Author: bugman
Date: Sat Jan 31 17:54:04 2015
New Revision: 27432
URL: http://svn.gna.org/viewcvs/relax?rev=27432&view=rev
Log:
Updated the Structure.test_align_CaM_BLOSUM62 system test script.
The MSA algorithm and pairwise alignment algorithms are now specified in the
structure.sequence_alignment user function calls.
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=27432&r1=27431&r2=27432&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
Sat Jan 31 17:54:04 2015
@@ -17,11 +17,11 @@
structure.read_pdb('%s.pdb' % code, dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures')
# First align then superimpose the N-domains - aligning 1OSA onto 1J70 to act
as a scaffold.
-structure.sequence_alignment(pipes=['1J7O', '1OSA'], matrix='BLOSUM62',
gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0)
+structure.sequence_alignment(pipes=['1J7O', '1OSA'], msa_algorithm='Central
Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0,
gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
structure.superimpose(pipes=['1J7O', '1OSA'], atom_id='@N,C,CA,O', method='fit
to first')
# Then align then superimpose the C-domains - aligning 1J7P onto the 1OSA
scaffold.
-structure.sequence_alignment(pipes=['1OSA', '1J7P'], matrix='BLOSUM62',
gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0,
end_gap_extend_penalty=0.0)
+structure.sequence_alignment(pipes=['1OSA', '1J7P'], msa_algorithm='Central
Star', pairwise_algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=10.0,
gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0)
structure.superimpose(pipes=['1OSA', '1J7P'], atom_id='@N,C,CA,O', method='fit
to first')
# Write out the result.
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
