r24369 - in /branches/frame_order_cleanup: lib/structure/represent/rotor.py pipe_control/pymol_control.py -- July 01, 2014 - 11:46

Author: bugman
Date: Tue Jul  1 11:46:58 2014
New Revision: 24369

URL: http://svn.gna.org/viewcvs/relax?rev=24369&view=rev
Log:
Renamed the residues of the rotor geometric object representation.

The rotor axis atoms now belong to the RTX residue and the propeller blades 
to the RTB residue.  The
'RT' at the start represents the rotor and this will allow all the geometric 
objects to be better
isolated.


Modified:
    branches/frame_order_cleanup/lib/structure/represent/rotor.py
    branches/frame_order_cleanup/pipe_control/pymol_control.py

Modified: branches/frame_order_cleanup/lib/structure/represent/rotor.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/represent/rotor.py?rev=24369&r1=24368&r2=24369&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/represent/rotor.py       
(original)
+++ branches/frame_order_cleanup/lib/structure/represent/rotor.py       Tue 
Jul  1 11:46:58 2014
@@ -83,18 +83,18 @@
 
         # The central point.
         mid_point = closest_point_ax(line_pt=axis_pt, axis=axis, 
point=centre)
-        pos_index = mol.atom_add(pdb_record='HETATM', atom_name='CTR', 
res_name='AX', res_num=1, pos=mid_point, element='PT')
+        pos_index = mol.atom_add(pdb_record='HETATM', atom_name='CTR', 
res_name='RTX', res_num=1, pos=mid_point, element='PT')
 
         # Centre of the propellers.
         prop1 = mid_point + axis_norm * span
         prop1_index = pos_index + 1
-        mol.atom_add(pdb_record='HETATM', atom_name='PRP', res_name='PRC', 
res_num=2, pos=prop1, element='O')
+        mol.atom_add(pdb_record='HETATM', atom_name='PRP', res_name='RTX', 
res_num=2, pos=prop1, element='O')
         mol.atom_connect(index1=pos_index, index2=prop1_index)
 
         # Centre of the propellers.
         prop2 = mid_point - axis_norm * span
         prop2_index = pos_index + 2
-        mol.atom_add(pdb_record='HETATM', atom_name='PRP', res_name='PRC', 
res_num=3, pos=prop2, element='O')
+        mol.atom_add(pdb_record='HETATM', atom_name='PRP', res_name='RTX', 
res_num=3, pos=prop2, element='O')
         mol.atom_connect(index1=pos_index, index2=prop2_index)
 
         # Create the rotor propellers.
@@ -147,11 +147,11 @@
             blade_origin = centre
 
         # Add an atom for the blage origin.
-        blade_origin_index = mol.atom_add(pdb_record='HETATM', 
atom_name='BLO', res_name='PRB', res_num=res_num, pos=blade_origin, 
element='O')
+        blade_origin_index = mol.atom_add(pdb_record='HETATM', 
atom_name='BLO', res_name='RTB', res_num=res_num, pos=blade_origin, 
element='O')
 
         # The centre edge point of the blade.
         mid_point = blade_origin + blades[i] * blade_length
-        mid_pt_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD', 
res_name='PRB', res_num=res_num, pos=mid_point, element='N')
+        mid_pt_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD', 
res_name='RTB', res_num=res_num, pos=mid_point, element='N')
         mol.atom_connect(index1=mid_pt_index, index2=blade_origin_index)
 
         # Build the blade.
@@ -172,13 +172,13 @@
 
             # The positive edge.
             pos_point = dot(R, mid_point - blade_origin) + blade_origin
-            pos_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD', 
res_name='PRB', res_num=res_num, pos=pos_point, element='N')
+            pos_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD', 
res_name='RTB', res_num=res_num, pos=pos_point, element='N')
             mol.atom_connect(index1=pos_index, index2=pos_last_index)
             mol.atom_connect(index1=pos_index, index2=blade_origin_index)
 
             # The negative edge.
             neg_point = dot(transpose(R), mid_point - blade_origin) + 
blade_origin
-            neg_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD', 
res_name='PRB', res_num=res_num, pos=neg_point, element='N')
+            neg_index = mol.atom_add(pdb_record='HETATM', atom_name='BLD', 
res_name='RTB', res_num=res_num, pos=neg_point, element='N')
             mol.atom_connect(index1=neg_index, index2=neg_last_index)
             mol.atom_connect(index1=neg_index, index2=blade_origin_index)
 

Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=24369&r1=24368&r2=24369&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py  (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py  Tue Jul  1 
11:46:58 2014
@@ -629,8 +629,8 @@
     if id == None:
         raise RelaxError("The PyMOL object ID must be supplied.")
 
-    # Rotor objects:  Set up the rotor axis (the residues AX and PRC).
-    pymol_obj.exec_cmd("select (%s & resn AX,PRC)" % id)
+    # Rotor objects:  Set up the rotor axis.
+    pymol_obj.exec_cmd("select (%s & resn RTX)" % id)
     pymol_obj.exec_cmd("show stick, 'sele'")
     pymol_obj.exec_cmd("color red, 'sele'")
     pymol_obj.exec_cmd("cmd.delete('sele')")
@@ -643,7 +643,7 @@
     pymol_obj.exec_cmd("cmd.delete('sele')")
 
     # Rotor objects:  Set up the propellers.
-    pymol_obj.exec_cmd("select (%s & resn PRB)" % id)
+    pymol_obj.exec_cmd("select (%s & resn RTB)" % id)
     pymol_obj.exec_cmd("show stick, 'sele'")
     pymol_obj.exec_cmd("set stick_radius, 0.15, 'sele'")
     pymol_obj.exec_cmd("cmd.delete('sele')")