Author: bugman
Date: Mon Oct 31 11:53:56 2011
New Revision: 14945
URL: http://svn.gna.org/viewcvs/relax?rev=14945&view=rev
Log:
The generation script for the free rotor frame order test model 2 creates a
PDB for the axis system.
The generate_distribution.py now creates the axis.pdb file which encoded the
rotation axis of the
domain distribution. The animate.py will also display this rotation axis.
Added:
1.3/test_suite/shared_data/frame_order/free_rotor2/axis.pdb
Modified:
1.3/test_suite/shared_data/frame_order/free_rotor2/animate.py
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.log
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.py
Modified: 1.3/test_suite/shared_data/frame_order/free_rotor2/animate.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor2/animate.py?rev=14945&r1=14944&r2=14945&view=diff
==============================================================================
--- 1.3/test_suite/shared_data/frame_order/free_rotor2/animate.py (original)
+++ 1.3/test_suite/shared_data/frame_order/free_rotor2/animate.py Mon Oct 31
11:53:56 2011
@@ -33,3 +33,21 @@
pymol.command('load ../1J7P_1st_NH.pdb')
pymol.command('hide everything, 1J7P_1st_NH')
pymol.command('show spheres, 1J7P_1st_NH')
+
+# Load the pivot-CoM axes.
+pymol.command('load ../system.pdb')
+pymol.command('show sticks, system')
+pymol.command('label system, resn')
+pymol.command('select sele, system and resi 1')
+pymol.command('color blue, sele')
+pymol.command('select sele, system and resi 2')
+pymol.command('color blue, sele')
+pymol.command('select sele, system and resi 3')
+pymol.command('color yellow, sele')
+
+# The original rotation axis.
+pymol.command('load axis.pdb')
+pymol.command('show sticks, axis')
+pymol.command('color orange, axis')
+pymol.command('select sele, axis and name N')
+pymol.command('label sele, resn')
Added: 1.3/test_suite/shared_data/frame_order/free_rotor2/axis.pdb
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor2/axis.pdb?rev=14945&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/frame_order/free_rotor2/axis.pdb (added)
+++ 1.3/test_suite/shared_data/frame_order/free_rotor2/axis.pdb Mon Oct 31
11:53:56 2011
@@ -1,0 +1,9 @@
+REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.1, 1-AUG-2007
+REMARK 40 CREATED BY RELAX (HTTP://NMR-RELAX.COM)
+ATOM 1 C AXE 1 37.254 0.500 16.747 1.00 0.00
C
+ATOM 2 N AXE 1 49.262 15.346 13.490 1.00 0.00
N
+TER 3 AXE 1
+CONECT 1 2
+CONECT 2 1
+MASTER 0 0 0 0 0 0 0 0 2 1 2 0
+END
Modified:
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.log
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.log?rev=14945&r1=14944&r2=14945&view=diff
==============================================================================
---
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.log
(original)
+++
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.log
Mon Oct 31 11:53:56 2011
@@ -47,6 +47,7 @@
# Tilt the rotation axis by 30 degrees.
rot_axis = cross(axis, array([0, 0, 1]))
+#rot_axis = rot_axis / norm(rot_axis)
axis_angle_to_R(rot_axis, 30.0 * 2.0 * pi / 360.0, R)
print("Tilt axis: %s" % repr(rot_axis))
print("CoM-pivot axis: %s" % repr(axis))
@@ -71,6 +72,14 @@
# Save the PDB file.
structure.write_pdb('distribution.pdb', compress_type=2, force=True)
+
+# Create a PDB for the motional axis system.
+end_pt = axis * norm(pivot - com) + pivot
+structure.delete()
+structure.add_atom(atom_name='C', res_name='AXE', res_num=1, pos=pivot,
element='C')
+structure.add_atom(atom_name='N', res_name='AXE', res_num=1, pos=end_pt,
element='N')
+structure.connect_atom(index1=0, index2=1)
+structure.write_pdb('axis.pdb', compress_type=0, force=True)
----------------------------------------------------------------------------------------------------
relax> pipe.create(pipe_name='generate', pipe_type='N-state')
@@ -1528,3 +1537,105 @@
MASTER
END
+relax> structure.delete()
+Deleting the following structural data:
+
+Models.
+
+Index Model number
+0 None
+1 1
+2 2
+3 3
+4 4
+5 5
+6 6
+7 7
+8 8
+9 9
+10 10
+11 11
+12 12
+13 13
+14 14
+15 15
+16 16
+17 17
+18 18
+19 19
+20 20
+21 21
+22 22
+23 23
+24 24
+25 25
+26 26
+27 27
+28 28
+29 29
+30 30
+31 31
+32 32
+33 33
+34 34
+35 35
+36 36
+37 37
+38 38
+39 39
+40 40
+41 41
+42 42
+43 43
+44 44
+45 45
+46 46
+47 47
+48 48
+49 49
+50 50
+51 51
+52 52
+53 53
+54 54
+55 55
+56 56
+57 57
+58 58
+59 59
+60 60
+61 61
+62 62
+63 63
+64 64
+65 65
+66 66
+67 67
+68 68
+69 69
+70 70
+71 71
+
+
+relax> structure.add_atom(atom_name='C', res_name='AXE', res_num=1,
pos=array([ 37.254 , 0.5 , 16.7465]), element='C', atom_num=None,
chain_id=None, segment_id=None, pdb_record=None)
+Adding molecule 'None' to model None (from the original molecule number None
of model None)
+
+relax> structure.add_atom(atom_name='N', res_name='AXE', res_num=1,
pos=array([ 49.26247678, 15.34637518, 13.4901042 ]), element='N',
atom_num=None, chain_id=None, segment_id=None, pdb_record=None)
+
+relax> structure.connect_atom(index1=0, index2=1)
+
+relax> structure.write_pdb(file='axis.pdb', dir=None, model_num=None,
compress_type=0, force=True)
+Opening the file 'axis.pdb' for writing.
+
+Creating the PDB records
+
+REMARK
+HET
+HETNAM
+FORMUL
+ATOM, HETATM, TER
+CONECT
+
+MASTER
+END
+
Modified:
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.py?rev=14945&r1=14944&r2=14945&view=diff
==============================================================================
---
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.py
(original)
+++
1.3/test_suite/shared_data/frame_order/free_rotor2/generate_distribution.py
Mon Oct 31 11:53:56 2011
@@ -26,6 +26,7 @@
# Tilt the rotation axis by 30 degrees.
rot_axis = cross(axis, array([0, 0, 1]))
+#rot_axis = rot_axis / norm(rot_axis)
axis_angle_to_R(rot_axis, 30.0 * 2.0 * pi / 360.0, R)
print("Tilt axis: %s" % repr(rot_axis))
print("CoM-pivot axis: %s" % repr(axis))
@@ -50,3 +51,11 @@
# Save the PDB file.
structure.write_pdb('distribution.pdb', compress_type=2, force=True)
+
+# Create a PDB for the motional axis system.
+end_pt = axis * norm(pivot - com) + pivot
+structure.delete()
+structure.add_atom(atom_name='C', res_name='AXE', res_num=1, pos=pivot,
element='C')
+structure.add_atom(atom_name='N', res_name='AXE', res_num=1, pos=end_pt,
element='N')
+structure.connect_atom(index1=0, index2=1)
+structure.write_pdb('axis.pdb', compress_type=0, force=True)
r14945 - /1.3/test_suite/shared_data/frame_order/free_rotor2/