r14501 - /1.3/specific_fns/model_free/pymol.py -- August 29, 2011 - 13:28

Author: bugman
Date: Mon Aug 29 13:28:13 2011
New Revision: 14501

URL: http://svn.gna.org/viewcvs/relax?rev=14501&view=rev
Log:
Completely converted the PyMOL model-free macro creation from Molmol to PyMOL 
commands.

This now reproduces the Molmol 'classic' representation.


Modified:
    1.3/specific_fns/model_free/pymol.py

Modified: 1.3/specific_fns/model_free/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/pymol.py?rev=14501&r1=14500&r2=14501&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/pymol.py (original)
+++ 1.3/specific_fns/model_free/pymol.py Mon Aug 29 13:28:13 2011
@@ -421,26 +421,21 @@
     def _pymol_classic_colour(self, res_num=None, width=None, 
rgb_array=None):
         """Colour the given peptide bond."""
 
-        # Ca to C bond.
-        self.commands.append("SelectBond 'atom1.name = \"CA\"  & atom2.name 
= \"C\" & res.num = " + repr(res_num-1) + "'")
-        self.commands.append("StyleBond neon")
-        self.commands.append("RadiusBond " + repr(width))
-        self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + 
repr(rgb_array[1]) + " " + repr(rgb_array[2]))
-
-        # C to N bond.
-        self.commands.append("SelectBond 'atom1.name = \"C\"  & atom2.name = 
\"N\" & res.num = " + repr(res_num-1) + "'")
-        self.commands.append("StyleBond neon")
-        self.commands.append("RadiusBond " + repr(width))
-        self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + 
repr(rgb_array[1]) + " " + repr(rgb_array[2]))
-
-        # N to Ca bond.
-        self.commands.append("SelectBond 'atom1.name = \"N\"  & atom2.name = 
\"CA\" & res.num = " + repr(res_num) + "'")
-        self.commands.append("StyleBond neon")
-        self.commands.append("RadiusBond " + repr(width))
-        self.commands.append("ColorBond " + repr(rgb_array[0]) + " " + 
repr(rgb_array[1]) + " " + repr(rgb_array[2]))
-
-        # Blank line.
+        # Blank line (to make the macro file easier to read for the user).
         self.commands.append("")
+
+        # Define the colour.
+        colour_name = 'pept_colour_%i' % res_num
+        self.commands.append("set_color %s, [%s, %s, %s]" % (colour_name, 
rgb_array[0], rgb_array[1], rgb_array[2]))
+
+        # The peptide bond.
+        self.commands.append("select pept_bond, (name ca,n and resi %i) or 
(name ca,c,o and resi %i)" % (res_num, res_num-1))
+        self.commands.append("as sticks, pept_bond")
+        self.commands.append("set_bond stick_radius, %s, pept_bond" % width)
+        self.commands.append("color %s, pept_bond" % colour_name)
+
+        # Delete the selection.
+        self.commands.append("delete pept_bond")
 
 
     def _pymol_classic_correlation_time(self, res_num, te, colour_start, 
colour_end, colour_list):
@@ -485,11 +480,14 @@
         self.commands.append("hide")
 
         # Show the backbone bonds as lines.
-        self.commands.append("select bb, (name ca,n,c)")
+        self.commands.append("select bb, (name ca,n,c,o)")
         self.commands.append("show lines, bb")
 
         # Colour the backbone black.
         self.commands.append("color black, bb")
+
+        # Delete the selection.
+        self.commands.append("delete bb")
 
         # Set the background colour to white.
         self.commands.append("bg_color white")