Author: bugman
Date: Thu May 23 19:22:07 2013
New Revision: 19716
URL: http://svn.gna.org/viewcvs/relax?rev=19716&view=rev
Log:
Created a directory for the results of the CPMGFit program using Hansen's
truncated CPMG data.
The script 'cpmgfit.py' has been added to create the input files for CPMGFit
and execute the
program. The input and batch files have been added to the repository as well.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/cpmgfit.py
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh
(with props)
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:70@xxxx
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:71@xxxx
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/cpmgfit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/cpmgfit.py?rev=19716&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/cpmgfit.py
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/cpmgfit.py
Thu May 23 19:22:07 2013
@@ -1,0 +1,118 @@
+"""Script for calculating R2eff values, generating input files for CPMGFit,
and executing CPMGFit.
+
+To run:
+
+$ ../../../../../relax cpmgfit.py
+"""
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from status import Status; status = Status()
+
+
+# Create the data pipe.
+pipe.create(pipe_name='R2eff', pipe_type='relax_disp')
+
+# The path to the data files.
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
+
+# Load the sequence.
+sequence.read('fake_sequence.in', dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen',
res_num_col=1, res_name_col=2)
+
+# Name the spins so they can be matched to the assignments.
+spin.name(name='N')
+
+# 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 = [
+ ['500_reference.in', '500_MHz'+sep+'reference.in_sparky',
None, 500e6],
+ ['500_66.667.in', '500_MHz'+sep+'66.667.in_sparky',
66.6666, 500e6],
+ ['500_133.33.in', '500_MHz'+sep+'133.33.in_sparky',
133.3333, 500e6],
+ ['500_133.33.in.bis', '500_MHz'+sep+'133.33.in.bis_sparky',
133.3333, 500e6],
+ ['500_200.in', '500_MHz'+sep+'200.in_sparky',
200.0000, 500e6],
+ ['500_266.67.in', '500_MHz'+sep+'266.67.in_sparky',
266.6666, 500e6],
+ ['500_333.33.in', '500_MHz'+sep+'333.33.in_sparky',
333.3333, 500e6],
+ ['500_400.in', '500_MHz'+sep+'400.in_sparky',
400.0000, 500e6],
+ ['500_466.67.in', '500_MHz'+sep+'466.67.in_sparky',
466.6666, 500e6],
+ ['500_533.33.in', '500_MHz'+sep+'533.33.in_sparky',
533.3333, 500e6],
+ ['500_533.33.in.bis', '500_MHz'+sep+'533.33.in.bis_sparky',
533.3333, 500e6],
+ ['500_600.in', '500_MHz'+sep+'600.in_sparky',
600.0000, 500e6],
+ ['500_666.67.in', '500_MHz'+sep+'666.67.in_sparky',
666.6666, 500e6],
+ ['500_733.33.in', '500_MHz'+sep+'733.33.in_sparky',
733.3333, 500e6],
+ ['500_800.in', '500_MHz'+sep+'800.in_sparky',
800.0000, 500e6],
+ ['500_866.67.in', '500_MHz'+sep+'866.67.in_sparky',
866.6666, 500e6],
+ ['500_933.33.in', '500_MHz'+sep+'933.33.in_sparky',
933.3333, 500e6],
+ ['500_933.33.in.bis', '500_MHz'+sep+'933.33.in.bis_sparky',
933.3333, 500e6],
+ ['500_1000.in', '500_MHz'+sep+'1000.in_sparky',
1000.0000, 500e6],
+ ['800_reference.in', '800_MHz'+sep+'reference.in_sparky',
None, 800e6],
+ ['800_66.667.in', '800_MHz'+sep+'66.667.in_sparky',
66.6666, 800e6],
+ ['800_133.33.in', '800_MHz'+sep+'133.33.in_sparky',
133.3333, 800e6],
+ ['800_133.33.in.bis', '800_MHz'+sep+'133.33.in.bis_sparky',
133.3333, 800e6],
+ ['800_200.in', '800_MHz'+sep+'200.in_sparky',
200.0000, 800e6],
+ ['800_266.67.in', '800_MHz'+sep+'266.67.in_sparky',
266.6666, 800e6],
+ ['800_333.33.in', '800_MHz'+sep+'333.33.in_sparky',
333.3333, 800e6],
+ ['800_400.in', '800_MHz'+sep+'400.in_sparky',
400.0000, 800e6],
+ ['800_466.67.in', '800_MHz'+sep+'466.67.in_sparky',
466.6666, 800e6],
+ ['800_533.33.in', '800_MHz'+sep+'533.33.in_sparky',
533.3333, 800e6],
+ ['800_533.33.in.bis', '800_MHz'+sep+'533.33.in.bis_sparky',
533.3333, 800e6],
+ ['800_600.in', '800_MHz'+sep+'600.in_sparky',
600.0000, 800e6],
+ ['800_666.67.in', '800_MHz'+sep+'666.67.in_sparky',
666.6666, 800e6],
+ ['800_733.33.in', '800_MHz'+sep+'733.33.in_sparky',
733.3333, 800e6],
+ ['800_800.in', '800_MHz'+sep+'800.in_sparky',
800.0000, 800e6],
+ ['800_866.67.in', '800_MHz'+sep+'866.67.in_sparky',
866.6666, 800e6],
+ ['800_933.33.in', '800_MHz'+sep+'933.33.in_sparky',
933.3333, 800e6],
+ ['800_933.33.in.bis', '800_MHz'+sep+'933.33.in.bis_sparky',
933.3333, 800e6],
+ ['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:
+ # Load the peak intensities.
+ spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height')
+
+ # 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.
+ frq.set(id=id, frq=H_frq)
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ 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.in.bis', '500_200.in', '500_266.67.in',
'500_333.33.in', '500_400.in', '500_466.67.in', '500_533.33.in',
'500_533.33.in.bis', '500_600.in', '500_666.67.in', '500_733.33.in',
'500_800.in', '500_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.in.bis', '800_200.in', '800_266.67.in',
'800_333.33.in', '800_400.in', '800_466.67.in', '800_533.33.in',
'800_533.33.in.bis', '800_600.in', '800_666.67.in', '800_733.33.in',
'800_800.in', '800_866.67.in', '800_933.33.in', '800_933.33.in.bis',
'800_1000.in'])
+
+# Select only a few spins.
+deselect.all()
+select.spin(':70')
+select.spin(':71')
+
+# Set up the model.
+relax_disp.select_model('R2eff')
+
+# Calculate the R2eff values.
+calc()
+
+state.save('x')
+
+# Set up the model.
+relax_disp.select_model('LM63')
+
+# Generate the input files.
+relax_disp.cpmgfit_input(force=True)
+
+# Execute CPMGFit.
+relax_disp.cpmgfit_execute()
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh?rev=19716&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh
Thu May 23 19:22:07 2013
@@ -1,0 +1,4 @@
+#! /bin/sh
+
+cpmgfit -xmgr -f spin_:70@xxxx
+cpmgfit -xmgr -f spin_:71@xxxx
Propchange:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh
------------------------------------------------------------------------------
svn:eol-style = native
Propchange:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/batch_run.sh
------------------------------------------------------------------------------
svn:executable = *
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:70@xxxx
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_%3A70%40N.in?rev=19716&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:70@xxxx
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:70@xxxx
Thu May 23 19:22:07 2013
@@ -1,0 +1,45 @@
+title :70@N
+fields 2 18.7892743865 11.7432964915
+function CPMG
+R2 1 10 20
+Rex 0 100.0 100
+tex 0 10.0 100
+xmgr
+@ xaxis label "1/tcp (1/ms)"
+@ yaxis label "R2(tcp) (rad/s)"
+@ xaxis ticklabel format decimal
+@ yaxis ticklabel format decimal
+@ xaxis ticklabel char size 0.8
+@ yaxis ticklabel char size 0.8
+@ world xmin 0.0
+data
+0.066667 16.045541 0.296491 11.743296
+0.133333 14.877925 0.234000 11.743296
+0.200000 14.357820 0.301228 11.743296
+0.266667 12.664495 0.299527 11.743296
+0.333333 12.363205 0.271194 11.743296
+0.400000 11.092532 0.285045 11.743296
+0.466667 10.566090 0.295090 11.743296
+0.533333 9.805807 0.235226 11.743296
+0.600000 9.564301 0.281865 11.743296
+0.666667 9.015634 0.275269 11.743296
+0.733333 8.607765 0.266371 11.743296
+0.800000 8.279997 0.274045 11.743296
+0.866667 8.474536 0.251836 11.743296
+0.933333 8.158973 0.220777 11.743296
+1.000000 7.988631 0.264123 11.743296
+0.066667 22.224914 0.157014 18.789274
+0.133333 21.230874 0.123960 18.789274
+0.200000 20.603704 0.162258 18.789274
+0.266667 20.327797 0.154694 18.789274
+0.333333 18.855377 0.159253 18.789274
+0.400000 18.537531 0.141982 18.789274
+0.466667 17.508069 0.139421 18.789274
+0.533333 16.035604 0.113450 18.789274
+0.600000 15.168192 0.145221 18.789274
+0.666667 14.431802 0.138125 18.789274
+0.733333 14.034137 0.131017 18.789274
+0.800000 12.920148 0.131678 18.789274
+0.866667 12.653673 0.139552 18.789274
+0.933333 12.610864 0.103480 18.789274
+1.000000 11.969303 0.135988 18.789274
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:71@xxxx
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_%3A71%40N.in?rev=19716&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:71@xxxx
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results/lm63/spin_:71@xxxx
Thu May 23 19:22:07 2013
@@ -1,0 +1,30 @@
+title :71@N
+fields 2 18.7892743865 11.7432964915
+function CPMG
+R2 1 10 20
+Rex 0 100.0 100
+tex 0 10.0 100
+xmgr
+@ xaxis label "1/tcp (1/ms)"
+@ yaxis label "R2(tcp) (rad/s)"
+@ xaxis ticklabel format decimal
+@ yaxis ticklabel format decimal
+@ xaxis ticklabel char size 0.8
+@ yaxis ticklabel char size 0.8
+@ world xmin 0.0
+data
+0.066667 7.044342 0.174267 11.743296
+0.133333 6.781033 0.137976 11.743296
+0.200000 6.467623 0.171372 11.743296
+0.266667 6.333340 0.179931 11.743296
+0.333333 6.323238 0.162322 11.743296
+0.400000 6.005245 0.166673 11.743296
+0.466667 5.767052 0.168136 11.743296
+0.533333 5.476968 0.134411 11.743296
+0.600000 5.469949 0.157734 11.743296
+0.666667 5.295113 0.168230 11.743296
+0.733333 5.435648 0.163755 11.743296
+0.800000 5.410400 0.165309 11.743296
+0.866667 5.437554 0.158582 11.743296
+0.933333 5.176844 0.144974 11.743296
+1.000000 5.227232 0.162255 11.743296
r19716 - in /branches/relax_disp/test_suite/shared_data/dispersion/Hansen/cpmgfit_results: ./ lm63/