Author: bugman
Date: Thu May 22 18:37:42 2014
New Revision: 23354
URL: http://svn.gna.org/viewcvs/relax?rev=23354&view=rev
Log:
Updated the CaM frame order test model superimposition script.
The Ca2+ atoms are now deleted from the structures before superimposition so
that the centroid
matches that used in the frame order analysis.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.log
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.py
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.log
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.log?rev=23354&r1=23353&r2=23354&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.log
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.log
Thu May 22 18:37:42 2014
@@ -1,8 +1,8 @@
- relax repository checkout rNone
- None
+ relax repository checkout r23353
+
svn+ssh://svn.gna.org/svn/relax/branches/frame_order_cleanup
Molecular dynamics by NMR data analysis
@@ -29,6 +29,9 @@
structure.read_pdb('1J7P_1st_NH.pdb', set_mol_name='C-dom', set_model_num=1)
structure.read_pdb('1J7P_1st_NH_rot.pdb', set_mol_name='C-dom',
set_model_num=2)
+# Delete the calciums to match the data pipe CoM (from only 15N and 1H
spins).
+structure.delete(atom_id='@CA')
+
# Superimpose.
structure.superimpose(method='fit to first', centre_type='CoM')
@@ -38,17 +41,22 @@
relax> pipe.create(pipe_name='superimpose', pipe_type='N-state', bundle=None)
-relax> structure.read_pdb(file='1J7P_1st_NH.pdb', dir=None, read_mol=None,
set_mol_name='C-dom', read_model=None, set_model_num=1, alt_loc=None,
merge=False)
+relax> structure.read_pdb(file='1J7P_1st_NH.pdb', dir=None, read_mol=None,
set_mol_name='C-dom', read_model=None, set_model_num=1, alt_loc=None,
verbosity=1, merge=False)
Internal relax PDB parser.
Opening the file '1J7P_1st_NH.pdb' for reading.
Adding molecule 'C-dom' to model 1 (from the original molecule number 1 of
model None)
-relax> structure.read_pdb(file='1J7P_1st_NH_rot.pdb', dir=None,
read_mol=None, set_mol_name='C-dom', read_model=None, set_model_num=2,
alt_loc=None, merge=False)
+relax> structure.read_pdb(file='1J7P_1st_NH_rot.pdb', dir=None,
read_mol=None, set_mol_name='C-dom', read_model=None, set_model_num=2,
alt_loc=None, verbosity=1, merge=False)
Internal relax PDB parser.
Opening the file '1J7P_1st_NH_rot.pdb' for reading.
Adding molecule 'C-dom' to model 2 (from the original molecule number 1 of
model None)
+
+relax> structure.delete(atom_id='@CA', verbosity=1, spin_info=True)
+Deleting structural data from the current pipe.
+Deleting all spin specific structural info.
+Deleting all interatomic vectors.
relax> structure.superimpose(models=None, method='fit to first',
atom_id=None, centre_type='CoM', centroid=None)
Validating models:
@@ -56,26 +64,26 @@
Superimposition of structural models [1, 2] using the 'fit to first'
algorithm.
Calculating the centre of mass.
- Total mass: M = 1085.12894
- Centre of mass: R = array([ 48.105998313011526, -9.256453511856387,
30.742193705588587])
+ Total mass: M = 1004.9729400000001
+ Centre of mass: R = array([ 47.63725241103505 , -9.48986557536564 ,
30.825358289766502])
Calculating the centre of mass.
- Total mass: M = 1085.12894
- Centre of mass: R = array([ 26.83678090574195 , -12.379064173184801,
28.341541283932589])
+ Total mass: M = 1004.9729400000001
+ Centre of mass: R = array([ 26.7775022253435 , -11.940472562813483,
28.633503719413586])
Calculating the rotational and translational displacements from model 1 to
model 2 using the Kabsch algorithm.
-Start CoM: [ 48.105998313011526, -9.256453511856387,
30.742193705588587]
-End CoM: [ 26.836780905741950, -12.379064173184801,
28.341541283932589]
-Translation vector: [ -21.269217407269576, -3.122610661328414,
-2.400652421655998]
-Translation distance: 21.630844609250556
+Start CoM: [ 47.637252411035050, -9.489865575365640,
30.825358289766502]
+End CoM: [ 26.777502225343500, -11.940472562813483,
28.633503719413586]
+Translation vector: [ -20.859750185691549, -2.450606987447843,
-2.191854570352916]
+Translation distance: 21.117264947761672
Rotation matrix:
- [[ -0.313343039541484, 0.937381760589709, 0.152090678493596]
- [ -0.889228800536162, -0.233411682389844, -0.393435035070547]
- [ -0.333299084709100, -0.258523541360706, 0.906684784638187]]
-Rotation axis: [ 0.071200484289399, 0.256167842033371,
-0.964006497771110]
-Rotation euler angles: [ 5.623469076122531, 0.435439405668396,
5.081265529106499]
-Rotation angle (deg): 108.665039652996725
+ [[ -0.313343136727067, 0.937381687553936, 0.152090928409876]
+ [ -0.889228712298167, -0.233411620017465, -0.393435271506466]
+ [ -0.333299228757862, -0.258523862495048, 0.906684640120288]]
+Rotation axis: [ 0.071200441865536, 0.256168058141030,
-0.964006443477639]
+Rotation euler angles: [ 5.623468683852550, 0.435439748282942,
5.081265879629926]
+Rotation angle (deg): 108.665045075655243
relax> structure.write_pdb(file='superimpose.pdb', dir=None, model_num=None,
compress_type=0, force=True)
Opening the file 'superimpose.pdb' for writing.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.py?rev=23354&r1=23353&r2=23354&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.py
Thu May 22 18:37:42 2014
@@ -7,6 +7,9 @@
structure.read_pdb('1J7P_1st_NH.pdb', set_mol_name='C-dom', set_model_num=1)
structure.read_pdb('1J7P_1st_NH_rot.pdb', set_mol_name='C-dom',
set_model_num=2)
+# Delete the calciums to match the data pipe CoM (from only 15N and 1H
spins).
+structure.delete(atom_id='@CA')
+
# Superimpose.
structure.superimpose(method='fit to first', centre_type='CoM')
r23354 - in /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam: superimpose.log superimpose.py