Author: bugman
Date: Wed Oct 9 16:19:16 2013
New Revision: 21020
URL: http://svn.gna.org/viewcvs/relax?rev=21020&view=rev
Log:
Created a relax script for analysing Remco Sprangers' ClpP data with the 'MQ
NS 2-site' model.
This currently does not work, as the model is absent.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Spranger_ClpP/analysis.py
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Spranger_ClpP/analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Spranger_ClpP/analysis.py?rev=21020&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Spranger_ClpP/analysis.py
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Spranger_ClpP/analysis.py
Wed Oct 9 16:19:16 2013
@@ -1,0 +1,122 @@
+"""Script for optimising the 'MQ NS 2-site' model.
+
+This performs the analysis of:
+
+ Remco Sprangers, Anna Gribun, Peter M. Hwang, Walid A. Houry, and Lewis
E. Kay (2005) Quantitative NMR spectroscopy of supramolecular complexes:
Dynamic side pores in ClpP are important for product release, PNAS, 102 (46),
16678-16683. (doi: http://dx.doi.org/10.1073/pnas.0507370102)
+"""
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from auto_analyses.relax_disp import Relax_disp
+from data_store import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Analysis variables.
+#####################
+
+# The dispersion models.
+MODELS = ['R2eff', 'MQ NS CPMG 2-site']
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 11
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
+MC_NUM = 3
+
+# The results directory.
+RESULTS_DIR = 'temp'
+
+
+# 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')
+
+# The path to the data files.
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Spranger_ClpP'
+
+# Create the sequence.
+spin.create(res_num=135, spin_name='S')
+spin.create(res_num=135, spin_name='F')
+spin.create(res_num=137, spin_name='S')
+spin.create(res_num=137, spin_name='F')
+
+# Set the isotope for field strength scaling.
+spin.isotope(isotope='13C')
+
+# The spectral data - spectrum ID, peak list file name, intensity column,
CPMG frequency (Hz), spectrometer frequency in Hertz.
+ncyc_frq = 800/12.
+data = [
+ ['600_ref', '600.out', 6, None, 600e6],
+ ['600_ncyc12', '600.out', 7, ncyc_frq * 12, 600e6],
+ ['600_ncyc1', '600.out', 8, ncyc_frq * 1, 600e6],
+ ['600_ncyc10', '600.out', 9, ncyc_frq * 10, 600e6],
+ ['600_ncyc2', '600.out', 10, ncyc_frq * 2, 600e6],
+ ['600_ncyc8', '600.out', 11, ncyc_frq * 8, 600e6],
+ ['600_ncyc3', '600.out', 12, ncyc_frq * 3, 600e6],
+ ['600_ncyc6', '600.out', 13, ncyc_frq * 6, 600e6],
+ ['600_ncyc4', '600.out', 14, ncyc_frq * 4, 600e6],
+ ['600_ncyc5', '600.out', 15, ncyc_frq * 5, 600e6],
+ ['600_ncyc1b', '600.out', 16, ncyc_frq * 1, 600e6],
+ ['600_ncyc2b', '600.out', 17, ncyc_frq * 2, 600e6],
+ ['600_ncyc3b', '600.out', 18, ncyc_frq * 3, 600e6],
+ ['800_ref', '800.out', 6, None, 800e6],
+ ['800_ncyc12', '800.out', 7, ncyc_frq * 12, 800e6],
+ ['800_ncyc1', '800.out', 8, ncyc_frq * 1, 800e6],
+ ['800_ncyc10', '800.out', 9, ncyc_frq * 10, 800e6],
+ ['800_ncyc2', '800.out', 10, ncyc_frq * 2, 800e6],
+ ['800_ncyc8', '800.out', 11, ncyc_frq * 8, 800e6],
+ ['800_ncyc3', '800.out', 12, ncyc_frq * 3, 800e6],
+ ['800_ncyc6', '800.out', 13, ncyc_frq * 6, 800e6],
+ ['800_ncyc4', '800.out', 14, ncyc_frq * 4, 800e6],
+ ['800_ncyc5', '800.out', 15, ncyc_frq * 5, 800e6],
+ ['800_ncyc1b', '800.out', 16, ncyc_frq * 1, 800e6],
+ ['800_ncyc2b', '800.out', 17, ncyc_frq * 2, 800e6],
+ ['800_ncyc3b', '800.out', 18, ncyc_frq * 3, 800e6]
+]
+
+# Loop over the spectra.
+for id, file, int_col, cpmg_frq, H_frq in data:
+ # Load the peak intensities.
+ spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height', res_num_col=1, spin_name_col=2, int_col=int_col)
+
+ # Set the relaxation dispersion experiment type.
+ relax_disp.exp_type(spectrum_id=id, exp_type='CPMG')
+
+ # Set the relaxation dispersion CPMG frequencies.
+ relax_disp.cpmg_frq(spectrum_id=id, cpmg_frq=cpmg_frq)
+
+ # Set the NMR field strength of the spectrum.
+ spectrometer.frequency(id=id, frq=H_frq)
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ relax_disp.relax_time(spectrum_id=id, time=0.015)
+
+# Specify the duplicated spectra.
+spectrum.replicated(spectrum_ids=['600_ncyc1', '600_ncyc1b'])
+spectrum.replicated(spectrum_ids=['600_ncyc2', '600_ncyc2b'])
+spectrum.replicated(spectrum_ids=['600_ncyc3', '600_ncyc3b'])
+spectrum.replicated(spectrum_ids=['800_ncyc1', '800_ncyc1b'])
+spectrum.replicated(spectrum_ids=['800_ncyc2', '800_ncyc2b'])
+spectrum.replicated(spectrum_ids=['800_ncyc3', '800_ncyc3b'])
+
+# Peak intensity error analysis.
+#spectrum.error_analysis(subset=['600_ref', '600_ncyc12', '600_ncyc1',
'600_ncyc10', '600_ncyc2', '600_ncyc8', '600_ncyc3', '600_ncyc6',
'600_ncyc4', '600_ncyc5', '600_ncyc1b', '600_ncyc2b', '600_ncyc3b'])
+#spectrum.error_analysis(subset=['800_ref', '800_ncyc12', '800_ncyc1',
'800_ncyc10', '800_ncyc2', '800_ncyc8', '800_ncyc3', '800_ncyc6',
'800_ncyc4', '800_ncyc5', '800_ncyc1b', '800_ncyc2b', '800_ncyc3b'])
+spectrum.error_analysis()
+
+
+# Auto-analysis execution.
+##########################
+
+# Do not change!
+Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM)
+
+
+
r21020 - /branches/relax_disp/test_suite/shared_data/dispersion/Spranger_ClpP/analysis.py