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Frequently Asked Questions
- How do I retrieve ConSurf-DB results based on List of PDB id's?
For this exact purpose we added a perl script that retrieves ConSurf-DB results directly from ConSurfDB website according to the input list (see the example bellow). Download and execute the perl script together with your PDB id's list in a separate folder (ConSurfDB files would be downloaded to this folder)
Click here to download the Script - ConSurfDB_list_feature.zip
- Read the list input file and covert to uppercase.
- Split and seperate the chains from the PDB id's.
- Look for the representative pdb ib and chain for each entry
- Retrieve each chain from the ConSurfDB website
- the program takes a single command line parameter, all other parameters
- the working directory for the script is the directory of the given input file. all files are created there.
- a log file ConSurfDB_list.log is created in the working directory
- a corrected list file - Corrected_list.dat (with representative chains) is created in the working directory
input_file - List of PDB id's and chains for example - 2DU3 A,B,C,D
Example of input_file - List of PDB id's with chains: