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List:       relax-commits
Subject:    r2708 - /branches/tensor_pdb/generic_fns/pymol.py
From:       edward.dauvergne () domain ! hid
Date:       2006-10-31 7:57:10
Message-ID: E1GeoUg-0004ri-JT () subversion ! gna ! org
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Author: bugman
Date: Tue Oct 31 08:57:07 2006
New Revision: 2708

URL: http://svn.gna.org/viewcvs/relax?rev=2708&view=rev
Log:
The 'pymol.view()' user function now works.

A number of calls to pipes located at 'self.relax.data.molmol' where changed to
'self.relax.data.pymol'.  The Molmol 'InitAll' and loading functions where changed to \
the PyMOL equivalents.  Now PyMOL executes and opens up the PDB file.


Modified:
    branches/tensor_pdb/generic_fns/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=2708&r1=2707&r2=2708&view=diff
 ==============================================================================
--- branches/tensor_pdb/generic_fns/pymol.py (original)
+++ branches/tensor_pdb/generic_fns/pymol.py Tue Oct 31 08:57:07 2006
@@ -95,7 +95,7 @@
 
 
     def open_pdb(self, run=None):
-        """Function for opening the PDB file in Molmol."""
+        """Function for opening the PDB file in PyMOL."""
 
         # Argument.
         if run:
@@ -105,11 +105,11 @@
         if not self.pipe_open_test():
             return
 
-        # Run InitAll to remove everything from molmol.
-        self.pipe_write("InitAll yes")
-
-        # Open the PDB.
-        self.pipe_write("ReadPdb " + self.relax.data.pdb[self.run].file_name)
+        # Reinitialise PyMOL.
+        self.pipe_write("reinitialise")
+
+        # Open the PDB file.
+        self.pipe_write("load " + self.relax.data.pdb[self.run].file_name)
 
 
     def pipe_open(self):
@@ -140,7 +140,7 @@
 
         # Test if the pipe has been broken.
         try:
-            self.relax.data.molmol.write('\n')
+            self.relax.data.pymol.write('\n')
         except IOError:
             return 0
 
@@ -159,7 +159,7 @@
             self.pipe_open()
 
         # Write the command to the pipe.
-        self.relax.data.molmol.write(command + '\n')
+        self.relax.data.pymol.write(command + '\n')
 
         # Place the command in the command history.
         if store_command:


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