r2763 - in /branches/tensor_pdb: generic_fns/pymol.py prompt/pymol.py -- November 07, 2006 - 07:29

Author: bugman
Date: Tue Nov  7 06:50:05 2006
New Revision: 2763

URL: http://svn.gna.org/viewcvs/relax?rev=2763&view=rev
Log:
'pymol.tensor_pdb()' has been modified to change the representation of 'COM', 
'AXS', and 'SIM'.

The centre of mass 'COM' is shown as the 'dots' representation and is 
coloured blue.

The diffusion tensor axes 'AXS' are shown as the 'sticks' representation, is 
coloured cyan, and the
atoms labelled to show 'Dpar', 'Dx', 'Dy', and 'Dz' in PyMOL.

The Monte Carlo simulations axes are coloured cyan.


Modified:
    branches/tensor_pdb/generic_fns/pymol.py
    branches/tensor_pdb/prompt/pymol.py

Modified: branches/tensor_pdb/generic_fns/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pymol.py?rev=2763&r1=2762&r2=2763&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pymol.py (original)
+++ branches/tensor_pdb/generic_fns/pymol.py Tue Nov  7 06:50:05 2006
@@ -207,6 +207,59 @@
         self.pipe_write("load " + file)
 
 
+        # Centre of mass.
+        #################
+
+        # Select the COM residue.
+        self.pipe_write("select resn COM")
+
+        # Show the centre of mass as the dots representation.
+        self.pipe_write("show dots, 'sele'")
+
+        # Colour it blue.
+        self.pipe_write("color blue, 'sele'")
+
+
+        # The diffusion tensor axes.
+        ############################
+
+        # Select the AXS residue.
+        self.pipe_write("select resn AXS")
+
+        # Hide everything.
+        self.pipe_write("hide ('sele')")
+
+        # Show as 'sticks'.
+        self.pipe_write("show sticks, 'sele'")
+
+        # Colour it cyan.
+        self.pipe_write("color cyan, 'sele'")
+
+        # Select the N atoms of the AXS residue (used to display the axis 
labels).
+        self.pipe_write("select (resn AXS and elem N)")
+
+        # Label the atoms.
+        self.pipe_write("label 'sele', name")
+
+
+
+        # Monte Carlo simulations.
+        ##########################
+
+        # Select the SIM residue.
+        self.pipe_write("select resn SIM")
+
+        # Colour it.
+        self.pipe_write("colour cyan, 'sele'")
+
+
+        # Clean up.
+        ###########
+
+        # Remove the selection.
+        self.pipe_write("cmd.delete('sele')")
+
+
     def view(self, run=None):
         """Function for running PyMOL."""
 

Modified: branches/tensor_pdb/prompt/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/pymol.py?rev=2763&r1=2762&r2=2763&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/pymol.py (original)
+++ branches/tensor_pdb/prompt/pymol.py Tue Nov  7 06:50:05 2006
@@ -263,6 +263,25 @@
         The tensor PDB file is read in using the command:
 
             load file
+
+        The centre of mass residue 'COM' is displayed using the commands:
+
+            select resn COM
+            show dots, 'sele'
+            color blue, 'sele'
+
+        The axes of the diffusion tensor, the residue 'AXS', is displayed 
using the commands:
+
+            select resn AXS
+            hide ('sele')
+            show sticks, 'sele'
+            color cyan, 'sele'
+            label 'sele', name
+
+        The simulation axes, the residues 'SIM', are displayed using the 
commands:
+
+            select resn SIM
+            colour cyan, 'sele'
         """
 
         # Function intro text.