r2710 - in /branches/tensor_pdb: generic_fns/pymol.py prompt/pymol.py -- October 31, 2006 - 09:01

Author: bugman
Date: Tue Oct 31 09:01:00 2006
New Revision: 2710

URL: http://svn.gna.org/viewcvs/relax?rev=2710&view=rev
Log:
Implemented the 'pymol.tensor_pdb()' user function.

The numerous Molmol commands have been replaced by a single PyMOL load 
command.


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=2710&r1=2709&r2=2710&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pymol.py (original)
+++ branches/tensor_pdb/generic_fns/pymol.py Tue Oct 31 09:01:00 2006
@@ -199,32 +199,8 @@
         if not self.run in self.relax.data.run_names:
             raise RelaxNoRunError, self.run
 
-        # To overlay the structure with the diffusion tensor, select all and 
reorient to the PDB frame.
-        self.pipe_write("SelectAtom ''")
-        self.pipe_write("SelectBond ''")
-        self.pipe_write("SelectAngle ''")
-        self.pipe_write("SelectDist ''")
-        self.pipe_write("SelectPrim ''")
-        self.pipe_write("RotateInit")
-        self.pipe_write("MoveInit")
-
-        # Read in the tensor PDB file and force Molmol to recognise the 
CONECT records (not that it will show the bonds)!
-        self.pipe_write("ReadPdb " + file)
-        file_parts = split(file, '.')
-        self.pipe_write("SelectMol '@" + file_parts[0] + "'")
-        self.pipe_write("CalcBond 1 1 1")
-
-        # Apply the 'ball/stick' style to the tensor.
-        self.pipe_write("SelectAtom '0'")
-        self.pipe_write("SelectBond '0'")
-        self.pipe_write("SelectAtom ':TNS'")
-        self.pipe_write("SelectBond ':TNS'")
-        self.pipe_write("XMacStand ball_stick.mac")
-
-        # Touch up.
-        self.pipe_write("RadiusAtom 1")
-        self.pipe_write("SelectAtom ':TNS@C*'")
-        self.pipe_write("RadiusAtom 1.5")
+        # Read in the tensor PDB file.
+        self.pipe_write("load " + file)
 
 
     def view(self, run=None):

Modified: branches/tensor_pdb/prompt/pymol.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/prompt/pymol.py?rev=2710&r1=2709&r2=2710&view=diff
==============================================================================
--- branches/tensor_pdb/prompt/pymol.py (original)
+++ branches/tensor_pdb/prompt/pymol.py Tue Oct 31 09:01:00 2006
@@ -260,39 +260,9 @@
         geometric object must be created using the complementary 
'pdb.create_tensor_pdb()' user
         function.
 
-        To display the diffusion tensor, the multiple commands will be 
executed.  To overlay the
-        structure with the diffusion tensor, everything will be selected and 
reoriented and moved to
-        their original PDB frame positions:
-
-            SelectAtom ''
-            SelectBond ''
-            SelectAngle ''
-            SelectDist ''
-            SelectPrim ''
-            RotateInit
-            MoveInit
-
-        Next the tensor PDB file is read in, selected, and the covalent 
bonds of the PDB CONECT
-        records calculated:
-
-            ReadPdb file
-            SelectMol '@file'
-            CalcBond 1 1 1
-
-        Then only the atoms and bonds of the geometric object are selected 
and the 'ball/stick'
-        style applied:
-
-            SelectAtom '0'
-            SelectBond '0'
-            SelectAtom ':TNS'
-            SelectBond ':TNS'
-            XMacStand ball_stick.mac
-
-        The appearance is finally touched up:
-
-            RadiusAtom 1
-            SelectAtom ':TNS@C*'
-            RadiusAtom 1.5
+        The tensor PDB file is read in using the command:
+
+            load file
         """
 
         # Function intro text.