Molecular Modeling and Bioinformatics : LSHEBA Examples (Cont'd)

LSHEBA (Local Structual Homology by Environment-Based Alignment)

Examples (Cont'd)

IV. Other Output:

1. Detail information of matched residues:

This output lists the residue id, secondary structure code, accessibility, and polarity of the matched residues.

%./lsheba -m (query.env/.pdb) (subject.env/.pdb)

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2. GEMM format output:

This format can be parsed to GEMM and it is stored in a file. Default output will be on the screen.

% ./lsheba -g (query.env/.pdb) (subject.env/.pdb)

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3. Transformation matrix:

The transformation matrix of each domain will be saved in one file and default output is on the screen.

%./lsheba -x (query.env/.pdb) (subject.env/.pdb)

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