Author: bugman
Date: Sun Mar 3 13:39:38 2013
New Revision: 18599
URL: http://svn.gna.org/viewcvs/relax?rev=18599&view=rev
Log:
Updates for the full frame order analysis script in the test suite.
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
Modified:
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py?rev=18599&r1=18598&r2=18599&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
Sun Mar 3 13:39:38 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2012 Edward d'Auvergne
#
+# Copyright (C) 2004-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -24,9 +24,6 @@
This script should be run from the directory where it is found with the
commands:
$ ../../../../../relax full_analysis.py
-
-$ mpirun -n 3 ../../../../../relax --multi mpi4py full_analysis.py
-
The free rotor pseudo-elliptic cone model is not used in this script as the
cone X and Y opening angles cannot be differentiated with simply RDC and PCS
data, hence this model is perfectly approximated by the free rotor isotropic
cone.
"""
@@ -102,8 +99,8 @@
structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..', set_mol_name='C-dom')
# Set up the 15N and 1H spins.
-structure.load_spins(spin_id='@N', ave_pos=False)
-structure.load_spins(spin_id='@H', ave_pos=False)
+structure.load_spins(spin_id='@N', mol_name_target='CaM', ave_pos=False)
+structure.load_spins(spin_id='@H', mol_name_target='CaM', ave_pos=False)
spin.isotope(isotope='15N', spin_id='@N')
spin.isotope(isotope='1H', spin_id='@H')
@@ -112,18 +109,52 @@
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
dipole_pair.unit_vectors()
+# The lanthanides and data files.
+ln = ['dy', 'tb', 'tm', 'er']
+pcs_files = [
+ 'pcs_dy.txt',
+ 'pcs_tb.txt',
+ 'pcs_tm.txt',
+ 'pcs_er.txt'
+]
+pcs_files_subset = [
+ 'pcs_dy_subset.txt',
+ 'pcs_tb_subset.txt',
+ 'pcs_tm_subset.txt',
+ 'pcs_er_subset.txt'
+]
+rdc_files = [
+ 'rdc_dy.txt',
+ 'rdc_tb.txt',
+ 'rdc_tm.txt',
+ 'rdc_er.txt'
+]
+
+# The spectrometer frequencies.
+pcs_frq = [
+ 700.0000000, # Dy3+.
+ 700.0000000, # Tb3+.
+ 700.0000000, # Tm3+.
+ 700.0000000, # Er3+.
+]
+rdc_frq = [
+ 900.00000000, # Dy3+.
+ 900.00000000, # Tb3+.
+ 900.00000000, # Tm3+.
+ 900.00000000, # Er3+.
+]
+
# Loop over the alignments.
-ln = ['dy', 'tb', 'tm', 'er']
for i in range(len(ln)):
# Load the RDCs.
- rdc.read(align_id=ln[i], file='rdc_%s.txt'%ln[i], spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
+ rdc.read(align_id=ln[i], file=rdc_files[i], dir='.', spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
# The PCS (only a subset of ~5 spins for fast initial optimisations).
- pcs.read(align_id=ln[i], file='pcs_%s_subset.txt'%ln[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ pcs.read(align_id=ln[i], file=pcs_files_subset[i], dir='.',
mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
# The temperature and field strength.
- temperature(id=ln[i], temp=303)
- frq.set(id=ln[i], frq=900e6)
+ temperature(id=ln[i], temp=303.0)
+ frq.set(id=ln[i], frq=rdc_frq[i], units="MHz")
# Load the N-domain tensors (the full tensors).
script('../tensors.py')
@@ -137,7 +168,7 @@
red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom']
ids = ['dy', 'tb', 'tm', 'er']
for i in range(len(full)):
- # Initialise the reduced tensor.
+ # Initialise the reduced tensors (fitted during optimisation).
align_tensor.init(tensor=red[i], align_id=ids[i], params=(0, 0, 0, 0, 0))
# Set the domain info.
@@ -153,6 +184,9 @@
# Link the domains to the PDB files.
frame_order.domain_to_pdb(domain='N', pdb='1J7O_1st_NH.pdb')
frame_order.domain_to_pdb(domain='C', pdb='1J7P_1st_NH_rot.pdb')
+
+# Allow the average domain to be translated during optimisation.
+#frame_order.ave_pos_translate()
# Set the initial pivot point.
pivot = array([ 37.254, 0.5, 16.7465])
@@ -168,7 +202,7 @@
# Load the complete PCS data into the already filled data pipe.
for i in range(len(ln)):
- pcs.read(align_id=ln[i], file='pcs_%s.txt'%ln[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ pcs.read(align_id=ln[i], file=pcs_files[i], mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
r18599 - /branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py