MantisBT - Rosetta
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0000174Rosetta[All Projects] Bad Codingpublic2013-02-21 08:522013-03-25 09:27
smlewis 
 
lowminoralways
newopen 
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integration tests
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0000174: 4FXN is a strange (bad?) choice for use in tests
4FXN is used in many integration tests:

9:51:15 somarriba ~/LOCAL/super_pure_dont_change/rosetta_tests/integration> find . -name "*4fxn*" | grep -v ".svn"
./tests/loop_modeling/inputs/4fxn.start_0001.pdb
./tests/loop_modeling/inputs/cc4fxn_03_05.200_v1_3.gz
./tests/loop_modeling/inputs/4fxn.loop_file
./tests/loop_modeling/inputs/cc4fxn_09_05.200_v1_3.gz
./tests/torsion_restricted_sampling/input/4fxn.start.pdb
./tests/torsion_restricted_sampling/input/4fxn.loop
./tests/KIC_refine/input/4fxn.start.pdb
./tests/KIC_refine/input/4fxn.loop
./tests/next_generation_KIC/input/4fxn.start.pdb
./tests/next_generation_KIC/input/4fxn.loop
./tests/kinematic_looprelax/input/4fxn.start.pdb
./tests/kinematic_looprelax/input/4fxn.loop
./tests/rosetta_scripts_loops/4fxn.loop_file
./new/loop_modeling/inputs/4fxn.start_0001.pdb
./new/loop_modeling/inputs/cc4fxn_03_05.200_v1_3.gz
./new/loop_modeling/inputs/4fxn.loop_file
./new/loop_modeling/inputs/cc4fxn_09_05.200_v1_3.gz

but, the PDB says it's obsolete (as of 1997!):

http://pdb.rcsb.org/pdb/explore/obsolete.do?obsoleteId=4FXN [^]

reports:
4FXN was obsoleted on 1997-03-12 and superseded by 2FOX
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Issue History
2013-02-21 08:52smlewisNew Issue
2013-03-25 09:27smlewisNote Added: 0000214

Notes
(0000214)
smlewis   
2013-03-25 09:27   
Also, for the loop_modeling itest (that's the CCD test), the first loop chosen (LOOP 54 64 0 0.0 X) is directly adjacent to an FMN that's missing in the input and ignored by Rosetta.