Author: bugman
Date: Tue Jul 8 11:26:46 2014
New Revision: 24476
URL: http://svn.gna.org/viewcvs/relax?rev=24476&view=rev
Log:
Added the full optimisation results for the large angle double rotor frame
order model.
This is for the CaM test data using the new frame_order.py optimisation
script.
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_fixed_piv.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_sim.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_true.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.log.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py
- copied, changed from r24471,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_sim.pdb.gz
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.bz2
(with props)
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.pdb.gz
(with props)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos.pdb.gz?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_fixed_piv.pdb.gz?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_fixed_piv.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_sim.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_sim.pdb.gz?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_sim.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_true.pdb.gz?rev=24476&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/ave_pos_true.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.bz2?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.log.bz2?rev=24476&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.log.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.pdb.gz?rev=24476&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Copied:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py
(from r24471,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py?p2=branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py&p1=branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py&r1=24471&r2=24476&rev=24476&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py
Tue Jul 8 11:26:46 2014
@@ -16,14 +16,14 @@
C_COM = array([26.837, -12.379, 28.342], float64)
# The Z-axis as the inter CoM vector.
- z_axis = N_COM - C_COM
+ z_axis = C_COM - N_COM
disp = norm(z_axis)
z_axis /= disp
# The eigenframe (partly from the system_create.log file).
eigensystem = transpose(array([
+ [ -7.778375610280605e-01, 6.284649244351433e-01,
-7.532653237683726e-04],
[-0.487095774865268, -0.60362450312215, -0.63116968030708 ],
- [ -7.778375610280605e-01, 6.284649244351433e-01,
-7.532653237683726e-04],
z_axis
], float64))
@@ -38,8 +38,8 @@
AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -21.269217407269576,
-3.122610661328414, -2.400652421655998]
AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623469076122531,
0.435439405668396, 5.081265529106499]
EIGEN_ALPHA, EIGEN_BETA, EIGEN_GAMMA, PIVOT_DISP = eigen_system()
-CONE_SIGMA_MAX = 10.5 * 2.0 * pi / 360.0 # 0.1832595714594046
-CONE_SIGMA_MAX_2 = 11.5 * 2.0 * pi / 360.0 # 0.20071286397934787
+CONE_SIGMA_MAX = 85.0 / 2.0 * 2.0 * pi / 360.0 # 0.7417649320975901
+CONE_SIGMA_MAX_2 = 55.0 / 2.0 * 2.0 * pi / 360.0 # 0.4799655442984406
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -63,7 +63,7 @@
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], 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)
@@ -101,7 +101,7 @@
frame_order.ref_domain('N')
# Set the initial pivot point.
-pivot = array([ 26.837, -12.379, 28.342])
+pivot = array([41.739, 6.03, -0.764])
frame_order.pivot(pivot, fix=True)
# Set the paramagnetic centre.
@@ -130,12 +130,12 @@
state.save('frame_order_true', force=True)
# Grid search (low quality for speed).
-frame_order.num_int_pts(num=100)
-grid_search(inc=[None, None, None, None, None, None, None, 7, 7, 7, 7, 7])
+frame_order.num_int_pts(num=200)
+grid_search(inc=[7, None, None, None, None, None, None, 7, 7, 7, 7, 7])
# Iterative optimisation with increasing precision.
-num_int_pts = [100, 1000, 10000, 50000]
-func_tol = [1e-2, 1e-3, 5e-3, 1e-4]
+num_int_pts = [1000, 10000, 50000]
+func_tol = [1e-2, 5e-3, 1e-4]
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise('simplex', func_tol=func_tol[i])
@@ -148,14 +148,14 @@
# Optimise the pivot and model, again iterating with increasing precision.
frame_order.pivot(pivot, fix=False)
-num_int_pts = [100, 1000, 10000, 50000]
-func_tol = [1e-2, 1e-3, 5e-3, 1e-4]
+num_int_pts = [1000, 10000, 50000]
+func_tol = [1e-2, 5e-3, 1e-4]
for i in range(len(num_int_pts)):
frame_order.num_int_pts(num=num_int_pts[i])
minimise('simplex', func_tol=func_tol[i])
# Test Monte Carlo simulations (at low quality for speed).
-frame_order.num_int_pts(num=100)
+frame_order.num_int_pts(num=10000)
monte_carlo.setup(number=5)
monte_carlo.create_data()
monte_carlo.initial_values()
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.bz2?rev=24476&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.pdb.gz?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_fixed_piv.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_sim.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_sim.pdb.gz?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_sim.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.bz2?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Added:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.pdb.gz?rev=24476&view=auto
==============================================================================
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Propchange:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_true.pdb.gz
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py?rev=24476&r1=24475&r2=24476&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py
Tue Jul 8 11:26:46 2014
@@ -49,8 +49,8 @@
# The rotation axes from the system_create.py script.
self.axes = [
- [-0.487095774865268, -0.60362450312215, -0.63116968030708 ],
- [ -7.778375610280605e-01, 6.284649244351433e-01,
-7.532653237683726e-04]
+ [-0.487095774865268, -0.60362450312215, -0.63116968030708 ],
# y-axis
+ [ -7.778375610280605e-01, 6.284649244351433e-01,
-7.532653237683726e-04] # x-axis
]
r24476 - /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/