Author: bugman
Date: Tue Jun 3 08:53:25 2014
New Revision: 23613
URL: http://svn.gna.org/viewcvs/relax?rev=23613&view=rev
Log:
Optimisation of the rotor model to the rigid CaM frame order test data.
The optimisation script and all results files have been added to the
repository.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_fixed_piv.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_true.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.log.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.py
- copied, changed from r23612,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_fixed_piv.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_true.pdb.gz
(with props)
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos.pdb.gz?rev=23613&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos.pdb.gz
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_fixed_piv.pdb.gz?rev=23613&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_fixed_piv.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_true.pdb.gz?rev=23613&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/ave_pos_true.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.bz2?rev=23613&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.bz2
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svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.log.bz2?rev=23613&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.log.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.pdb.gz?rev=23613&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Copied:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.py
(from r23612,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/frame_order.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.py?p2=branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.py&p1=branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/frame_order.py&r1=23612&r2=23613&rev=23613&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.py
Tue Jun 3 08:53:25 2014
@@ -1,4 +1,4 @@
-# Script for optimising the rigid frame order test model of CaM.
+# Script for optimising the rotor frame order test model of CaM to the rigid
data.
# Python module imports.
from numpy import array
@@ -7,13 +7,16 @@
# The real parameter values.
AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623468683852550,
0.435439748282942, 5.081265879629926]
+AXIS_THETA = 0.9600799785953431
+AXIS_PHI = 4.0322755062196229
+CONE_SIGMA_MAX = 0.0
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
# Read the structures.
-structure.read_pdb('1J7O_1st_NH.pdb', dir='..', set_mol_name='N-dom')
-structure.read_pdb('1J7P_1st_NH_rot.pdb', dir='..', set_mol_name='C-dom')
+structure.read_pdb('1J7O_1st_NH.pdb', dir='../..', set_mol_name='N-dom')
+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)
@@ -30,17 +33,17 @@
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_%s.txt'%ln[i], dir='..',
spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
# The PCS.
- 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_%s.txt'%ln[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.
spectrometer.temperature(id=ln[i], temp=303)
spectrometer.frequency(id=ln[i], frq=900e6)
# Load the N-domain tensors (the full tensors).
-script('../tensors.py')
+script('../../tensors.py')
# Define the domains.
domain(id='N', spin_id=":1-78")
@@ -62,7 +65,7 @@
align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
# Select the model.
-frame_order.select_model('rigid')
+frame_order.select_model('rotor')
# Set the reference domain.
frame_order.ref_domain('N')
@@ -84,6 +87,9 @@
value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
value.set(param='ave_pos_beta', val=AVE_POS_BETA)
value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='axis_theta', val=AXIS_THETA)
+value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='cone_sigma_max', val=CONE_SIGMA_MAX)
calc()
# Create the PDB representation of the true state.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_fixed_piv.pdb.gz?rev=23613&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_fixed_piv.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_true.pdb.gz?rev=23613&view=auto
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order_true.pdb.gz
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svn:mime-type = application/octet-stream
r23613 - /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/