Author: bugman
Date: Wed Nov 15 09:49:05 2006
New Revision: 2852
URL: http://svn.gna.org/viewcvs/relax?rev=2852&view=rev
Log:
Updated all the sample scripts to use the new PDB reading user function name
'structure.read_pdb()'.
Modified:
1.3/sample_scripts/angles.py
1.3/sample_scripts/dasha.py
1.3/sample_scripts/diff_min.py
1.3/sample_scripts/full_analysis.py
1.3/sample_scripts/mf_multimodel.py
1.3/sample_scripts/model-free.py
1.3/sample_scripts/noe.py
1.3/sample_scripts/palmer.py
1.3/sample_scripts/relax_fit.py
Modified: 1.3/sample_scripts/angles.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/angles.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/angles.py (original)
+++ 1.3/sample_scripts/angles.py Wed Nov 15 09:49:05 2006
@@ -1,5 +1,5 @@
name = 'spheroid'
run.create(name, 'mf')
-pdb(name, "Ap4Aase_new_3.pdb")
+structure.read_pdb(name, "Ap4Aase_new_3.pdb")
diffusion_tensor.init(name, (1.698e7, 1.417e7, 67.174, -83.718),
param_types=3)
angles(name)
Modified: 1.3/sample_scripts/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/dasha.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/dasha.py (original)
+++ 1.3/sample_scripts/dasha.py Wed Nov 15 09:49:05 2006
@@ -16,7 +16,7 @@
sequence.read(name, 'noe.500.out')
# Load a PDB file.
- #pdb(name, 'example.pdb')
+ #structure.read_pdb(name, 'example.pdb')
# Load the relaxation data.
relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
Modified: 1.3/sample_scripts/diff_min.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/diff_min.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/diff_min.py (original)
+++ 1.3/sample_scripts/diff_min.py Wed Nov 15 09:49:05 2006
@@ -22,7 +22,7 @@
sequence.read(name, 'noe.500.out')
# Load a PDB file.
- pdb(name, 'example.pdb')
+ structure.read_pdb(name, 'example.pdb')
# Load the relaxation data.
relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
Modified: 1.3/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/full_analysis.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/full_analysis.py (original)
+++ 1.3/sample_scripts/full_analysis.py Wed Nov 15 09:49:05 2006
@@ -171,7 +171,7 @@
model_free.remove_tm(run=name)
# Load the PDB file.
- pdb(name, '1F3Y.pdb')
+ structure.read_pdb(name, '1F3Y.pdb')
# Add an arbitrary diffusion tensor which will be optimised.
if self.diff_model == 'sphere':
@@ -377,7 +377,7 @@
# Load the PDB file.
if not local_tm:
- pdb(name, '1F3Y.pdb')
+ structure.read_pdb(name, '1F3Y.pdb')
# Load the relaxation data.
relax_data.read(name, 'R1', '600', 599.719 * 1e6, 'r1.600.out')
Modified: 1.3/sample_scripts/mf_multimodel.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/mf_multimodel.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/mf_multimodel.py (original)
+++ 1.3/sample_scripts/mf_multimodel.py Wed Nov 15 09:49:05 2006
@@ -16,7 +16,7 @@
sequence.read(name, 'noe.500.out')
# Load a PDB file.
- #pdb(name, 'example.pdb')
+ #structure.read_pdb(name, 'example.pdb')
# Load the relaxation data.
relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
Modified: 1.3/sample_scripts/model-free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model-free.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/model-free.py (original)
+++ 1.3/sample_scripts/model-free.py Wed Nov 15 09:49:05 2006
@@ -11,7 +11,7 @@
sequence.read(name, 'noe.500.out')
# Load a PDB file.
-#pdb(name, 'example.pdb')
+#structure.read_pdb(name, 'example.pdb')
# Load the relaxation data.
relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
Modified: 1.3/sample_scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/noe.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/noe.py (original)
+++ 1.3/sample_scripts/noe.py Wed Nov 15 09:49:05 2006
@@ -5,7 +5,7 @@
run.create(name, 'noe')
# Load the sequence from a PDB file.
-pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
+structure.read_pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
# Load the reference spectrum and saturated spectrum peak intensities.
noe.read(name, file='ref.list', spectrum_type='ref')
Modified: 1.3/sample_scripts/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/palmer.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/palmer.py (original)
+++ 1.3/sample_scripts/palmer.py Wed Nov 15 09:49:05 2006
@@ -27,7 +27,7 @@
sequence.read(name, 'noe.500.out')
# PDB.
- #pdb(name, 'Ap4Aase_new_3.pdb')
+ #structure.read_pdb(name, 'Ap4Aase_new_3.pdb')
# Load the relaxation data.
relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
Modified: 1.3/sample_scripts/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/relax_fit.py?rev=2852&r1=2851&r2=2852&view=diff
==============================================================================
--- 1.3/sample_scripts/relax_fit.py (original)
+++ 1.3/sample_scripts/relax_fit.py Wed Nov 15 09:49:05 2006
@@ -5,7 +5,7 @@
run.create(name, 'relax_fit')
# Load the sequence from a PDB file.
-pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
+structure.read_pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
# Load the peak intensities.
relax_fit.read(name, file='T2_ncyc1.list', relax_time=0.0176)
r2852 - /1.3/sample_scripts/