\_666.67.in', `500\_733.33.in', `500\_800.in',
`500\linebreak[0]{}\_866.67.in', `500\_933.33.in', `500\_933.33.in.bis',
`500\_1000.in']) \\
+spectrum.error\_analysis(subset=[`800\_reference.in', `800\_66.667.in',
`800\_133.33.in', `800\_133.33\linebreak[0]{}.in.bis', `800\_200.in',
`800\_266.67.in', `800\_333.33.in', `800\_400.in', `800\_466.67.in',
`800\_533\linebreak[0]{}.33.in', `800\_533.33.in.bis', `800\_600.in',
`800\_666.67.in', `800\_733.33.in', `800\_800.in',
`800\linebreak[0]{}\_866.67.in', `800\_933.33.in', `800\_933.33.in.bis',
`800\_1000.in']) \\
+ \\
+\# Deselect unresolved spins. \\
+deselect.read(file=`unresolved', dir=`500\_MHz', res\_num\_col=1) \\
+deselect.read(file=`unresolved', dir=`800\_MHz', res\_num\_col=1) \\
+ \\
+ \\
+ \\
+\# Auto-analysis execution. \\
+\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# \\
+ \\
+\# Do not change! \\
+Relax\_disp(pipe\_name=pipe\_name, pipe\_bundle=pipe\_bundle, models=MODELS,
grid\_inc=GRID\_INC, mc\_sim\linebreak[0]{}\_num=MC\_NUM, modsel=MODSEL) \\
+\end{exampleenv}
+
% Tutorial - adding models.
r20138 - /branches/relax_disp/docs/latex/relax_disp.tex