r8180 - /1.3/generic_fns/pymol.py -- December 10, 2008 - 14:15

Author: bugman
Date: Wed Dec 10 14:15:47 2008
New Revision: 8180

URL: http://svn.gna.org/viewcvs/relax?rev=8180&view=rev
Log:
Bug fix for the vector_dist() function.

The PyMOL structure loading command should not use the file root but the full 
file name!!!  A few
unused 'id' file root variables were also deleted.


Modified:
    1.3/generic_fns/pymol.py

Modified: 1.3/generic_fns/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol.py?rev=8180&r1=8179&r2=8180&view=diff
==============================================================================
--- 1.3/generic_fns/pymol.py (original)
+++ 1.3/generic_fns/pymol.py Wed Dec 10 14:15:47 2008
@@ -196,9 +196,6 @@
 
     # Test if the current data pipe exists.
     pipes.test()
-
-    # The file root.
-    id = file_root(file)
 
     # Read in the cone PDB file.
     pymol.pipe_write("load " + file)
@@ -324,81 +321,78 @@
     # Test if the current data pipe exists.
     pipes.test()
 
+    # Read in the tensor PDB file.
+    pymol.pipe_write("load " + file)
+
+
+    # Centre of mass.
+    #################
+
+    # Select the COM residue.
+    pymol.pipe_write("select resn COM")
+
+    # Show the centre of mass as the dots representation.
+    pymol.pipe_write("show dots, 'sele'")
+
+    # Colour it blue.
+    pymol.pipe_write("color blue, 'sele'")
+
+
+    # The diffusion tensor axes.
+    ############################
+
+    # Select the AXS residue.
+    pymol.pipe_write("select resn AXS")
+
+    # Hide everything.
+    pymol.pipe_write("hide ('sele')")
+
+    # Show as 'sticks'.
+    pymol.pipe_write("show sticks, 'sele'")
+
+    # Colour it cyan.
+    pymol.pipe_write("color cyan, 'sele'")
+
+    # Select the N atoms of the AXS residue (used to display the axis 
labels).
+    pymol.pipe_write("select (resn AXS and elem N)")
+
+    # Label the atoms.
+    pymol.pipe_write("label 'sele', name")
+
+
+
+    # Monte Carlo simulations.
+    ##########################
+
+    # Select the SIM residue.
+    pymol.pipe_write("select resn SIM")
+
+    # Colour it.
+    pymol.pipe_write("colour cyan, 'sele'")
+
+
+    # Clean up.
+    ###########
+
+    # Remove the selection.
+    pymol.pipe_write("cmd.delete('sele')")
+
+
+def vector_dist(file=None):
+    """Display the XH bond vector distribution.
+
+    @keyword file:   The vector distribution PDB file.
+    @type file:     str
+    """
+
+    # Test if the current data pipe exists.
+    pipes.test()
+
     # The file root.
     id = file_root(file)
 
-    # Read in the tensor PDB file.
+    # Read in the vector distribution PDB file.
     pymol.pipe_write("load " + file)
-
-
-    # Centre of mass.
-    #################
-
-    # Select the COM residue.
-    pymol.pipe_write("select resn COM")
-
-    # Show the centre of mass as the dots representation.
-    pymol.pipe_write("show dots, 'sele'")
-
-    # Colour it blue.
-    pymol.pipe_write("color blue, 'sele'")
-
-
-    # The diffusion tensor axes.
-    ############################
-
-    # Select the AXS residue.
-    pymol.pipe_write("select resn AXS")
-
-    # Hide everything.
-    pymol.pipe_write("hide ('sele')")
-
-    # Show as 'sticks'.
-    pymol.pipe_write("show sticks, 'sele'")
-
-    # Colour it cyan.
-    pymol.pipe_write("color cyan, 'sele'")
-
-    # Select the N atoms of the AXS residue (used to display the axis 
labels).
-    pymol.pipe_write("select (resn AXS and elem N)")
-
-    # Label the atoms.
-    pymol.pipe_write("label 'sele', name")
-
-
-
-    # Monte Carlo simulations.
-    ##########################
-
-    # Select the SIM residue.
-    pymol.pipe_write("select resn SIM")
-
-    # Colour it.
-    pymol.pipe_write("colour cyan, 'sele'")
-
-
-    # Clean up.
-    ###########
-
-    # Remove the selection.
-    pymol.pipe_write("cmd.delete('sele')")
-
-
-def vector_dist(file=None):
-    """Display the XH bond vector distribution.
-
-    @keyword file:   The vector distribution PDB file.
-    @type file:     str
-    """
-
-    # Test if the current data pipe exists.
-    pipes.test()
-
-    # The file root.
-    id = file_root(file)
-
-    # Read in the vector distribution PDB file.
-    pymol.pipe_write("load " + id)
 
 
     # Create a surface.