r27370 - /trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py -- January 29, 2015 - 18:30

Author: bugman
Date: Thu Jan 29 18:30:04 2015
New Revision: 27370

URL: http://svn.gna.org/viewcvs/relax?rev=27370&view=rev
Log:
Corrections for the Structure.test_align_CaM_BLOSUM62 system test.

The CaM N and C domains can not be aligned together in a global MSA as they 
would align very well to
themselves, causing the atomic coordinate assembly function to fail.


Modified:
    trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py

Modified: 
trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py?rev=27370&r1=27369&r2=27370&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py    
  (original)
+++ trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py    
  Thu Jan 29 18:30:04 2015
@@ -16,8 +16,11 @@
     # Load the structure.
     structure.read_pdb('%s.pdb' % code, dir=status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures')
 
-# Backbone heavy atom align all structures.
-structure.align(pipes=codes, atom_id='@N,C,CA,O', method='fit to first', 
matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, 
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
+# First align the N-domains - aligning 1OSA onto 1J70 to act as a scaffold.
+structure.align(pipes=['1J7O', '1OSA'], atom_id='@N,C,CA,O', method='fit to 
first', matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, 
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
+
+# Then align the C-domains - aligning 1J7P onto the 1OSA scaffold.
+structure.align(pipes=['1OSA', '1J7P'], atom_id='@N,C,CA,O', method='fit to 
first', matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, 
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
 
 # Write out the result.
 structure.write_pdb('devnull', force=True)