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List: relax-commits
Subject: r2710 - in /branches/tensor_pdb: generic_fns/pymol.py prompt/pymol.py
From: edward.dauvergne () domain ! hid
Date: 2006-10-31 8:01:01
Message-ID: E1GeoYP-0004wJ-QQ () subversion ! gna ! org
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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The numerous Molmol commands have been replaced by a single PyMOL load command.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.
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