Author: bugman
Date: Mon Oct 5 11:34:48 2009
New Revision: 9566
URL: http://svn.gna.org/viewcvs/relax?rev=9566&view=rev
Log:
Added a script for creating Molmol macros to represent the model-free motions.
Added:
1.3/sample_scripts/mf_molmol_plot.py
Added: 1.3/sample_scripts/mf_molmol_plot.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/mf_molmol_plot.py?rev=9566&view=auto
==============================================================================
--- 1.3/sample_scripts/mf_molmol_plot.py (added)
+++ 1.3/sample_scripts/mf_molmol_plot.py Mon Oct 5 11:34:48 2009
@@ -1,0 +1,56 @@
+###############################################################################
+#
#
+# Copyright (C) 2009 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+"""Script for generating Molmol macros for highlighting model-free motions.
+
+Note that the most important macros are:
+ 'amp_fast' - The order parameters for fast motions (< 200 ps).
+ 'amp_slow' - The order parameters for slow motions (> 200 ps).
+ 'time_fast' - The correlation time for fast motions (< 200 ps).
+ 'time_slow' - The correlation time for slow motions (> 200 ps).
+ 'Rex' - Chemical exchange relaxation.
+
+These are more important than 'S2', 'S2f', 'S2s', 'te', 'tf', and 'ts' as
they are model independent
+reporters of the motions of the molecule. Note that which model is selected
is not important,
+rather the motions that that model represents is of interest. A standard
concept in mathematical
+modelling is that simpler models can approximate more complex ones. But
this does not mean that the
+more complex motion is not present, just that it cannot be statistically
differentiated from the
+data being analysed.
+
+Please read the documentation for the molmol.write() user function before
using this script.
+"""
+
+# Load the program state.
+state.load(file='final_state', dir=None)
+
+# Create the Molmol macros.
+molmol.write(data_type='S2', colour_start='red', colour_end='blue',
force=True)
+molmol.write(data_type='S2f', force=True)
+molmol.write(data_type='S2s', force=True)
+molmol.write(data_type='amp_fast', colour_start='red', colour_end='blue',
force=True)
+molmol.write(data_type='amp_slow', colour_start='red', colour_end='blue',
force=True)
+molmol.write(data_type='te', force=True)
+molmol.write(data_type='tf', force=True)
+molmol.write(data_type='ts', force=True)
+molmol.write(data_type='time_fast', force=True)
+molmol.write(data_type='time_slow', force=True)
+molmol.write(data_type='Rex', force=True)
r9566 - /1.3/sample_scripts/mf_molmol_plot.py