No interface for protein – Interface Analyzer

[Anonymous]

I’m trying to run interfaceanalyzer on a PDB with two chains (A and . I first tried using the -fixedchains flag to specify the two separate chains for determining the interface, but get the following error:

~/Applications/rosetta3.4/rosetta_source/build/src/release/macos/10.7/64/x86/gcc/4.2/InterfaceAnalyzer.default.macosgccrelease -database ~/Applications/rosetta3.4/rosetta_database/ -l list3 -tracer_data_print false -out:file:score_only score.sc -pack_separated true -add_regular_scores_to_scorefile true -fixedchains A -pose_metrics::inter_group_neighbors_calculator 3

ERROR: Option matching -pose_metrics:inter_group_neighbors_calculator not found in command line top-level context

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I also tried running it with the other pose_metrics flag option

~/Applications/rosetta3.4/rosetta_source/build/src/release/macos/10.7/64/x86/gcc/4.2/InterfaceAnalyzer.default.macosgccrelease -database ~/Applications/rosetta3.4/rosetta_database/ -l list3 -tracer_data_print false -out:file:score_only score.sc -pack_separated true -add_regular_scores_to_scorefile true -pose_metrics::interface_cutoff 3

and it runs but in the .out it prints:

protocols.analysis.InterfaceAnalyzerMover: NO INTERFACE FOR: 1AUT_PAR1_renum_ppk_0030_0002_0001_0002_0005_0001

and then in the score file, nres_int = 0.

I’m no expert but it seems like it’s not detecting the interface between chain A and chain B.

[Anonymous]

interface_cutoff 3 may be too small, in many application such interface cutoff is 8 – 10 A

[Author]

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