MotiveValidator:MotifExtractor Help

MotifExtractor is a simple automated script for extracting the motifs of interest from biomolecule structure files. You may define one or more motifs to be extracted from a set of biomolecules stored in PDB format.

Requirements

• Windows: .NET 4.5 or newer
• Linux and MacOS: MONO 3.2.3 or newer

Input

• A folder with a set of biomolecules in PDB format.
• A .json file with settings, defining the motif(s) to be extracted. The key parameters of the .json file are encoded in attributes, that you will need to edit depending on what you want to extract and from where:

1. Location of the folder with biomolecules - attribute "InputFolders". When writing the path to your folder, note that backslashes must be escaped (so C:\Data\pdb should be written as C:\\Data\\pdb), or forward slash can be used (C:/Data/pdb).
2. Name of query residue - attributes "Id", "Name", and "Residues". Write the 3-letter code for the residue of interest.

Output

A .zip archive containing

• Folders with motifs in PDB format.
• CSV files with list of motifs and their unique identifier (motif index).

Execution

• Windows

Open the utility cmd, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as "MotiveQuery.exe path_to_output motifs.json" (without the "). For example:

MotiveQuery c:\data\nag_motifs motifs.json

• Linux and MacOS

Open a terminal, go to the location where you unzipped MotifExtractor, and, after you have edited the .json file according to your needs, run MotifExtractor as "mono MotiveQuery.exe path_to_output motifs.json" (without the ").